US Pat. No. 9,169,512

METHODS AND COMPOSITIONS FOR NUCLEIC ACID AMPLIFICATION

Gen-Probe Incorporated, ...

1. A method for simultaneously amplifying at least two different target nucleic acid sequences contained in a sample comprising
the steps of:
(a) contacting a sample with at least two different amplification oligomer complexes that hybridize to different target nucleic
acid sequences and with at least two target capture oligomers that hybridize to different target nucleic acid sequences, wherein
each of said amplification oligomer complexes comprises a first amplification oligomer member that is directly joined to a
second amplification oligomer member;

(b) providing conditions for hybridizing each of said two amplification oligomer complexes and each of said target capture
oligomers to their target nucleic acids present in said sample, and for hybridizing a capture region of said target capture
oligomers to a solid support structure;

(c) performing a wash step to remove all unhybridized amplification oligomer complexes;
(d) pre-amplifying said target nucleic acid sequences using said amplification oligomer complexes in an isothermal amplification
reaction, thereby generating a first amplification product for each target nucleic acid hybridized by an amplification oligomer
complex;

(e) splitting said pre-amplified sample from step (d) into at least two separate secondary target specific amplification reactions;
(f) amplifying said pre-amplified sample in each of said secondary target specific amplification reactions using target specific
amplification oligomers, thereby generating second amplification products; and

(g) detecting said second amplification products from at least one of said secondary target specific amplification reactions,
wherein said detecting step determines the presence of at least one of said at least two different target nucleic acids.

US Pat. No. 9,248,449

INTERLOCKING CAP AND RECEPTACLE WITH DETENT FEATURE

GEN-PROBE INCORPORATED, ...

1. A cap securable to a receptacle and comprising:
a lower portion configured for insertion into a receptacle opening;
an upper portion having an opening formed therein, the opening defining an open end that is configured for engaging a portion
of an automated receptacle transport mechanism;

a plurality of locking arms extending toward the lower portion of the cap and configured for engaging a portion of a receptacle
to secure the cap to the receptacle when the lower portion of the cap is inserted into the receptacle opening;

a plurality of longitudinally extending, linear ribs disposed on an inner surface of the opening formed in the upper portion
of the cap; and

a detent formed in at least one of the linear ribs and configured for engaging a portion of the automated receptacle transport
mechanism.

US Pat. No. 9,171,279

RECEPTACLE RACK HAVING AN ELECTRONIC MEMORY ELEMENT

GEN-PROBE INCORPORATED, ...

1. A receptacle rack comprising:
a sample receptacle holding structure defining a plurality of sample receptacle-receiving pockets, each configured to receive
and hold a sample receptacle;

machine-readable position data associated with each sample receptacle-receiving pocket and comprising information relating
to a position of each sample receptacle-receiving pocket; and

an electronic memory element configured to store information relating to sample receptacles held within receptacle-receiving
pockets of the sample receptacle rack and the information relating to a position of each sample receptacle-receiving pocket.

US Pat. No. 9,206,484

COMPOSITIONS, METHODS AND KITS TO DETECT HERPES SIMPLEX VIRUS NUCLEIC ACIDS

GEN-PROBE INCORPORATED, ...

1. A method for specifically detecting a Herpes Simplex Virus-1 (HSV-1) target nucleic acid in a sample comprising the steps
of:
(a) providing a sample suspected of containing at least a HSV-1 target nucleic acid;
(b) contacting said sample with at least two amplification oligomers, wherein a first of said amplification oligomers comprises
a target hybridizing sequence 15 to 25 nucleotides in length and configured to target a sequence in a region of the HSV-1
US8.5 ORF corresponding to nucleotides 124 to 156 of SEQ ID NO:1, and wherein a second of said amplification oligomers comprises
a target hybridizing sequence comprising SEQ ID NO:10; and

(c) performing a nucleic acid detection reaction with a detection probe configured to detect a sequence in a region corresponding
to nucleotides 173 to 196 of SEQ ID NO:1 that detects an amplification product to determine whether a HSV-1 target nucleic
acid is present in said sample.

US Pat. No. 9,446,911

APPARATUS FOR TRANSFERRING REACTION RECEPTACLES BETWEEN A PLURALITY OF RECEPTACLE-RECEIVING STRUCTURES

GEN-PROBE INCORPORATED, ...

11. An apparatus for transferring one or more receptacles between a plurality of receptacle-receiving structures comprising:
a linear transport track having opposed ends, wherein the receptacle-receiving structures are disposed at different locations
adjacent to said transport track;

a receptacle carrier operatively engaged with said transport track and adapted to carry a receptacle and translate along said
transport track in a first or second direction between said opposed ends, wherein said receptacle carrier is further adapted
to selectively stop at a transfer position with respect to any of the receptacle-receiving structures disposed adjacent said
transport track, and wherein said receptacle carrier includes a receptacle moving mechanism adapted to move a receptacle with
respect to said receptacle carrier to move a receptacle into said receptacle carrier, move a receptacle out of said receptacle
carrier, or alternately move a receptacle into and out of said receptacle carrier;

a carrier rotation system adapted to rotate at least a portion of said receptacle carrier about an axis of rotation; and
a transfer position locating system adapted to automatically determine, for each receptacle-receiving structure, a location
of a transfer position of the receptacle carrier with respect to the receptacle-receiving structure to enable the receptacle
carrier to transfer a receptacle between the receptacle carrier and the receptacle-receiving structure.

US Pat. No. 9,328,392

COMPOSITIONS AND REACTION MIXTURES FOR THE DETECTION OF NUCLEIC ACIDS FROM MULTIPLE TYPES OF HUMAN PAPILLOMAVIRUS

Gen-Probe Incorporated, ...

1. A mixture of oligomers for detecting multiple types of human papillomavirus (HPV) nucleic acids, wherein the mixture includes
first amplification oligomers, comprising a target binding region and a 5? promoter sequence, and second amplification oligomers,
comprising a target binding region, wherein pairs of the first and second amplification oligomers hybridize to opposing strands
of HPV nucleic acids for transcription mediated amplification of HPV nucleic acids between pairs of hybridized first and second
amplification oligomers, wherein:
(a) the first amplification oligomers comprise nucleic acid sequences selected from the group consisting of SEQ ID Nos. 18,
20, 22, 24, 28, 30, 32, 34, 36, RNA equivalents thereof, complements thereof, and combinations thereof; and

(b) the second amplification oligomers comprise nucleic acid sequences selected from the group consisting of SEQ ID Nos. 38,
39, 40, 41, RNA equivalents thereof, complements thereof, and combinations thereof.

US Pat. No. 9,175,353

COMPOSITIONS, KITS AND METHODS FOR DETECTION OF CAMPYLOBACTER NUCLEIC ACID

Gen-Probe Incorporated, ...

1. A method for specifically detecting a Campylobacter target nucleic acid in a sample comprising the steps of:
(a) contacting a sample suspected of containing at least a Campylobacter target nucleic acid with at least two amplification oligomers that stably hybridize to a C. jejuni target nucleic acid and a C. coli, a C. lari, or a C. coli and a C. lari target nucleic acid, wherein a first of said amplification oligomers comprises SEQ ID NO:26 or SEQ ID NO:32 and wherein a
second of said amplification oligomers comprises a target hybridizing sequence 15 to 45 nucleotides in length and configured
to target a sequence in a region of a Campylobacter 16S rRNA gene corresponding to nucleotides 170 to 226 of GenBank Accession No.: AF393202.1, gi:20378208;

(b) performing an in vitro nucleic acid amplification reaction wherein any of a C. jejuni target nucleic acid, a C. coli target nucleic acid and a C. lari target nucleic acid present in said sample is used as a template for generating an amplification product; and

(c) performing a nucleic acid detection reaction that detects said amplification product to determine whether a Campylobacter target nucleic acid was present in said sample.

US Pat. No. 9,347,098

REACTION MIXTURES FOR QUANTITATIVE AMPLIFICATION AND DETECTION OVER A WIDE DYNAMIC RANGE

GEN-PROBE INCORPORATED, ...

1. A nucleic acid amplification reaction mixture comprising at least two primers and at least two probes, wherein:
(a) the at least two primers hybridize to the same strand of a target nucleic acid sequence but each primer hybridizes to
a distinct nucleotide sequence on the strand,

wherein each primer is present in the reaction mixture at a different amount Px, where x is an integer between 1 and the number of primers in the mixture, and wherein the at least two primers comprise
a first inner primer and a second outer primer;

(b) each primer is capable of simultaneously and independently producing one of at least two amplicons from the target nucleic
acid sequence under amplification conditions,

wherein for each amplicon, a number of copies Ax is capable of being produced, wherein each Ax differs by at least two orders of magnitude, and

wherein the at least two amplicons comprise a first amplicon capable of being produced from the first inner primer and a second
amplicon capable of being produced from the second outer primer, wherein the first amplicon is shorter than the second amplicon;

(c) the at least two amplicons are detectable by hybridization with the at least two probes, wherein one of the at least two
probes is specific to a nucleotide sequence common to both the first and second amplicons and another of the at least two
probes is specific to a nucleotide sequence contained within the second amplicon but not within the first amplicon, and each
probe is detectable within a detection range Cx(a) to Cx(b),

wherein Cx(a) is the minimum detectable number of copies of amplicon and Cx(b) is the maximum detectable number of copies of amplicon for probe x,

wherein for each probe, Cx+1(a) is greater than Cx(a) and Cx+1(b) is greater than Cx(b) such that the at least two probes together are detectable across a dynamic range of from about 103 to 107, wherein for each amplicon-probe combination, Ax is between Cx(a) and Cx(b), and wherein the at least two probes are capable of producing distinguishable detection signals.

US Pat. No. 9,566,582

MULTI-WELL TRAY

GEN-PROBE INCORPORATED, ...

1. A single piece multi-well tray for use in an automated instrument and comprising:
an elongated base having a first end and a second end, said base comprising a top surface and opposed side walls extending
from the top surface to a bottom surface, a first end wall extending between said side walls, and an arm extending outwardly
from the first end of the base and configured to be engaged by a transport mechanism for transporting the tray within the
instrument, wherein the arm comprises a bridge extending outwardly from the first end wall and a post having one end attached
to the bridge and an opposite end that is not attached to the bridge and wherein the post extends from the bridge so as to
define a gap between the opposite end of the post and the first end wall;

a plurality of wells depending from the top surface and disposed between the opposed side walls, each having an opening at
the top surface, wherein the wells are arranged in at least one row extending between the first end and the second end of
the base, and wherein the wells do not extend below the bottom surface of the side walls; and

snap fingers disposed at the second end of the base and configured to grasp an element of the instrument for securing the
tray to the element, wherein the snap fingers comprise opposed spaced-apart tabs defining a slot therebetween configured to
receive the element of the instrument.

US Pat. No. 9,117,192

METHOD FOR READING MACHINE-READABLE LABELS

GEN-PROBE INCORPORATED, ...

1. In an apparatus comprising a plurality of rack-receiving locations, each configured to receive a rack holding at least
one receptacle, and a label reading device configured to read a rack-identifying machine-readable label disposed on the rack
and machine-readable labels disposed on the at least one receptacle held on the rack, wherein the label reading device is
disposed adjacent to one of the rack-receiving locations, a method for reading machine-readable labels disposed on receptacles
carried on a receptacle rack and associating receptacle data read from each machine-readable label disposed on the at least
one receptacle with one of the rack-receiving locations, said method comprising:
(a) placing a rack holding at least one receptacle having a machine readable label disposed thereon in the rack-receiving
location disposed adjacent to the label reading device;

(b) during or after performing step (a), reading the machine-readable label of each receptacle having a machine-readable label
to obtain receptacle data for each receptacle having a machine-readable label;

(c) during or after performing step (a), reading the rack-identifying machine readable label to obtain rack identifying data;
(d) storing the receptacle data obtained in step (b) and the rack identifying data obtained in step (c) and associating the
receptacle data obtained in step (b) with the rack identifying data obtained in step (c);

(e) removing the rack from the rack-receiving location disposed adjacent to the label-reading device;
(f) placing the rack removed in step (e) in one of the other rack-receiving locations;
(g) during or after performing step (f), reading the rack-identifying machine readable label to obtain rack identifying data;
(h) acquiring location data identifying the rack-receiving location in which the rack was placed in step (f); and
(i) retrieving the receptacle data stored in step (d) that is associated with the rack-identifying data obtained in step (g)
and associating the retrieved receptacle data with the location data acquired in step (h) to thereby associate the retrieved
receptacle data with the rack-receiving location in which the rack was placed in step (f).

US Pat. No. 9,249,472

COMPOSITIONS, METHODS AND KITS TO DETECT ADENOVIRUS NUCLEIC ACIDS

GEN-PROBE INCORPORATED, ...

1. A composition for use in an Adenovirus target nucleic acid amplification assay comprising
(I) at least three amplification oligomers capable of stably hybridizing to Adenovirus target nucleic acid to generate an
amplicon during an amplification reaction, wherein the at least three amplification oligomers are

(a) a first amplification oligomer consisting of a target hybridizing sequence as set forth in SEQ ID NO:27,
(b) a second amplification oligomer consisting of a target hybridizing sequence as set forth in SEQ ID NO:28, and
(c) a third amplification oligomer consisting of target hybridizing sequences as set forth in (i) SEQ ID NO:25 and/or SEQ
ID NO:26, (ii) SEQ ID NO:33 and/or SEQ ID NO:34, or (iii) SEQ ID NO:31 and/or SEQ ID NO:26; and

(II) at least one labelled detection probe oligonucleotide configured to specifically hybridize to a portion of said amplicon.

US Pat. No. 9,393,565

METHOD AND APPARATUS FOR EFFECTING AUTOMATED MOVEMENT OF A MAGNET IN AN INSTRUMENT FOR PERFORMING A MAGNETIC SEPARATION PROCEDURE

GEN-PROBE INCORPORATED, ...

1. A method for removing a conduit from a distal end of each of a plurality of fluid transfer probes, comprising:
a) effecting powered linear translation of a movable slide in a direction transverse to the axes of the probes from a first
location with respect to a receptacle carrier to a second location with respect to the receptacle carrier, wherein the slide
includes a lateral surface with conduit-stripping portions thereon, wherein when the slide is in the first location, no portion
of the slide is in a position to be engaged by any of the probes, and when the slide is in the second location, the conduit-stripping
portions of the slide are in positions to be engaged by the distal ends of the probes, wherein the slide comprises one or
more magnets mounted thereon such that, when the slide is in the first location, the one or more magnets have substantially
no effect on magnetically-responsive solid supports contained in a receptacle device held in the receptacle carrier, the receptacle
device comprising multiple receptacles that each have a wall and contain a fluid, and wherein the multiple receptacles of
the receptacle device held in the receptacle carrier are positioned so as to be operatively engageable by the probes, and
when the slide is in the second location, the one or more magnets are positioned adjacent to the receptacle device held in
the receptacle carrier so that the magnets will draw at least a portion of the magnetically-responsive solid supports to the
walls of the multiple receptacles;

b) removing the receptacle device from the receptacle carrier; and
c) after step b), and with the slide in the second location, effecting powered axial movement of the probes with respect to
the slide to engage the distal ends of the probes with the conduit-stripping portions of the slide and to strip the conduits
from the probes.

US Pat. No. 9,255,293

INTEGRATED CAPTURE AND AMPLIFICATION OF TARGET NUCLEIC ACID FOR SEQUENCING

GEN-PROBE INCORPORATED, ...

1. A method of preparing a target nucleic acid, comprising
contacting a target nucleic acid with a capture probe and an immobilized probe, the capture probe comprising a first segment
that hybridizes to the target nucleic acid and a second segment that hybridizes to the immobilized probe, wherein the target
nucleic acid hybridizes to the first segment of the capture probe, and the second segment of the capture probe hybridizes
to the immobilized probe, thereby forming a capture hybrid capturing the target nucleic acid; and

performing a PCR amplification of the captured target nucleic acid without a step of dissociating the capture hybrid before
initiating thermocycling in the PCR amplification; wherein the PCR amplification is performed in the same vessel as the contacting
step and wherein the amplified target nucleic acid comprises at least one mutation that is present in less than 10% of molecules
of the target nucleic acid.

US Pat. No. 9,181,593

COMPOSITIONS AND METHODS TO DETECT ATOPOBIUM VAGINAE NUCLEIC ACID

Gen-Probe Incorporated, ...

1. A method for detecting in a sample a 16S rRNA of A. vaginae or a gene encoding a 16S rRNA of A. vaginae, comprising the steps of:
a. providing a sample, wherein said sample is suspected of containing an Atopobium vaginae bacterium;

b. contacting said sample with at least two amplification oligomers, wherein a first amplification oligomer comprises a target
hybridizing sequence that consists of SEQ ID NO:2, and wherein a second amplification oligomer comprises a target hybridizing
sequence that consists of SEQ ID NO:27, and wherein said first and second amplification oligomers are configured to specifically
hybridize to a target sequence within a 16S rRNA of A. vaginae or a gene encoding a 16S rRNA of A. vaginae in the presence of one or more of Gardnerella vaginalis, Prevotella sp, anaerobic gram positive cocci, Mobiluncus sp, Mycoplasma hominis, Eggerthella hongkongensis, Megasphaera sp, and/or Leptotrichia sanguinegens;
c. performing an in vitro isothermal nucleic acid amplification reaction wherein any target nucleic acid present in said sample
is used as a template for generating an amplification product; and

d. contacting said in vitro nucleic acid amplification reaction with a detection probe oligomer that comprises a nucleotide
sequence consisting of SEQ ID NO:4 or SEQ ID NO:17 and providing conditions for a detection reaction to determine the presence
or absence of an amplification product;
wherein the detection of the presence of an amplification product indicates the presence of at least 100 CFU/ml of Atopobium vaginae bacterium in the sample.

US Pat. No. 9,046,507

METHOD, SYSTEM AND APPARATUS FOR INCORPORATING CAPACITIVE PROXIMITY SENSING IN AN AUTOMATED FLUID TRANSFER PROCEDURE

GEN-PROBE INCORPORATED, ...

1. A method for monitoring the status of a fluid transfer probe, the method comprising:
(A) moving a fluid transfer probe known to have a protective tip on its distal end with respect to a secondary structure;
(B) during step (A), measuring a first capacitance reference signal from the fluid transfer probe with the protective tip
disposed on its distal end;

(C) moving a fluid transfer probe known to lack a protective tip on its distal end with respect to the secondary structure;
(D) during step (B), measuring a second capacitance reference signal from the fluid transfer probe lacking a protective tip;
(E) deriving a reference value from either or both of the first capacitance reference signal and the second capacitance reference
signal; and

(F) determining whether or not a fluid transfer probe has a protective tip engaged on its distal end by:
(1) moving the fluid transfer probe with respect to the secondary structure,
(2) measuring a capacitance signal from the fluid transfer probe as the fluid transfer probe is moved with respect to the
secondary structure, and

(3) comparing at least one characteristic of the measured capacitance signal with the reference value.
US Pat. No. 9,194,008

HYBRIDIZATION ASSAY DETECTION PROBES FOR DETECTING HUMAN PAPILLOMA VIRUS IN A SAMPLE

Gen-Probe Incorporated, ...

1. A method of detecting a HPV Type 16 nucleic acid in a sample comprising the steps of:
a) contacting an HPV type 16 amplification product with at least one hybridization assay detection probe that forms a detectable
probe: HPV type 16 target hybrid under stringent hybridization conditions, wherein the at least one hybridization assay detection
probe comprises a detectable label joined to a contiguous nucleic acid sequence that is from 21 to 27 nucleotides in length,
(a) contained within a sequence consisting of SEQ ID NO:13 or an RNA equivalent thereof, and contains a sequence consisting
of SEQ ID NO:34 or an RNA equivalent thereof, or (b) contained within a sequence consisting of SEQ ID NO:14 or an RNA equivalent
thereof, and contains a sequence consisting of SEQ ID NO:33 or an RNA equivalent thereof; and

b) detecting a signal from the probe: HPV type 16 target hybrid, thereby indicating the presence of HPV type 16 in the sample.

US Pat. No. 9,162,228

INTERLOCKING CAP AND RECEPTACLE FOR AUTOMATED PROCESSES

GEN-PROBE INCORPORATED, ...

1. A cap securable to a receptacle and comprising:
a lower portion for inserting into a receptacle opening;
an upper portion having an opening formed therein, the opening defining an open end that is configured for engagement by a
receptacle transport mechanism;

a plurality of locking arms extending toward the lower portion of the cap and configured for engaging a portion of a receptacle
to secure the cap to the receptacle when the lower portion is inserted into the receptacle opening, each of the locking arms
extending axially from an annular flange extending radially with respect to a centerline of the cap and defining a gap between
an outer surface of the lower portion and an inner surface of each locking arm, wherein the gap is sized to receive a lip
surrounding the receptacle opening when the lower portion is inserted into the receptacle opening and the locking arms securely
engage the lip surrounding the receptacle opening; and

a plurality of longitudinally extending linear ribs disposed on an inner surface of the cap, the inner surface of the cap
being defined by the opening formed in the upper portion, wherein each of the linear ribs has associated therewith at least
one of: (i) an enlarged portion proximate a distal end thereof, and (ii) a recess disposed on an outer surface of the upper
portion, wherein the recess corresponds in length with the associated rib and is disposed on the outer surface opposite the
associated rib.

US Pat. No. 9,109,262

COMPOSITIONS AND METHODS TO DETECT CANDIDA ALBICANS NUCLEIC ACID

Gen-Probe Incorporated, ...

1. A set of oligomers for use in amplifying a Candida albicans 26S rRNA sequence or DNA encoding the 26S rRNA sequence, the set of oligomers comprising first and second amplification oligomers,
wherein the first amplification oligomer consists of the base sequence of SEQ ID NO:1, the DNA equivalent of SEQ ID NO:1,
or a combination RNA/DNA equivalent of SEQ ID NO: 1, and wherein the second amplification oligomer is a promoter-primer comprising
a 5? promoter sequence and a target binding region consisting of the base sequence of SEQ ID NO:6, the DNA equivalent of SEQ
ID NO:6, or a combination RNA/DNA equivalent of SEQ ID NO:6.
US Pat. No. 9,909,189

DISTINGUISHING PCA3 MESSENGER RNA SPECIES IN BENIGN AND MALIGNANT PROSTATE TISSUES

Gen-Probe Incorporated, ...

1. A cDNA molecule encoding a differentially expressed prostate cancer antigen 3 (PCA3) mRNA containing an additional sequence
between exon 3and exon 4a, thereby giving rise to a long PCA3 mRNA, wherein the additional sequence is at least 90% identical
to the sequence of positions 27-254 of SEQ ID NO: 1 or the complement thereof.
US Pat. No. 9,657,352

COMPOSITIONS AND METHODS FOR DETECTING BV-ASSOCIATED BACTERIAL NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

1. A combination of at least two oligomers for detecting in a sample a Megasphaera sp. 16S rRNA or a gene encoding a Megasphaera sp. 16S rRNA, said oligomer combination comprising:
a first amplification oligomer comprising a first target-hybridizing sequence consisting of 14 to 32 contiguous nucleotides
contained in the sequence of SEQ ID NO: 38 and that includes at least the sequence of SEQ ID NO: 37; and

a second amplification oligomer that is a promoter primer comprising
(i) a second target-hybridizing sequence consisting of 22 to 31 contiguous nucleotides contained in the sequence of SEQ ID
NO: 40 and that includes at least the sequence of SEQ ID NO: 21 and

(ii) a T7 promoter sequence located 5? to the second target-hybridizing sequence.
US Pat. No. 9,663,829

COMPOSITIONS AND METHODS FOR DETECTING BV-ASSOCIATED BACTERIAL NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

3. A method for detecting in a sample a Gardnerella vaginalis (GV) target nucleic acid, wherein the target nucleic acid is a GV 16S rRNA or a gene encoding the 16S rRNA, the method comprising:
(a) contacting a sample, the sample suspected of containing a GV bacterium, with at least two oligomers for amplifying a GV
nucleic acid target region corresponding to the target nucleic acid, the oligomer combination comprising

(i) a first amplification oligomer comprising a nucleotide sequence, wherein the nucleotide sequence consists of a first target-hybridizing
sequence selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:8, and wherein the first amplification oligomer does
not comprise an additional target hybridizing sequence; and

(ii) a second amplification oligomer that is a promoter primer or promoter provider and that comprises a first region nucleotide
sequence and a second region nucleotide sequence, wherein (i) the first region nucleotide sequence consists of a second target-hybridizing
sequence selected from the group consisting of SEQ ID NO:36, SEQ ID NO:38, and SEQ ID NO:39, and (ii) the second region nucleotide
sequence consists of a promoter sequence located 5? to the second target-hybridizing sequence, and wherein the second amplification
oligomer does not comprise a target hybridizing region in addition to the second target hybridizing region;

(b) performing an in vitro nucleic acid amplification reaction, wherein any GV target nucleic acid present in the sample is
used as a template for generating an amplification product; and

(c) detecting the presence or absence of the amplification product, thereby indicating the presence or absence of GV in the
sample.

US Pat. No. 9,399,796

METHODS AND COMPOSITIONS FOR NUCLEIC ACID AMPLIFICATION

GEN-PROBE INCORPORATED, ...

1. A pre-amplification reaction mixture for use in simultaneously amplifying at least two different target nucleic acid sequences
contained in a sample to generate first amplification products, wherein the pre-amplification reaction mixture comprises
(a) an enzyme selected from the group consisting of: a polymerase, an RNA-dependent DNA polymerase, a DNA-dependent DNA polymerase,
a DNA-dependent RNA polymerase, a reverse transcriptase, an RNase, or a combination thereof;

(b) an immobilized probe attached to a solid support;
(c) at least two different target capture oligomers, wherein each of said target capture oligomers comprises (i) a target
specific sequence and (ii) an immobilized probe-binding region that binds to the immobilized probe; and

(d) at least two different amplification oligomer complexes, wherein each of said amplification oligomer complexes comprises
a first amplification oligomer member having a first target specific sequence that is joined to a second amplification oligomer
member having a second target specific sequence, wherein the first amplification oligomer member is a non-promoter primer
and the second amplification oligomer member is a promoter primer,

wherein each of said target capture oligomers and each of said amplification oligomer complexes specifically hybridizes to
a different target nucleic acid sequence, and wherein each target nucleic acid sequence is specifically targeted by one of
said target capture oligomers and one of said amplification oligomer complexes, and

wherein the pre-amplification reaction mixture does not contain any target-specific amplification oligomers that are not joined
to form one of the at least two amplification oligomer complexes.

US Pat. No. 9,372,156

SYSTEM FOR PROCESSING CONTENTS OF A RECEPTACLE TO DETECT AN OPTICAL SIGNAL EMITTED BY THE CONTENTS

GEN-PROBE INCORPORATED, ...

1. A system for processing the contents of one or more receptacles to detect an optical signal, if any, emitted by the contents
of each receptacle, the system comprising:
an incubator including a temperature-controlled chamber configured to receive one or more receptacles;
at least one signal detector configured to detect an optical signal, if any, emitted by the contents of a receptacle disposed
within said chamber in an operative position with respect to the signal detector;

a receptacle carrier disposed within said chamber and comprising one or more receptacle stations, each receptacle station
being configured to receive and hold one or more receptacles; and

at least one magnet holder attached to said receptacle carrier and holding one or more magnets in a fixed position adjacent
to an associated receptacle carrier station so as to expose the contents of each of one or more receptacles carried in the
associated receptacle station to a magnetic field when each of the receptacles is in the operative position with respect to
said at least one signal detector, and wherein said receptacle carrier, including said one or more receptacle stations, said
magnet holder, and said one or more magnets, is automatically moveable relative to said at least one signal detector.

US Pat. No. 9,273,365

METHOD FOR DETECTING CHIKUNGUNYA VIRUS

GEN-PROBE INCORPORATED, ...

1. A kit for amplifying and detecting a Chikungunya virus (CHIKV) nucleic acid sequence, comprising:
(a) a first primer up to 100 bases long, wherein the 3? terminal sequence of said first primer consists of SEQ ID NO:108,
and wherein said first primer comprises a first primer 5? phage T7 promoter sequence that is not complementary to CHIKV nucleic
acids;

(b) a second primer up to 100 bases long, wherein the 3? terminal sequence of said second primer is selected from the group
consisting of SEQ ID NO:148, SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:174, SEQ ID NO:175 and SEQ ID NO:176,
and wherein said second primer optionally comprises a second primer 5? sequence that is not complementary to CHIKV nucleic
acids; and

(c) a hybridization probe for detecting a nucleic acid amplification product synthesized using said primers, wherein said
primers and said hybridization probe are in packaged combination with each other.

US Pat. No. 9,469,881

COMPOSITIONS AND METHODS FOR DETECTION OF HEPATITIS A VIRUS NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

1. A combination of at least two oligomers for amplifying a HAV target region comprising:
a first oligomer comprising an HAV target-specific sequence length of 18 to 27 nt contained in the sequence of SEQ ID NO:93;
and a second oligomer comprising an HAV target specific sequence comprising the sequence of SEQ ID NO:63, joined at its 5?
end to a promoter sequence.

US Pat. No. 9,810,622

SAMPLE TESTING SYSTEMS AND METHODS WITH AUTOMATED CLEANING

GEN-PROBE INCORPORATED, ...

24. A method of operating a sample testing system, the system comprising a test receptacle support structure and an optical
element positioned for transmitting electromagnetic radiation emitted or reflected by a sample disposed in a test receptacle
supported by the test receptacle support structure, the method comprising using an automated transport arm to:
detachably couple a cleaning member to a working end of the transport arm;
move the detachably-coupled cleaning member into a position proximate to and/or contacting the optical element, such that
the cleaning member thereby cleans and/or sterilizes the optical element; and

decouple the cleaning member from the working end of the transport arm.

US Pat. No. 9,604,185

APPARATUS FOR INDEXING AND AGITATING FLUID CONTAINERS

GEN-PROBE INCORPORATED, ...

1. A fluid container mixing apparatus comprising:
a container support platform configured to hold one or more fluid containers, wherein the container support platform is constructed
and arranged to be movable in such a manner to index the fluid containers to sequentially place each of the containers in
one or more predetermined positions and to be movable in an orbital path about an orbital center;

an indexing drive system configured to effect powered indexing movement of the container support platform; and
a vortex drive system configured to effect powered movement of the container support platform in the orbital path, wherein
the vortex drive system comprises:

a vortex drive motor;
a vortexing pulley coupled to the vortex drive motor to effect powered rotation of the vortexing pulley;
first, second, and third vortexing idler pulleys;
an eccentric coupling associated with each of the vortexing idler pulleys, each of the eccentric couplings extending from
the associated vortexing idler pulley at a position that is offset with respect to an axis of rotation of the associated vortexing
idler pulley; and

a belt coupling the vortexing pulley to the first and second vortexing idler pulleys so that rotation of the vortexing pulley
imparts rotation to the first and second vortexing idler pulleys,

wherein the container support platform is coupled to the eccentric couplings of the vortexing idler pulleys such that rotation
of the first and second vortexing idler pulleys imparts powered movement of the container support platform in the orbital
path via the eccentric couplings, and wherein the third vortexing idler pulley is a follower pulley that rotates with the
powered movement of the container support platform in the orbital path but is not coupled to the vortexing pulley by the belt
coupling the vortexing pulley to the first and second vortexing idler pulleys.

US Pat. No. 9,051,601

METHODS OF NONSPECIFIC TARGET CAPTURE OF NUCLEIC ACIDS

Gen-Probe Incorporated, ...

1. A method for isolating nucleic acid from a sample, comprising the steps of:
a. mixing a sample containing nucleic acids with a non-specific capture probe comprising a first region that is a randomized
poly(k) sequence at a length of 18 residues comprising G and T nucleotides or G and U nucleotides attached to a second region
that is a first specific binding partner (SBP);

b. incubating a reaction mixture containing a support and the mixture of nucleic acids and non-specific capture probe in conditions
that allow hybridization of the first region with all or a portion of the nucleic acids in the sample and that allow for hybridization
of the SBP with a second specific binding partner (SBP?) immobilized to the support, thereby forming a hybridization complex;
and

c. separating the support from the solution phase of the reaction mixture, thereby isolating the nucleic acids away from other
components in the sample.

US Pat. No. 10,087,494

ASSAY FOR DETECTION OF HUMAN PARVOVIRUS NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

1. An amplification oligomer combination for amplifying human parvovirus genotypes 1, 2, and 3, the oligomer combination comprising:a) at least one primer oligomer member comprising a target binding sequence that is SEQ ID NO:48 or SEQ ID NO:50;
b) a first promoter-based oligomer member comprising a sequence that is SEQ ID NO:73; and
c) a second promoter-based oligomer member comprising a sequence that is SEQ ID NO:78.
US Pat. No. 9,845,509

COMPOSITIONS AND METHODS TO DETECT LEGIONELLA PNEUMOPHILA NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

1. A method for the amplification of Legionella pneumophila 23S nucleic acid present in a sample, the method comprising the steps of:
(A) contacting the sample with a capture probe that hybridizes to a Legionella pneumophila 23S target nucleic acid and separating the target nucleic acid away from other components of the sample;

(B) contacting the separated target nucleic acid from step (A) with a set of oligonucleotides, the set of oligonucleotides
comprising:

(i) a first amplification oligonucleotide, the base sequence of which consists of SEQ ID NO:87;
(ii) a second amplification oligonucleotide, the base sequence of which consists of SEQ ID NO:71 joined at its 5? end to a
promoter sequence; and

(iii) a blocker oligonucleotide, the base sequence of which is at least 80% identical to SEQ ID NO:84; and
(C) performing a transcription associated amplification reaction to generate amplification product from the target nucleic
acid using the set of oligonucleotides.

US Pat. No. 9,512,467

METHODS AND COMPOSITIONS FOR THE SELECTION AND OPTIMIZATION OF OLIGONUCLEOTIDE TAG SEQUENCES

GEN-PROBE INCORPORATED, ...

1. A method for identifying a nucleic acid tag sequence for use in a nucleic acid assay, comprising:
a) generating a pool of nucleic acid sequences, wherein the pool is at least three nucleic acid sequences;
b) screening the pool of nucleic acid sequences to identify two or more nucleic acid sequences having two or more performance
characteristics;

c) selecting one or more nucleic acid sequences, each for use as tag sequence in a nucleic acid assay;
d) comparing a nucleic acid sequence or sequences from the pool of nucleic acid sequences against a database having one or
more nucleic acid sequences to determine complementarity of the nucleic acid sequences from the pool of nucleic acid sequences
to the database having one or more sequences,

e) generating a sub-pool of nucleic acid sequences, wherein the sub-pool is a collection of nucleic acid sequences with complementarity
that is less than 95% to the nucleic acid sequence(s) in the database, that is less than 90% to the nucleic acid sequence(s)
in the database; that is less than 80% to the nucleic acid sequence(s) in the database, that is less than 70% to the nucleic
acid sequence(s) in the database, or that is less than 50% to the nucleic acid sequence(s) in the database;

f) screening the sub-pool of nucleic acid sequences for one or more performance characteristics selected from melting temperature,
activity in an enzyme reaction, G-C content, nucleobase composition, length, hybridization energy, multimer formation, internal
structure formation, G-quartet formation, and hairpin-stability,

g) selecting one or more nucleic acid sequences from the sub-pool for use as tag sequences in a nucleic acid assay;
h) synthesizing at least two different oligonucleotides for use in a nucleic acid assay, wherein each of the synthesized oligonucleotides
has a tag sequence selected according to step g); and

i) measuring for each of the different oligonucleotides synthesized in step h) one or more of the following performance characteristics:
speed of amplification, limit of detection, interference, precision of replicates, performance against a specific target nucleic
acid sequence, or performance against multiple target nucleic acid sequences in a nucleic acid assay, and optionally comparing
the measurements to the measurements obtained for an untagged oligonucleotide; and

j) selecting one or more of the nucleic acid tag sequences used in step i) for use in a nucleic acid assay;
k) modifying the sequence of the tag sequence incorporated into an oligonucleotide from step h) to obtain a modified tag sequence
for incorporation into an oligonucleotide;

l) measuring for the oligonucleotide containing a modified tag sequence from step k) one or more of the following performance
characteristics: speed of amplification, limit of detection, interference, precision of replicates, performance against a
specific target nucleic acid sequence, or performance against multiple target nucleic acid sequences in a nucleic acid assay;
and

m) selecting one or more of the modified nucleic acid tag sequences used in step i) for use in a nucleic acid assay.

US Pat. No. 9,284,549

TAGGED OLIGONUCLEOTIDES AND THEIR USE IN NUCLEIC ACID AMPLIFICATION METHODS

GEN-PROBE INCORPORATED, ...

1. A method for the selective amplification of at least one target nucleic acid sequence from a nucleic acid sample, said
method comprising the steps of:
(a) treating a nucleic acid sample comprising a target nucleic acid sequence with a tagged oligonucleotide comprising first
and second regions, said first region comprising a target hybridizing sequence which hybridizes to a 3?-end of said target
nucleic acid sequence and said second region comprising a tag sequence situated 5? to said target hybridizing sequence, wherein
said second region does not stably hybridize to a target nucleic acid containing said target nucleic acid sequence, and wherein
said target nucleic acid sequence is contained in each of a plurality of ribosomal nucleic acids from multiple species of
microorganisms;

(b) prior to initiating a primer extension reaction, reducing in said nucleic acid sample the effective concentration of unhybridized
tagged oligonucleotide having an active form in which a target hybridizing sequence of said unhybridized tagged oligonucleotide
is available for hybridization to said target nucleic acid sequence; and

(c) after step (b), initiating an extension reaction from the 3?-end of the tagged oligonucleotide with a DNA polymerase to
produce a primer extension product comprising a region complementary to the target nucleic acid sequence;

(d) separating the primer extension product from the target nucleic acid; and
(e) producing amplification products in a nucleic acid amplification reaction using first and second oligonucleotides, wherein
said first oligonucleotide comprises a hybridizing sequence which hybridizes to a 3?-end of the complement of said target
nucleic acid sequence and said second oligonucleotide comprises a hybridizing sequence which hybridizes to the complement
of said tag sequence, wherein said second oligonucleotide does stably hybridize to said target nucleic acid, and wherein each
of said amplification products comprises a base sequence which is substantially identical or complementary to the base sequence
of said target nucleic acid sequence and further comprises a base sequence which is substantially identical or complementary
to all or a portion of said tag sequence.

US Pat. No. 9,139,870

MULTIPHASE NUCLEIC ACID AMPLIFICATION

Gen-Probe Incorporated, ...

1. A method of quantifying a target nucleic acid sequence in a sample, comprising the steps of:
(a) contacting the sample with a first amplification oligonucleotide, specific for a first portion of the target nucleic acid
sequence, under conditions allowing hybridization of the first amplification oligonucleotide to the first portion of the target
nucleic acid sequence, thereby generating a pre-amplification hybrid that comprises the first amplification oligonucleotide
and the target nucleic acid sequence;

(b) isolating the pre-amplification hybrid by target capture onto a solid support followed by washing to remove any of the
first amplification oligonucleotide that did not hybridize to the first portion of the target nucleic acid sequence in step
(a);

(c) amplifying, in a first phase amplification reaction mixture, at least a portion of the target nucleic acid sequence of
the pre-amplification hybrid isolated in step (b) in a first phase, substantially isothermal, transcription-associated amplification
reaction under conditions that support linear amplification thereof, but do not support exponential amplification thereof,
thereby resulting in a reaction mixture comprising a first amplification product,

wherein the first phase amplification reaction mixture comprises a second amplification oligonucleotide, the second amplification
oligonucleotide being complementary to a portion of an extension product of the first amplification oligonucleotide, and

wherein the first amplification product is not a template for nucleic acid synthesis during the first phase, substantially
isothermal, transcription-associated amplification reaction;

(d) combining the reaction mixture comprising the first amplification product with at least one component that participates
in exponential amplification of the first amplification product, but that is lacking from the reaction mixture comprising
the first amplification product, to produce a second phase amplification reaction mixture,

wherein the second phase amplification reaction mixture additionally comprises a sequence-specific hybridization probe;
(e) performing, in a second phase, substantially isothermal, transcription-associated amplification reaction in the second
phase amplification reaction mixture, an exponential amplification of the first amplification product, thereby synthesizing
a second amplification product;

(f) detecting, with the sequence-specific hybridization probe at regular time intervals, synthesis of the second amplification
product in the second phase amplification reaction mixture; and

(g) quantifying the target nucleic acid sequence in the sample using results from step (f).
US Pat. No. 9,588,069

METHODS FOR PERFORMING THERMAL MELT ANALYSIS

GEN-PROBE INCORPORATED, ...

1. A method for performing a thermal melt analysis on the contents of a receptacle contained within a thermal melt analysis
module, the method comprising the steps of:
(a) bringing a receptacle into thermal contact with a thermal block contained within the thermal melt analysis module, wherein
the contents of the receptacle are at an initial temperature that is lower than the temperature of the thermal block when
the receptacle is brought into thermal contact with the thermal block;

(b) allowing the receptacle to dwell in thermal contact with the thermal block for a predetermined dwell period so that the
temperature of the contents of the receptacle increases from the initial temperature to a temperature that is higher than
the initial temperature;

(c) during step (b), periodically measuring an optical signal emitted from the contents of the receptacle as the temperature
of the contents of the receptacle increases;

(d) detecting a change, if any, in the measured optical signal during step (c); and
(e) removing the receptacle from the thermal melt analysis module,
wherein the thermal block is maintained at a steady-state temperature during steps (a)-(d).

US Pat. No. 9,335,336

AUTOMATED SAMPLE HANDLING INSTRUMENTATION, SYSTEMS, PROCESSES, AND METHODS

GEN-PROBE INCORPORATED, ...

1. A processing station for automatically processing a biological sample, comprising:
(a) a rotatable platform configured to rotate around a central axis;
(b) two or more container holders arranged in spatially distinct locations on the rotatable platform, wherein each of the
container holders is configured to hold a container and wherein the rotatable platform is configured to mix a fluid sample
contained within the container;

(c) a capping/decapping mechanism configured to decap and cap a container positioned in one of the two or more container holders;
(d) an automated pipettor comprising a pipette tip configured to selectively aspirate an amount of fluid into the pipette
tip or dispense an amount of fluid from the pipette tip and to move the pipette tip with respect to the rotatable platform
to enable the pipette tip to access a container carried on the rotatable platform; and

(e) mucoid strand detection means for detecting the presence of a mucoid strand suspended from the pipette tip,
wherein the rotatable platform, the capping/decapping mechanism, the automated pipettor, and the mucoid strand detection means
are in operative communication with a controller programmed to:

(i) activate the rotatable platform to move a container positioned in one of the two or more container holders into a capping/decapping
position,

(ii) activate the capping/decapping mechanism to remove a cap from the container,
(iv) activate the rotatable platform to move the container to a fluid transfer position,
(v) activate the automated pipettor to move the pipette tip into the fluid sample within the container, aspirate an amount
of the fluid sample into the pipette tip, and withdraw the pipette tip from the fluid sample,

(vi) after the automated pipettor has aspirated the amount of the fluid sample from the container and withdrawn the pipette
tip from the fluid sample within the container but before the automated pipettor moves the pipette tip away from the container,
determine if there is a mucoid strand on the pipette tip with the mucoid strand detection means, and

(vii) if a mucoid strand is detected, activate the automated pipettor to dispense the aspirated fluid sample back into the
container.

US Pat. No. 9,243,286

METHODS OF USING OLIGONUCLEOTIDES COMPRISING A MOLECULAR SWITCH

GEN-PROBE INCORPORATED, ...

1. A method of detecting the presence or absence of a mutation or polymorphism in a sample comprising nucleic acids, the method
comprising:
(I) contacting said sample, under conditions suitable for hybridization, with an oligonucleotide comprising
(a) a nucleic acid anchor region complementary to a first sequence of nucleic acid residues of a target nucleic acid, and
(b) a switch domain comprising a bridging domain and a binding domain,
wherein said binding domain comprises 2-20 nucleic acid bases or analogs thereof complementary to said target nucleic acid
and said binding domain has less affinity for said target nucleic acid than said anchor region,

wherein said bridging domain is located between said anchor region and said binding domain and comprises 2-11 universal or
non-hydrogen bonding natural bases or analogs thereof that do not form a Watson-Crick hybridization complex with said target
nucleic acid or a mixture of universal and non-hydrogen bonding natural bases or analogs thereof that do not form a Watson-Crick
hybridization complex with said target nucleic acid, wherein two or more universal or non-hydrogen bonding natural bases or
analogs thereof or a mixture of universal and non-hydrogen bonding natural bases or analogs thereof in said bridging domain
are juxtaposed, and wherein said universal or non-hydrogen bonding natural bases or analogs thereof in said bridging domain
substitute for bases complementary to nucleotide bases of said target nucleic acid, and

wherein said switch domain is able to discriminate between (i) a sequence of nucleic acid residues of said target nucleic
acid that is complementary to said binding domain and (ii) a mismatch sequence of nucleic acid residues of said target nucleic
acid that contains at least one nucleic acid residue that is not complementary to said binding domain, under conditions wherein
said anchor region (a) forms a stable duplex with said first sequence of nucleic acid residues of said target nucleic acid,
wherein the at least one nucleic acid residue that is not complementary to said binding domain corresponds to the site of
the polymorphism or mutation to be detected; and

(II) detecting, under conditions wherein said anchor region (a) forms the stable duplex with said first sequence, the hybridization
status of said switch domain as an indication of the presence or absence of the mutation or polymorphism in said sample.

US Pat. No. 9,150,908

METHOD FOR DETECTING THE PRESENCE OF A NUCLEIC ACID IN A SAMPLE

GEN-PROBE INCORPORATED, ...

1. A method for detecting the presence of a nucleic acid in a sample, the method comprising performing within a housing of
a self-contained, stand-alone analyzer the automated steps of:
a) contacting the sample with a solid support such that a complex comprising the nucleic acid and the solid support is formed
in the sample, wherein the solid support comprises a magnetically-responsive particle, and wherein the complex is suspended
in a fluid component of the sample;

b) after step a), subjecting the complex contained in the sample to a magnetic field;
c) while the complex contained in the sample is subjected to the magnetic field, aspirating at least a portion of the fluid
component of the sample from the complex;

d) after step c), washing the solid support one or more times with a wash buffer, thereby providing a purified form of the
nucleic acid;

e) forming a reaction mixture with a pipette of the analyzer, wherein the reaction mixture comprises the purified form of
the nucleic acid and all reagents required to perform a nucleic acid amplification;

f) synthesizing amplification products in the reaction mixture, each of the amplification products comprising a nucleotide
sequence contained in the nucleic acid or its complement;

g) exposing an amplification product that is one of the amplification products synthesized in step f) to a probe having a
label, such that a hybrid comprising the probe and the amplification product is formed in solution in a mixture containing
the probe and the amplification products; and

h) in the mixture of step g), detecting the label after formation of the hybrid, wherein the formation of the hybrid in the
mixture is an indication of the presence of the nucleic acid in the sample,

wherein steps b)-d) are performed at a first station of the analyzer and step f) is performed at a second station of the analyzer,
and

wherein step f) is performed within an enclosure having a receptacle access opening, the receptacle access opening being closed
by a door of the enclosure during step f).

US Pat. No. 10,043,047

SYSTEMS AND METHODS FOR READING MACHINE-READABLE MARKS ON RACKS AND RECEPTACLES

GEN-PROBE INCORPORATED, ...

1. A sample instrument comprising:a moveable support configured to move from a first position to a second position, the moveable support defining a first pocket configured to receive a first object having a first machine-readable mark, and defining a second pocket configured to receive a second object having a second machine-readable mark, the moveable support comprising a first fiducial machine-readable mark containing information that identifies a location of the first fiducial machine-readable mark and a second fiducial machine-readable mark containing information that identifies a location of the second fiducial machine-readable mark; and
an image capture device having a field of view that captures a first image including the first fiducial machine-readable mark and, when the first object is received within the first pocket, the first machine-readable mark of the first object, and captures a second image as the moveable support moves from the first position to the second position that includes the second fiducial machine-readable mark and, when the second object is received within the second pocket, the second machine-readable mark of the second object; and
a processor configured to
decode the first machine-readable mark and the first fiducial machine-readable mark in the first image,
associate information decoded from the first machine-readable mark with a first location on the moveable support having a predetermined association with the first fiducial machine-readable mark,
decode the second machine-readable mark and the second fiducial machine-readable mark in the second image, and
associate information decoded from the second machine-readable mark with a second location on the moveable support having a predetermined association with the second fiducial machine-readable mark.

US Pat. No. 9,175,337

METHODS FOR AMPLIFYING NUCLEIC ACID USING TAG-MEDIATED DISPLACEMENT

Gen-Probe Incorporated, ...

1. A method of amplifying a nucleic acid target region, the method comprising:
contacting a target nucleic acid comprising the target region with
(1) a first amplification oligomer comprising
(a) a target-binding priming segment (T1) complementary to a 3?-end of the target region; and
(b) a first heterologous displacer tag (D1) located 5? to T1;
said contacting comprising conditions whereby the target nucleic acid serves as a template for extension from the first amplification
oligomer to produce a first amplification product comprising T1 and D1;

(2) a second amplification oligomer comprising a target-binding segment T2 complementary to a region of the first amplicon
that is the complement of a 5?-end of the target region, and wherein said contacting further comprises conditions whereby
the first amplicon serves as a template to produce a second amplicon comprising segments cT1 and cD1, complementary to T1
and D1, respectively;

(3) a third amplification oligomer comprising target-binding priming segment T1p having a nucleotide sequence corresponding to T1, or corresponding to the complement of a second amplicon target sequence
cT1? near or overlapping with cT1 and situated 5? to cD1; and

(4) a fourth amplification oligomer comprising a displacer priming segment D1p having a nucleotide sequence corresponding to D1;

wherein said contacting further comprises conditions whereby the second amplicon serves as a template for extension from both
the third and fourth amplification oligomers, wherein extension of T1p from a T1p:cT1/cT1? hybrid produces a third amplicon, and wherein extension of D1p from a D1p:cD1 hybrid produces a fourth amplicon while displacing the third amplicon.

US Pat. No. 9,109,263

COMPOSITIONS TO DETECT CANDIDA ALBICANS NUCLEIC ACID

Gen-Probe Incorporated, ...

1. A set of oligomers for use in amplifying a Candida albicans 26S rRNA sequence or DNA encoding the 26S rRNA sequence, the set of oligomers comprising first and second amplification oligomers,
wherein the first amplification oligomer consists of the base sequence of SEQ ID NO:19, the DNA equivalent of SEQ ID NO:19,
or a combination RNA/DNA equivalent of SEQ ID NO:19, and wherein the second amplification oligomer is a promoter-primer comprising
a 5? promoter sequence and a target binding region that consists of the base sequence of SEQ ID NO:24, the DNA equivalent
of SEQ ID NO:24, or a combination RNA/DNA equivalent of SEQ ID NO:24.
US Pat. No. 9,074,263

COMPOSITIONS AND REACTION MIXTURES FOR THE DETECTION OF NUCLEIC ACIDS FROM MULTIPLE TYPES OF HUMAN PAPILLOMAVIRUS

Gen-Probe Incorporated, ...

1. A combination of amplification oligomers for detecting human papillomavirus (HPV) of multiple HPV types, the combination
comprising first amplification oligonucleotides, comprising a target binding region and a 5? promoter sequence, and second
amplification oligonucleotides, comprising a target binding region, wherein pairs of the first and second amplification oligonucleotides
can hybridize to opposing strands of HPV nucleic acid for transcription mediated amplification of HPV nucleic acid between
hybridized pairs of the first and second amplification oligonucleotides, wherein
(a) the target binding regions of the first amplification oligomers consist of SEQ ID Nos. 19, 21, 23, 25, 29, 31, 33, 35,
and 37, respectively, and the target binding regions of the second amplification oligomers consist of SEQ ID Nos. 38, 39,
40, and 41, respectively; or complements thereof; RNA equivalents thereof; or RNA equivalents of the complements thereof;
or

(b) the target binding regions of the first amplification oligomers consists of SEQ ID Nos. 21, 23, 25, 29, 31, 33, 35, 37,
and 42, respectively, and the target binding regions of the second amplification oligomers consist of SEQ ID Nos. 38, 39,
40, and 41, respectively, or complements thereof; RNA equivalents thereof; or RNA equivalents of the complements thereof.

US Pat. No. 9,527,080

FLUID CARTRIDGE

GEN-PROBE INCORPORATED, ...

1. A cartridge consisting of:
a plurality of adjacently-positioned wells;
a top surface that is integrally molded with the wells, each of the wells depending from the top surface and having a bottom
surface and a discrete opening at the top surface, wherein at least a first well and a second well of the plurality of wells
are sealed, wherein at least a portion of the wells contain a fluid, and wherein the first and second wells contain the same
fluid;

a first fluid path connecting the first well with the second well, wherein the first fluid path is disposed adjacent a lower
portion of each of the first and second wells and above the respective bottom surfaces of the first and second wells;

a second fluid path connecting the first well with the second well, wherein the second fluid path is disposed adjacent an
upper portion of each of the first and second wells; and

optionally, an outer wall depending from a perimeter of the top surface.
US Pat. No. 9,109,264

COMPOSITIONS AND METHODS FOR DETECTING HEPATITIS B VIRUS

Gen-Probe Incorporated, ...

1. A composition of oligonucleotides for amplifying and detecting an HBV nucleic acid wherein said composition comprises at
least two amplification oligomers configured to generate an HBV amplicon from an HBV nucleic acid present in a test sample
at a concentration as low as 200 copies/ml of reaction mixture, wherein:
(a) the first amplification oligomer consists of a target hybridizing sequence, optionally, an upstream sequence that is not
complementary to an HBV target sequence, and a 5? promoter sequence for an RNA polymerase, wherein the target hybridizing
sequence consists of SEQ ID NO:25 or SEQ ID NO:28; and

(b) the second amplification oligomer consists of a target hybridizing sequence consisting of SEQ ID NO:15.

US Pat. No. 10,065,190

MULTI-WELL TRAY AND RACK THEREFORE

Gen-Probe Incorporated, ...

1. A multi-well tray for use in an automated process comprising:a base; and
one or more sets of wells, wherein each set of wells comprises:
a receptacle cap well formed in the base and comprising a side wall and a bottom wall defining interior surfaces of the receptacle cap well and a protrusion projecting upward from the bottom wall; and
a receptacle well formed in the base and comprising a side wall defining an interior surface of the receptacle well and a ledge extending from the side wall of the receptacle well and defining a perimeter of an end of a through-hole.
US Pat. No. 9,920,382

COMPOSITIONS AND METHODS FOR DETECTING NUCLEIC ACID FROM MOLLICUTES

GEN-PROBE INCORPORATED, ...

1. A method for the in vitro amplification of a nucleic acid in a sample, said nucleic acid being from one or more species
in the class Mollicutes, comprising the steps of:
(a.) contacting a sample with four tagged amplification oligomers, each of which individually comprises a target hybridizing
region and a tag region, wherein said four tagged amplification oligomers are each individually selected from the group consisting
of:

(i) a tagged amplification oligomer comprising a target hybridizing region that is from 15 to 50 nucleobases in length and
contains a nucleotide sequence that is configured to specifically hybridize to all or a portion of a region of a target nucleic
acid corresponding to residues 5065 to 5088 of SEQ ID NO:1;

(ii) a tagged amplification oligomer comprising a target hybridizing region that is from 15 to 50 nucleobases in length and
contains a nucleotide sequence that is configured to specifically hybridize to all or a portion of a region of a target nucleic
acid corresponding to residues 4752 to 4798 of SEQ ID NO:2;

(iii) a tagged amplification oligomer comprising a target hybridizing region that is from 15 to 50 nucleobases in length and
contains a nucleotide sequence that is configured to specifically hybridize to all or a portion of a region of a target nucleic
acid corresponding to residues 1954 to 2006 of SEQ ID NO:3; and

(iv) a tagged amplification oligomer comprising a target hybridizing region that is from 15 to 50 nucleobases in length and
contains a nucleotide sequence that is configured to specifically hybridize to all or a portion of a region of a target nucleic
acid corresponding to residues 1994 to 2036 of SEQ ID NO:4; and

(b.) providing suitable conditions for performing an in vitro amplification reaction.

US Pat. No. 9,630,179

FLUID CARTRIDGE

GEN-PROBE INCORPORATED, ...

1. A method for transferring a liquid from a fluid cartridge comprising a casing having a top surface, a fluid chamber comprising
a well formed in the casing with an opening at the top surface that is sealed to prevent or limit liquid evaporation through
the opening, a fluid reservoir adjacent to the fluid chamber and comprising a well formed in the casing with an opening at
the top surface that is sealed to prevent or limit liquid evaporation through the opening, wherein the fluid chamber and the
fluid reservoir contain the same liquid, wherein the opening of the fluid reservoir is larger than the opening of the fluid
chamber, and wherein the opening of the fluid chamber is sealed by a frangible seal secured to the top surface and covering
the opening of the fluid chamber, a first path between the fluid reservoir and the fluid chamber disposed proximate a lower
portion of the fluid reservoir and fluid chamber and providing liquid communication between the fluid reservoir and the fluid
chamber, and a second path between the fluid reservoir and fluid chamber disposed proximate a top portion of the fluid reservoir
and fluid chamber and providing fluid communication between the fluid reservoir and the fluid chamber, the method comprising:
(a) penetrating the frangible seal covering the opening of the fluid chamber with an automated pipettor;
(b) contacting the liquid contained in the fluid chamber with the automated pipettor; and
(c) withdrawing at least a portion of the liquid from the fluid chamber with the automated pipettor, thereby causing liquid
to flow from the fluid reservoir into the fluid chamber through the first path while air flows from the fluid chamber to the
fluid reservoir through the second path.

US Pat. No. 9,458,451

MULTI-CHANNEL OPTICAL MEASUREMENT INSTRUMENT

GEN-PROBE INCORPORATED, ...

1. A detector for detecting optical emissions of two or more different wavelengths or ranges of wavelengths from a sample,
wherein emissions of two or more different wavelengths are indicative of the presence, amount, or state of two or more analytes
of interest in the sample, the detector comprising:
two or more excitation channels fixed with respect to the sample and each other, wherein each excitation channel is adapted
to direct an excitation signal of a different prescribed excitation wavelength or range of excitation wavelengths toward the
sample and each excitation channel comprises:

a light emitting element adapted to emit excitation light; and
excitation optical elements defining an excitation optical path having an excitation optic axis, the excitation optical elements
being constructed and arranged to transmit at least a portion of the light emitted by the light-emitting element having the
prescribed excitation wavelength or range of excitation wavelengths toward the sample;

two or more emission channels fixed with respect to the sample, the excitation channels, and each other, wherein each emission
channel is adapted to receive and detect an emission signal of a different prescribed emission wavelength or range of emission
wavelengths from the sample and each emission channel comprises:

emission optical elements defining an emission optical path having an emission optic axis, the emission optical elements being
constructed and arranged to transmit at least a portion of any light emitted by the sample having the prescribed emission
wavelength or range of emission wavelengths; and

a light-detecting element adapted to detect light transmitted by the emission optical elements and to convert the detected
light to an electronic signal indicative of at least one of the presence and strength of the detected light;

a housing, wherein each excitation channel is disposed within a different excitation conduit within the housing and each emission
channel is disposed within a different emission conduit within the housing, and wherein the excitation optic axes of the excitation
channels and the emission optic axes of the emission channels are parallel to one another throughout their extents;

a solid, undivided optic lens constructed and arranged with respect to the excitation channels and the emission channels to
(1) direct excitation light transmitted by each excitation channel and impinging on a different portion of the optic lens
at a prescribed location and (2) receive emission signals emitted by contents of the sample and to direct at least a portion
of the received emission signals into each of the emission channels, wherein the optic lens is positioned with respect to
the excitation and emission channels so that the light emitting element and excitation optical elements of each excitation
channel and the emission optical elements and the light-detecting element of each emission channel are disposed on one side
of the optic lens, and wherein the detector includes no optic element on an opposite side of the optic lens between the optic
lens and the sample; and

signal discriminating circuitry comprising:
excitation modulation circuitry constructed and arranged to modulate the excitation signal of each excitation channel at a
predefined excitation frequency, wherein the excitation frequencies of at least two of the excitation channels are different;
and

detection circuitry constructed and arranged to identify that portion of the detected light that is substantially at the excitation
frequency.

US Pat. No. 9,371,556

SOLUTIONS, METHODS AND KITS FOR DEACTIVATING NUCLEIC ACIDS

GEN-PROBE INCORPORATED, ...

1. A homogenous solution for use in preventing nucleic acids from acting as templates in an amplification reaction when the
solution is combined with a nucleic acid deactivating agent, the solution consisting essentially of a corrosion-inhibiting
agent, a wetting agent, and a solubilizing agent, each of the agents remaining substantially in solution at 22° C.,
wherein the wetting agent and the solubilizing agent are each needed to maintain the other agent substantially in solution
in the presence of the corrosion-inhibiting agent,

wherein the amount of each agent is such that, when combined with a nucleic acid deactivating agent in an amount sufficient
for the solution to substantially deactivate nucleic acids, the corrosion-inhibiting agent reduces the corrosive properties
of the deactivating agent, the wetting agent improves the dispersion properties of the deactivating agent on a solid surface
and/or increases the solubility of the deactivating agent and/or other material that may be present on a solid surface or
in a solution, and the solubilizing agent increases the solubility of at least one of the deactivating agent, the corrosion-inhibiting
agent and the wetting agent, and

wherein the solution does not include a nucleic acid deactivating agent;
wherein the corrosion-inhibiting agent comprises sodium bicarbonate; the wetting agent comprises a detergent; and the solubilizing
agent comprises an emulsifying agent.

US Pat. No. 9,109,261

METHOD AND KIT FOR IDENTIFYING ANTIBIOTIC-RESISTANT MICROORGANISMS

Gen-Probe Incorporated, ...

1. A device for detecting nucleic acids encoding resistance to an antibiotic, comprising a solid support and a plurality of
detectably labeled solution-phase hybridization probes distributed among a plurality of loci thereon, said plurality of loci
comprising,
(a) a first locus that comprises one or more solution-phase hybridization probes that collectively hybridize to ribosomal
nucleic acids from a plurality of species of bacteria in the genus Staphylococcus, comprising Staphylococcus aureus and Staphylococcus epidermidis, but do not hybridize to ribosomal nucleic acids of bacteria in the genus Enterococcus,

(b) a second locus that comprises a probe mix containing
(i) one or more solution-phase hybridization probes that collectively hybridize to ribosomal nucleic acids from a plurality
of bacteria in the genus Enterococcus, comprising Enterococcus faecalis and Enterococcus faecium, but not Staphylococcus aureus or any other bacteria in the genus Staphylococcus, and

(ii) at least one solution-phase hybridization probe that hybridizes to ribosomal nucleic acids from Staphylococcus aureus but not from other species in the genus Staphylococcus or bacteria in the genus Enterococcus,

(c) a third locus that comprises a probe mix containing a first mecA solution-phase hybridization probe that consists of the
nucleotide sequence of SEQ ID NO:2 or the complement thereof, a second mecA solution-phase hybridization probe that consists
of the nucleotide sequence of SEQ ID NO:3 or the complement thereof, and a third mecA solution-phase hybridization probe that
consists of the nucleotide sequence of SEQ ID NO:5 or the complement thereof, and

(d) a fourth locus that comprises a solution-phase hybridization probe that hybridizes both to VanA nucleic acids and VanB
nucleic acids, wherein said solution-phase hybridization probe consists of the nucleotide sequence of SEQ ID NO:33 or the
complement thereof; wherein each of said plurality of loci is configured as a matrix that provides an identification of one
or more unknown nucleic acids from a sample, and wherein each of said detectably labeled solution-phase hybridization probes
comprises a polynucleotide sequence which is covalently attached to a non-nucleotide detectable moiety that emits a detectable
signal.

US Pat. No. 9,771,571

METHOD OF ISOLATING NUCLEIC ACID FROM SPECIMENS IN LIQUID-BASED CYTOLOGY PRESERVATIVES CONTAINING FORMALDEHYDE

GEN-PROBE INCORPORATED, ...

7. A reaction mixture for treating a specimen, wherein the specimen is a clinical sample comprising nucleic acids and is disposed
in a liquid-based cytology preservative containing formaldehyde, and wherein the reaction mixture comprises proteinase K and
2-imidazolidone.
US Pat. No. 9,732,374

METHOD FOR ANALYZING A PLURALITY OF SAMPLES

GEN-PROBE INCORPORATED, ...

1. An automated method for analyzing a plurality of samples, the method comprising performing within a housing of a self-contained
diagnostic system the steps of:
(a) loading the diagnostic system with the plurality of samples;
(b) after step (a), performing a first assay on a first sample subset of the plurality of samples, the first assay comprising:
(i) preparing each of a plurality of samples of the first sample subset using an aliquot of a first bulk reagent contained
in a first bulk reagent container, wherein the first bulk reagent comprises a solid support for directly or indirectly binding
and immobilizing a first target nucleic acid that may be present in one or more samples of the first sample subset; and

(ii) after step (b)(i), performing in each sample of the first sample subset a first amplification reaction for amplifying
a region of the first target nucleic acid, wherein a unit-dose reagent comprising a polymerase is used to perform the first
amplification reaction in each sample of the first sample subset, the unit does reagent being in an amount sufficient to perform
only one amplification reaction; and

(c) after step (a), performing a second assay on a second sample subset of the plurality of samples, the second assay comprising:
(i) preparing each of a plurality of samples of the second sample subset using an aliquot of a second bulk reagent contained
in a second bulk reagent container, wherein the second bulk reagent comprises a solid support for directly or indirectly binding
and immobilizing a second target nucleic acid that may be present in one or more samples of the second sample subset; and

(ii) after step (c)(i), and simultaneous with step (b)(ii), performing in each sample of the second sample subset a second
amplification reaction for amplifying a region of the second target nucleic acid, wherein an aliquot of a third bulk reagent
contained in a third bulk reagent container and comprising a polymerase is used to perform the second amplification reaction
in each sample of the second sample subset wherein the first assay does not use a bulk reagent comprising a polymerase for
performing an amplification reaction, and wherein the second assay does not use a unit-dose reagent comprising a polymerase
for performing an amplification reaction, the unit-dose reagent being in an amount sufficient to perform only a single amplification
reaction,

wherein the diagnostic system stores the unit-dose reagent for each of the first amplification reactions and the bulk reagents
prior to performing the first and second assays.

US Pat. No. 9,476,094

POLYNUCLEOTIDE SEQUENCING METHOD

GEN-PROBE INCORPORATED, ...

1. A method for determining the sequence of a polynucleotide, consisting essentially of the sequential steps of:
(i) contacting a polynucleotide processive enzyme immobilised in a fixed position having a metal nanoparticle positioned on
or proximal to the enzyme with a target polynucleotide to form a complex;

(ii) contacting the complex with one or more nucleoside triphosphates selected from the group consisting of dATP, dTTP, dGTP,
and dCTP, under conditions sufficient to induce polynucleotide processive enzyme activity;

(iii) generating a non-linear optical signal in the area encompassing at least a portion of the immobilized enzyme; and
(iv) detecting an effect as the complex interacts with the one or more nucleoside triphosphates, by measurement of the non-linear
optical signal, wherein the non-linear optical signal measurement consists of measuring the second or third harmonic signals,
thereby determining the sequence of the polynucleotide.

US Pat. No. 10,053,742

COMPOSITIONS AND METHODS FOR DETECTING HEV NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

1. A combination of at least two oligomers for determining the presence or absence of hepatitis E virus (HEV) in a sample, said oligomer combination comprising:at least two amplification oligomers for amplifying a target region of an HEV target nucleic acid, wherein
(a) at least one amplification oligomer is selected from the group consisting of
(i) an oligomer comprising a target-hybridizing sequence consisting of a sequence that is from about 14 to about 23 contiguous nucleotides contained in the sequence of SEQ ID NO:63 and that includes at least the sequence of SEQ ID NO:26, including RNA equivalents and DNA/RNA chimerics thereof, and
(ii) an oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:28, including RNA equivalents and DNA/RNA chimerics thereof; and
(b) at least one amplification oligomer that is a promoter primer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 or SEQ ID NO:56, including RNA equivalents and DNA/RNA chimerics thereof and further comprising a promoter sequence joined to the 5? end of the target hybridizing sequence.
US Pat. No. 10,047,407

DETECTION OF NUCLEIC ACIDS FROM MULTIPLE TYPES OF HUMAN PAPILLOMAVIRUS

GEN-PROBE INCORPORATED, ...

5. A method of determining the presence or absence of a human papillomavirus (HPV) nucleic acid type in group C1 in a sample, comprising the steps of:(a) contacting a sample with a detection probe oligomer comprising:
(i) a target-specific sequence consisting of a nucleotide sequence selected from the group consisting of SEQ ID NOs:13, 46, 45, complements thereof, and RNA equivalents thereof; and
(ii) a detectable label; and
(b) performing a detection reaction to detect a signal from the detectable label, wherein the signal indicates the presence of a human papillomavirus (HPV) nucleic acid type in group C1 in the sample.

US Pat. No. 9,945,780

USE OF A FLUORESCENT MATERIAL TO DETECT FAILURE OR DETERIORATED PERFORMANCE OF A FLUOROMETER

GEN-PROBE INCORPORATED, ...

1. A system for monitoring the performance of a fluorometer in a dynamic environment, comprisinga fluorometer comprising two or more channels, each channel having a separate light source, optical focus and filter assembly, and optical signal detector, and wherein each channel is configured to focus the light source at a detection zone;
a support comprising two or more fluorescent reference standards, each fluorescent reference standard corresponding to a single channel of the fluorometer, wherein the support is arranged to accommodate two or more removable receptacle vessels; and
a drive mechanism configured to adjust the relative horizontal positioning between the reference standards and the fluorometer such that each of the two or more fluorescent reference standards can be positioned in or out of optical communication with its corresponding channel of the fluorometer.
US Pat. No. 9,593,383

COMPOSITIONS, KITS AND RELATED METHODS FOR THE DETECTION AND/OR MONITORING OF LISTERIA

GEN-PROBE INCORPORATED, ...

1. A method for detecting Listeria in a sample, the method comprising:
performing a nucleic acid amplification assay to generate an amplification product from a Listeria nucleic acid using a set of oligonucleotides comprising a T7 provider oligonucleotide and a primer oligonucleotide, wherein
the T7 provider oligonucleotide has the sequence consisting of SEQ ID NO:55 and the primer oligonucleotide has the sequence
selected from the group consisting of SEQ ID NOs:64, 65, & 68, and

detecting the presence or absence of amplification product utilizing a detection oligonucleotide that specifically hybridizes
to the amplification product, wherein the detection oligonucleotide is a molecular torch having the sequence consisting of
SEQ ID NO:78,

wherein the presence of the amplification product indicates the presence of Listeria in the sample.

US Pat. No. 9,580,762

DETECTION OF WEST NILE VIRUS NUCLEIC ACIDS IN THE VIRAL 3? NON-CODING REGION

GEN-PROBE INCORPORATED, ...

1. A method of establishing whether a biological sample contains WNV (West Nile virus), the method comprising the steps of:
(a) obtaining nucleic acids from the biological sample;
(b) performing an in vitro nucleic acid amplification reaction comprising nucleic acids obtained in step (a) as templates,
and further comprising a hybridization probe labeled with one or more detectable labels selected from the group consisting
of: a chemiluminescent compound; a fluorophore moiety; and a quencher moiety, wherein said hybridization probe is up to 60
nucleotides in length and comprises a base sequence selected from the group consisting of SEQ ID NO:104, SEQ ID NO:105, SEQ
ID NO:106, SEQ ID NO:107, SEQ ID NO:108, SEQ ID NO:109, SEQ ID NO:110, SEQ ID NO:111, SEQ ID NO:112, SEQ ID NO:113, SEQ ID
NO:114, SEQ ID NO:115, and SEQ ID NO:116,

whereby there is synthesized, if nucleic acids obtained in step (a) comprise WNV nucleic acids, an amplification product terminating
at one end with the nucleotide sequence of SEQ ID NO:74 or the complement thereof, allowing for RNA and DNA equivalent bases,
and

wherein there is formed by complementary base pairing, if nucleic acids obtained in step (a) comprise WNV nucleic acids, a
nucleic acid duplex comprising the hybridization probe and a strand of the amplification product synthesized in step (b);

(c) determining whether the nucleic acid duplex formed in the in vitro nucleic acid amplification reaction; and
(d) establishing either that,
(i) the biological sample contains WNV if the nucleic acid duplex is determined to have formed in the in vitro nucleic acid
amplification reaction, or

(ii) the biological sample does not contain detectable amounts of WNV if the nucleic acid duplex is not determined to have
formed in the in vitro nucleic acid amplification reaction.

US Pat. No. 9,465,161

INDEXING SIGNAL DETECTION MODULE

GEN-PROBE INCORPORATED, ...

1. An apparatus for detecting a signal emission from each of a plurality of potential signal emission sources, said apparatus
comprising:
a plurality of signal transmission conduits corresponding in number to the number of signal emission sources, each signal
transmission conduit being associated with at least one of the signal emission sources and being configured to transmit a
signal emitted by the associated signal emission source between a first end and a second end thereof;

a conduit reformatter constructed and arranged to secure the first ends of the respective signal transmission conduits in
a first spatial arrangement corresponding to a spatial arrangement of the signal emission sources, such that the first end
of each signal transmission conduit is positioned to receive an emission signal emitted by an associated signal emission source,
and to secure the second ends of the respective signal transmission conduits in a second spatial arrangement different from
the first spatial arrangement;

a plurality of signal detectors configured to detect a signal emitted by each signal emission source, wherein each signal
detector is configured to generate an excitation light of a different predetermined wavelength and to detect light of a different
predetermined emission wavelength, and further wherein each of the plurality of signal emission sources is in optical communication
with a single signal transmission conduit; and

a signal detector carrier having mounted thereon the plurality of signal detectors, the signal detector carrier being configured
to carry the signal detectors and to move each signal detector in a path that sequentially places the signal detector in signal
detecting positions with respect to the second ends of the signal transmission conduits arranged in the second spatial arrangement.

US Pat. No. 9,404,147

CLOSED NUCLEIC ACID STRUCTURES

GEN-PROBE INCORPORATED, ...

1. A method of forming a closed nucleic acid structure comprising a target nucleic acid, the method comprising:
(a) providing a denatured target nucleic acid, at least one strand of the denatured target nucleic acid having a 5? phosphate,
a 5? segment, and a 3? segment;

(b) contacting the strand of the denatured target nucleic acid with a 3? blocked oligonucleotide having a 5? segment, a 3?
segment, and an intervening segment that links the 5? and 3? segments, the 3? segment being complementary to the 3? end segment
of the denatured target nucleic acid strand and the intervening segment having a common sequence with the 5? segment of the
denatured target nucleic acid strand;

(c) annealing the 3? segment of the 3? blocked oligonucleotide to the 3? segment of the denatured target nucleic acid strand,
whereby the 3? blocked oligonucleotide provides a template for extension of the denatured target nucleic acid strand;

(d) extending the denatured target nucleic acid strand to form a 3? extended nucleic acid strand having from 5?-3? a 5? phosphate
group, the target nucleic acid strand, a 3? extension complementary to the 5? and intervening segments of the 3? blocked oligonucleotide,
and a 3? hydroxyl group;

(e) separating the 3? blocked oligonucleotide from the 3? extended nucleic acid strand;
(f) contacting the 3? extended nucleic acid with a stem-loop adaptor having a 3? segment and a 5? segment, the 5? segment
having a 5? phosphate group and a sequence capable of forming a stem-loop structure and the 3? segment having a common sequence
with the 3? segment of the 3? blocked oligonucleotide and ending in a 3? hydroxyl group;

(g) allowing the 3? extended nucleic acid strand to intermolecularly hybridize with the stem-loop adaptor and intramolecularly
hybridize with itself; thereby forming a nicked intermediate wherein the 3? extended nucleic acid strand has a stem-loop structure,
the 5? phosphate group of the 3? extended nucleic acid strand is separated from the 3? hydroxyl group of the stem-loop adaptor
by a nick, and the 5? phosphate group of the stem-loop adaptor is separated from the 3? hydroxyl group of the 3? extended
nucleic acid strand by a nick; and

(h) providing a ligase that seals nicks between the ends of the stem-loop adaptor and the ends of the 3? extended nucleic
acid, thereby forming a closed nucleic acid structure including the strand of the target nucleic acid circularized by a stem-loop
structure.

US Pat. No. 9,234,249

COMPOSITIONS AND ASSAYS TO DETECT SWINE H1N1 INFLUENZA A VIRUS, SEASONAL H1 INFLUENZA A VIRUS AND SEASONAL H3 INFLUENZA A VIRUS NUCLEIC ACIDS

GEN-PROBE INCORPORATED, ...

1. A method for the detection of an influenza A virus from a sample, comprising the steps of:
(a) contacting an influenza A virus nucleic acid from a sample with a composition comprising at least two seasonal H1 influenza
A-specific amplification primers, wherein the at least two primers comprise nucleic acid sequences in combination(s) selected
from the group consisting of Combination 1: SEQ ID NO:63 and SEQ ID NO:64; Combination 2: SEQ ID NO:68 and SEQ ID NO:69; and
Combination 3: SEQ ID NO:72 and SEQ ID NO:73, or RNA equivalents thereof;

(b) providing conditions for amplifying the nucleic acid from step a by a polymerase chain reaction to generate an amplification
product from the nucleic acid; and

(c) detecting the presence or absence of amplification product from step b, wherein the presence of the amplification product
indicates that the sample contained an influenza A virus.

US Pat. No. 10,113,205

COMPOSITIONS TO DETECT SEASONAL H1 INFLUENZA A VIRUS NUCLEIC ACIDS

GEN-PROBE INCORPORATED, ...

1. A composition comprising:at least first and second seasonal H1 influenza A-specific amplification primers, wherein the first primer comprises a H1 influenza A-specific sequence consisting of SEQ ID NO:72 and the second primer comprises a H1 influenza A-specific sequence consisting of SEQ ID:73; and
a seasonal H1 influenza A-specific oligonucleotide detection probe having a H1 influenza A-specific sequence of at least 18 contiguous nucleotides, wherein said detection probe is complementary to a H1 influenza A nucleic acid sequence that is amplifiable by the first and second primers, and wherein said detection probe comprises at least a first detectable label operably linked to said oligonucleotide detection probe.
US Pat. No. 10,047,406

COMPOSITIONS AND METHODS FOR DETECTING HEV NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

1. A combination of at least three oligomers for determining the presence or absence of hepatitis E virus (HEV) in a sample, said oligomer combination comprising:at least two amplification oligomers for amplifying a target region of an HEV target nucleic acid and at least one detectably labeled detection probe oligomer, wherein
(a) at least one amplification oligomer is
an oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:28, including RNA equivalents and DNA/RNA chimerics thereof;
(b) at least one amplification oligomer is a promoter primer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 or SEQ ID NO:56, including RNA equivalents and DNA/RNA chimerics thereof and further comprising a promoter sequence joined to the 5? end of the target hybridizing sequence of the promoter primer; and
(c) at least one detectably labeled detection probe oligomer comprises a target-hybridizing sequence that is from about 14 to about 28 nucleotides in length and is configured to specifically hybridize to a target sequence contained within SEQ ID NO:39 or the complement thererof.

US Pat. No. 9,724,693

METHOD AND APPARATUS FOR EFFECTING AUTOMATED MOVEMENT OF A MAGNET IN AN INSTRUMENT FOR PERFORMING A MAGNETIC SEPARATION PROCEDURE

GEN-PROBE INCORPORATED, ...

1. An apparatus comprising:
a receptacle carrier configured to carry a receptacle device comprising multiple receptacles, each of the multiple receptacles
having a wall and containing a solution which includes magnetically-responsive solid supports and to carry the receptacle
device throughout a fluid transfer process;

a fluid transfer device comprising a plurality of aspirator probes aligned in a side-by-side arrangement, wherein the multiple
receptacles of a receptacle device carried in the receptacle carrier are positioned so as to be operatively engageable by
the aspirator probes, wherein the receptacle carrier is configured to selectively move the receptacle device between a first
position with respect to the fluid transfer device and a second position with respect to the fluid transfer device, wherein
the fluid transfer device further comprises a probe moving mechanism adapted to move the plurality of probes in unison with
respect to the receptacle carrier, and wherein the probe moving mechanism and the receptacle carrier are configured so that
movement of the plurality of probes with respect to the receptacle carrier when the receptacle carrier is in the first position
will cause the distal end of each probe to engage an associated conduit carried on a receptacle device carried by the receptacle
carrier so that a conduit becomes mounted on the distal end of each probe; and

a magnet moving apparatus including at least one magnet generating a magnetic field, the magnet moving apparatus being configured
to effect linear translation of the at least one magnet in a direction transverse to the axes of the aspirator probes and
parallel to the direction of aspirator probe alignment between an operational position with respect to the multiple receptacles
of the receptacle device carried in the receptacle carrier and a non-operational position with respect to the multiple receptacles
of the receptacle device carried in the receptacle carrier,

wherein the receptacle carrier and the magnet moving apparatus are configured so that the magnetic field of the at least one
magnet draws the magnetically-responsive solid supports to an inner surface of the wall of each receptacle of the receptacle
device adjacent to the at least one magnet when the at least one magnet is in the operational position, and wherein the effect
of the magnetic field on the magnetically-responsive solid supports is less when the at least one magnet is in the non-operational
position than when the at least one magnet is in the operational position,

wherein the receptacle carrier and the magnet moving apparatus are configured so that when the receptacle device is positioned
in the first position with respect to the fluid transfer device, the receptacle device interferes with translation of the
magnet by the magnet moving apparatus from the non-operational position to the operational position,

wherein the magnet moving apparatus comprises a plurality of stripping elements, and the magnet moving apparatus is configured
to effect linear translation of the stripping elements when the magnet moving apparatus moves the at least one magnet between
the operational position and the non-operational position, each stripping element being associated with a corresponding aspirator
probe, and each stripping element being adapted to remove a conduit from the distal end of the associated aspirator probe,
and

wherein when the magnet is in the operational position, each stripping element is in a position to engage the associated aspirator
probe to strip the conduit mounted thereon, and when the magnet is in the non-operational position, no stripping element is
in a position to engage the associated aspirator probe to strip the conduit mounted thereon.

US Pat. No. 9,624,557

COMPOSITIONS, METHODS AND KITS TO DETECT HERPES SIMPLEX VIRUS NUCLEIC ACIDS

GEN-PROBE INCORPORATED, ...

1. A method for determining the presence or absence of Herpes Simplex Virus 1 (HSV-1) in a sample, said method comprising:
(1) contacting a sample, said sample suspected of containing HSV-1, with at least two oligomers for amplifying a target region
of an HSV-1 target nucleic acid, wherein the at least two amplification oligomers comprise

(a) a first amplification oligomer comprising a first target-hybridizing sequence that is from about 15 to about 27 contiguous
nucleotides contained in the sequence of SEQ ID NO:31 and that includes at least the sequence of SEQ ID NO:30; and

(b) a second amplification oligomer comprising a second target-hybridizing sequence that is from about 15 to about 27 contiguous
nucleotides contained in the sequence of SEQ ID NO:33 and that includes at least the sequence of SEQ ID NO:32;

(2) performing an in vitro nucleic acid amplification reaction, wherein any HSV-1 target nucleic acid present in said sample
is used as a template for generating an amplification product; and

(3) detecting the presence or absence of the amplification product, thereby indicating the presence or absence of HSV-1 in
said sample.

US Pat. No. 9,598,723

AUTOMATED ANALYZER FOR PERFORMING A NUCLEIC ACID-BASED ASSAY

GEN-PROBE INCORPORATED, ...

1. An automated analyzer for use in performing a nucleic acid-based assay, the analyzer comprising:
a separation station comprising a magnetic element for subjecting a sample to a magnetic field, the magnetic field being sufficient
to isolate a target nucleic acid immobilized on a solid support comprising a magnetically-responsive particle from other material
present in the sample, wherein the magnetic element is carried by a magnet moving structure configured to be automatically
movable between first and second positions, wherein the magnetic element does not have a substantial effect on the magnetically-responsive
particle when the magnet moving structure is in the first position, and wherein the magnetic element has a substantial effect
on the magnetically-responsive particle when the magnet moving structure is in the second position;

an amplification incubator adapted to receive a receptacle containing the target nucleic acid isolated in the separation station
and to incubate the contents of the receptacle, to which reagents for performing a nucleic acid amplification have been provided,
for a period of time and under conditions sufficient to permit a target sequence of the target nucleic acid to be amplified,
said incubator comprising: a housing having a side wall and including a receptacle access opening formed in the side wall
for allowing the receptacle to be moved laterally into or out of said housing through said receptacle access opening in the
side wall and a door configured for automated movement between a closed position in which said door cooperates with said housing
to close said receptacle access opening and an open position in which said door is positioned such that said receptacle access
opening permits a reaction receptacle to pass therethrough;

a robotic pipettor positioned to access the contents of the receptacle;
a detector for detecting a light signal emitted by the contents of a receptacle, wherein the separation station, the amplification
incubator, the robotic pipettor and the detector are contained within a housing of the analyzer; and

a computer controller in communication with the separation station, the amplification incubator, the robotic pipettor, and
the detector and programmed to (i) effect cooperative operation of the separation station, the amplification incubator, the
robotic pipettor, and the detector, (ii) control movement of a receptacle within the analyzer, (iii) control automated movement
of the magnet moving structure between the first and second positions; (iv) control automated movement of said door between
the closed position and the opened position, and (v) determine the presence of a target nucleic acid in the sample by:

separating immobilized target nucleic acid from non-immobilized components of the sample at the separation station;
forming a mixture with the robotic pipettor, the mixture comprising the separated target nucleic acid and all reagents necessary
for performing a nucleic acid amplification;

performing the nucleic acid amplification with the separated target nucleic acid to form an amplification product in the amplification
incubator;

detecting a signal associated with the amplification product with the detector; and
determining the presence of the target nucleic acid based on the signal detected with the detector.
US Pat. No. 9,212,397

COMPOSITIONS AND METHODS FOR DETECTING NUCLEIC ACID FROM MOLLICUTES

GEN-PROBE INCORPORATED, ...

1. A method for the in vitro amplification and detection of a nucleic acid in a sample, said nucleic acid being from one or
more species in the class Mollicutes, comprising the steps of:
(a.) contacting a sample with at least four tagged amplification oligomers and at least one additional amplification oligomer
for generating amplification product from one or more nucleic acids in said sample, wherein each of said at least four tagged
amplification oligomers, designated (i)-(iv), individually comprises a target hybridizing region and a tag region, wherein
said at least four tagged amplification oligomers are selected as follows:

(i) a tagged amplification oligomer comprising a target hybridizing region that is configured to specifically hybridize to
all or a portion of a region of a target nucleic acid corresponding to residues 5065 to 5088 of SEQ ID NO:1 and wherein said
target hybridizing region has a nucleotide sequence that is SEQ ID NO:38 or SEQ ID NO:39;

(ii) a tagged amplification oligomer comprising a target hybridizing region that is configured to specifically hybridize to
all or a portion of a region of a target nucleic acid corresponding to residues 4752 to 4798 of SEQ ID NO:2, and wherein said
target hybridizing region has a nucleotide sequence that is SEQ ID NO:46, SEQ ID NO:47, or SEQ ID NO:48;

(iii) a tagged amplification oligomer comprising a target hybridizing region that is configured to specifically hybridize
to all or a portion of a region of a target nucleic acid corresponding to residues 1954 to 2006 of SEQ ID NO:3, and wherein
said target hybridizing region has a nucleotide sequence that is SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, or SEQ ID NO:54;
and

(iv) a tagged amplification oligomer comprising a target hybridizing region that is configured to specifically hybridize to
all or a portion of a region of a target nucleic acid corresponding to residues 1994 to 2036 of SEQ ID NO:4, and wherein said
target hybridizing region has a nucleotide sequence that is SEQ ID NO:58 or SEQ ID NO:59;
and wherein the at least one additional amplification oligomer includes a promoter-based amplification oligomer comprising
a target hybridizing region having a nucleotide sequence that is SEQ ID NO:42;
(b.) performing an in vitro amplification reaction under suitable conditions to generate an initial amplification product
from said one or more target nucleic acids using said at least two tagged amplification oligomers and said at least one additional
amplification oligomer; and

(c.) detecting the initial amplification product generated in step (b.), wherein said detecting comprises contacting the initial
amplification product with a detection probe having a nucleotide sequence that is SEQ ID NO:14.

US Pat. No. 10,006,862

CONTINUOUS PROCESS FOR PERFORMING MULTIPLE NUCLEIC ACID AMPLIFICATION ASSAYS

GEN-PROBE INCORPORATED, ...

1. A method for determining the presence or absence of target nucleic acid sequences in a plurality of samples, the method comprising the steps of:a) loading a plurality of samples onto a self-contained, stand-alone analyzer having a view window situated above a generally horizontal work surface, each sample being contained within one of a plurality of receptacles, and each receptacle having an associated label containing machine-readable data;
b) reading each associated label with a label reading device, wherein the label reading device is in communication with a computer, and wherein the computer associates each sample with one of at least two assays, the at least two assays including a first nucleic acid amplification reaction for amplifying a first target nucleic acid sequence and a second nucleic acid amplification reaction for amplifying a second target nucleic acid sequence, and the first and second target nucleic acid sequences being different from each other;
c) exposing each sample to a solid support material, the solid support material being capable of immobilizing nucleic acids present in the samples;
d) isolating the solid support material within each sample and separating a fluid component of the samples from the solid support material;
e) after step d), washing the solid support material with a wash solution, thereby purifying the nucleic acids immobilized on the solid support material;
f) forming a plurality of reaction mixtures, each reaction mixture being associated with one of the samples and comprising the nucleic acids from the associated sample that are purified in step e), if any, a first subset of the reaction mixtures comprising a first amplification reagent for performing the first nucleic acid amplification reaction, and a second subset of the reaction mixtures comprising a second amplification reagent for performing the second nucleic acid amplification reaction, wherein the first subset of reaction mixtures does not contain an amplification reagent for amplifying the second target nucleic acid sequence, and wherein the second subset of reaction mixtures does not contain an amplification reagent for amplifying the first target nucleic acid sequence;
g) transferring the reaction mixtures to a heater disposed on the work surface;
h) in the heater, simultaneously subjecting a plurality of reaction mixtures from the first and second subsets of reaction mixtures to conditions sufficient to perform the first and second nucleic acid amplification reactions; and
i) determining the presence or absence of the first target nucleic acid sequence in each of the first subset of reaction mixtures and the presence or absence of the second target nucleic acid sequence in each of the second subset of reaction mixtures,
wherein a plurality of the reaction mixtures from the second subset of reaction mixtures are provided to the heater while a plurality of the reaction mixtures from the first subset of reaction mixtures are being subjected to conditions sufficient to perform the first nucleic acid amplification reaction,
wherein the determining step is performed during the subjecting step for the first subset of reaction mixtures, and
wherein steps b)-i) are automated steps performed on the analyzer.

US Pat. No. 9,962,705

METHOD AND APPARATUS FOR EFFECTING AUTOMATED MOVEMENT OF A MAGNET IN AN INSTRUMENT FOR PERFORMING A MAGNETIC SEPARATION PROCEDURE

Gen-Probe Incorporated, ...

1. An apparatus comprising:a fluid transfer device comprising a plurality of aspirator probes, each aspirator probe having a distal end, and each distal end being adapted to have a conduit mounted thereon;
a slide configured for linear translation between a first position and a second position in the apparatus and having a bottom plate comprising a plurality of conduit stripping elements formed therein, the slide including a first wall and a second wall extending upwardly from the bottom plate and defining a slot between the first and second walls, wherein the slot is configured to receive the plurality of aspirator probes, and wherein the plurality of conduit-stripping elements are disposed in a bottom surface of the slot each conduit-stripping element being associated with a corresponding one of the plurality of aspirator probes, and each conduit-stripping element being adapted to remove a conduit from the distal end of an associated aspirator probe that is aligned with the conduit-stripping element, wherein the plurality of conduit-stripping elements are movable with the slide, such that when the slide is in the first position, no conduit-stripping element is aligned with an aspirator probe to strip the conduit mounted thereon, and when the slide is in the second position, each conduit-stripping element is aligned with the associated aspirator probe, and wherein each conduit stripping element comprises a key-hole opening having a first portion with a transverse size sufficient to permit the conduit to pass therethrough and a second portion with a transverse size sufficient to permit the probe to pass therethrough, but not sufficient to permit the conduit to pass therethrough; and
a controller configured to:
cause the fluid transfer device to pass the distal end of the probe with the conduit disposed thereon through the first portion of the key-hole opening;
effect a linear translation of the slide so that the probe is in the second portion of the key-hole opening; and
withdraw the probe from the key-hole opening, the conduit being retained by the conduit-stripping element when the conduit is unable to pass through the second portion of the key-hole opening.
US Pat. No. 9,915,613

SYSTEMS AND METHODS FOR DISTINGUISHING OPTICAL SIGNALS OF DIFFERENT MODULATION FREQUENCIES IN AN OPTICAL SIGNAL DETECTOR

GEN-PROBE INCORPORATED, ...

1. A system for detecting an optical signal emitted from a receptacle, said system comprising:
an excitation source controlled by an excitation circuit to (a) generate an optical excitation signal having a predetermined
excitation wavelength that excites an emission moiety which emits an optical emission signal that is associated with the excitation
wavelength and has a predetermined emission wavelength and (b) modulate the optical excitation signal at a predetermined modulation
frequency;

excitation optics configured to direct the optical excitation signal at the receptacle;
a detector circuit including a photodetector configured to detect an optical signal including an optical emission signal emitted
from the receptacle and to convert the detected optical signal to an analog detection signal; and

a controller directly or indirectly connected to the detector circuit and programmed with a signal-digitizing algorithm to
digitize the analog detection signal and generate digitized detection data;

wherein the controller is further programmed with a digital signal-processing algorithm for determining from the digitized
detection data an amplitude of the optical emission signal at the predetermined modulation frequency to thereby ascertain
the portion of the detected optical signal corresponding to the associated optical emission signal.

US Pat. No. 9,822,397

METHOD AND APPARATUS FOR IDENTIFYING ANALYTE-CONTAINING SAMPLES USING SINGLE-READ DETERMINATION OF ANALYTE AND PROCESS CONTROL SIGNALS

GEN-PROBE INCORPORATED, ...

1. A method for determining the presence or absence of an analyte nucleic acid in a sample, the method comprising the steps
of:
(a) forming a reaction mixture comprising a sample suspected of containing an analyte nucleic acid, an internal control (IC)
nucleic acid that is distinct from the analyte nucleic acid, and reagents sufficient to synthesize amplicons using the analyte
nucleic acid and the IC nucleic acid as templates;

(b) after step (a), subjecting the reaction mixture to amplification reaction conditions, the amplification reaction conditions
permitting analyte amplicons to be synthesized from the analyte nucleic acid, if present in the sample, and IC amplicons to
be synthesized from the IC nucleic acid;

(c) exposing the reaction mixture to an analyte probe and an IC probe under conditions permitting the analyte probe to bind
to the analyte amplicons, if any, and the IC probe to bind to the IC amplicons synthesized in the reaction mixture during
step (b), wherein the analyte probe and the IC probe include first and second detectable labels, respectively, wherein signals
generated by the first and second detectable labels are indistinguishable from each other, and wherein the analyte probe is
specific for the analyte amplicons and the IC probe is specific for the IC amplicons; and

(d) detecting a combined signal generated by the first and second detectable labels, the combined signal being indicative
of the presence or absence of the analyte nucleic acid in the sample, wherein the analyte probe and the IC probe are both
free in solution during the detecting step, and wherein the detecting step is performed at a constant temperature.

US Pat. No. 9,726,607

SYSTEMS AND METHODS FOR DETECTING MULTIPLE OPTICAL SIGNALS

GEN-PROBE INCORPORATED, ...

1. A system for detecting two or more different optical emission signals emitted from each of a plurality of reaction receptacles,
wherein the reaction receptacles are disposed in a fixed arrangement with respect to each other, said system comprising:
(A) a plurality of optical sensors, each of said optical sensors being configured to detect one of the two or more optical
emission signals and being associated with one of the reaction receptacles so that each reaction receptacle has associated
therewith one optical sensor for each optical emission signal to be detected, whereby said optical sensors associated with
each of the plurality of reaction receptacles are arranged in a configuration that enables each optical sensor to detect the
associated optical emission signal emitted from the associated reaction receptacle;

(B) a transport mechanism constructed and arranged to effect relative movement between the plurality of reaction receptacles
and the optical sensors to sequentially place each reaction receptacle into a signal-detecting position with respect to one
of its associated optical sensors, wherein

(1) each optical sensor is configured to direct an optical excitation signal at an associated reaction receptacle that is
in a signal-detecting position with respect to the optical sensor and to detect an optical emission signal emitted from the
reaction receptacle that is associated with the excitation signal, and

(2) each optical sensor is further configured to modulate an excitation signal at an excitation frequency and direct the modulated
excitation signal at an associated receptacle, and wherein optical sensors configured to detect at least two different optical
emission signals are configured to direct excitation signals of two different excitation frequencies; and

(C) circuitry configured to discard any portion of an optical signal detected by an optical sensor having a frequency that
is inconsistent with the excitation frequency of the associated excitation signal.

US Pat. No. 9,523,133

OLIGONUCLEOTIDE PRIMER COMPOSITION

GEN-PROBE INCORPORATED, ...

1. A composition comprising an oligonucleotide primer,
wherein the base sequence of the oligonucleotide primer consists of a target-hybridizing sequence and an upstream phage T7
RNA polymerase promoter sequence,

wherein the base sequence of the upstream phage T7 RNA polymerase promoter sequence is the base sequence of SEQ ID NO:30,
wherein the base sequence of the target-hybridizing sequence is the base sequence of SEQ ID NO:15, and
wherein the composition further comprises a hybridization probe, and wherein the base sequence of the hybridization probe
is the base sequence of the molecular torch of SEQ ID NO:24.

US Pat. No. 10,086,342

MULTI-CHANNEL OPTICAL MEASUREMENT INSTRUMENT

Gen-Probe Incorporated, ...

1. A detector for detecting optical emissions of two or more different wavelengths or ranges of wavelengths from a sample, wherein emissions of two or more different wavelengths are indicative of the presence, amount, or state of two or more analytes of interest in the sample, the detector comprising:two or more excitation channels fixed with respect to the sample and each other, wherein each excitation channel is adapted to direct an excitation signal of a different prescribed excitation wavelength or range of excitation wavelengths toward the sample and each excitation channel comprises:
a light emitting element adapted to emit excitation light; and
excitation optical elements defining an excitation optical path having an excitation optic axis, the excitation optical elements being constructed and arranged to transmit at least a portion of the light emitted by the light-emitting element having the prescribed excitation wavelength or range of excitation wavelengths toward the sample;
two or more emission channels fixed with respect to the sample, the excitation channels, and each other, wherein each emission channel is adapted to receive and detect an emission signal of a different prescribed emission wavelength or range of emission wavelengths from the sample and each emission channel comprises:
emission optical elements defining an emission optical path having an emission optic axis, the emission optical elements being constructed and arranged to transmit at least a portion of any light emitted by the sample having the prescribed emission wavelength or range of emission wavelengths; and
a light-detecting element adapted to detect light transmitted by the emission optical elements and to convert the detected light to an electronic signal indicative of at least one of the presence and strength of the detected light;
a housing, wherein each excitation channel is disposed within a different excitation conduit within the housing and each emission channel is disposed within a different emission conduit within the housing, and wherein the excitation optic axes of the excitation channels and the emission optic axes of the emission channels are parallel to one another throughout their extents; and
a solid, undivided optic lens constructed and arranged with respect to the excitation channels and the emission channels to (1) direct excitation light transmitted by each excitation channel and impinging on a different portion of the optic lens at a prescribed location and (2) receive emission signals emitted by contents of the sample and to direct at least a portion of the received emission signals into each of the emission channels, wherein the optic lens is positioned with respect to the excitation and emission channels so that the light emitting element and excitation optical elements of each excitation channel and the emission optical elements and the light-detecting element of each emission channel are disposed on one side of the optic lens, and wherein the detector includes no optic element on an opposite side of the optic lens between the optic lens and the sample.

US Pat. No. 10,152,569

ALGORITHMS FOR SEQUENCE DETERMINATIONS

GEN-PROBE INCORPORATED, ...

18. A method of developing a consensus sequence from a plurality of sequencing reads of a nucleic acid target, comprising:(i) ligating a target nucleic acid of unknown sequence to a hairpin structure of known sequence to a form a circular nucleic acid target template in which the target nucleic acid forms an adjacent segment adjacent an anchor segment of known sequence:
(ii) performing sequencing by synthesis by extending a primer bound to the anchor segment with a polymerase reading around the circular nucleic acid target template multiple times to generate a population of raw target sequence reads comprising alternating reads of the anchor segment and the adjacent segment; and at least some of the raw target sequencing reads containing sequencing errors; and
(iii) performing the following computer implemented steps:
(a) receiving the population of raw target sequencing reads generated in step (ii);
(b) evaluating the accuracy of sequencing of the anchor segment in different raw target sequencing reads by comparing raw target sequencing reads of the anchor segment with the known sequence of the anchor segment;
(c) assigning a subset of the raw target sequencing reads into an accepted class based on reaching at least a threshold level of accuracy of the sequencing of the anchor segment;
(d) polling nucleobases at a position equidistant to the anchor segment sequence in raw target sequencing reads in the accepted class to determine a consensus nucleobase, which consensus nucleobase is assigned as the first nucleobase of a nascent sequence of the adjacent segment;
(e) assigning raw target sequencing reads having the consensus nucleobase determined in the prior polling step to remain in the accepted class and assigning raw target sequencing reads lacking the consensus nucleobase determined in the prior polling step to a rejected class;
(f) optionally reassigning a raw target sequencing read from the rejected class to the accepted class by scoring similarity of the raw target sequencing read to the nascent sequence and reintroducing the raw target sequencing read if the sequence similarity reaches at least a threshold level of similarity; and
(g) repeating steps (d), (e) and optionally (f), except that a repetition polls a position adjacent the position poled in the previous polling step for raw target sequencing reads having the consensus nucleobase polled in the previous step or in the case of a raw target sequencing read reassigned from the rejected class to the accepted class and not polled in the previous polling step or if polled and not having the consensus nucleobase in the previous polling step, the polling polls a position adjacent the position aligned with the last nucleobase of the nascent sequence to determine a consensus nucleobase, and the consensus nucleobases determined in successive repetitions are assigned as successive nucleobases in the nascent sequence of the adjacent segment; wherein step (f) is performed at least once
(h) outputting the sequence of at least part of the target nucleic acid.
US Pat. No. 10,073,094

COMPOSITIONS, METHODS AND KITS TO DETECT HERPES SIMPLEX VIRUS NUCLEIC ACIDS

GEN-PROBE INCORPORATED, ...

1. A method for determining the presence or absence of Herpes Simplex Virus 2 (HSV-2) in a sample, said method comprising:(1) contacting a sample, said sample suspected of containing HSV-2, with at least two oligomers for amplifying a target region of an HSV-2 target nucleic acid, wherein the at least two amplification oligomers comprise
(a) a first amplification oligomer comprising a first target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides (i) contained in the sequence of SEQ ID NO:49 and that includes at least the sequence of SEQ ID NO:48 or (ii) contained in the sequence of SEQ ID NO:43 and that includes at least the sequence of SEQ ID NO:42; and
(b) a second amplification oligomer comprising a second target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides (i) contained in the sequence of SEQ ID NO:51 and that includes at least the sequence of SEQ ID NO:50 or (ii) contained in the sequence of SEQ ID NO:45 and that includes at least the sequence of SEQ ID NO:44;
(2) performing an in vitro nucleic acid amplification reaction, wherein any HSV-2 target nucleic acid present in said sample is used as a template for generating an amplification product; and
(3) detecting the presence or absence of the amplification product, thereby indicating the presence or absence of HSV-2 in said sample.
US Pat. No. 9,932,628

DUAL REFERENCE CALIBRATION METHOD AND SYSTEM FOR QUANTIFYING POLYNUCLEOTIDES

Gen-Probe Incorporated, ...

1. A method of quantifying an analyte polynucleotide in a sample with an adjusted calibration curve using a local instrument, said method comprising the steps of:(a) obtaining first and second equations respectively defining first and second calibration curves specific for a quantitative assay,
wherein each of the first and second calibration curves relates normalized indicia of amplification for analyte polynucleotide standards to indicia of amplification for a fixed amount of an internal calibrator polynucleotide that co-amplified therewith as a function of starting amounts of the analyte polynucleotide in amplification reactions of the assay, wherein the first calibration curve was not determined using the local instrument or was previously determined and stored for later use, and the second calibration curve was not determined using the local instrument or was previously determined and stored for later use, and
wherein each of the calibration curves is different from the other;
(b) obtaining an adjustment calibrator comprising an amount of the analyte polynucleotide and said fixed amount of the internal calibrator polynucleotide;
(c) co-amplifying, in a nucleic acid amplification reaction carried out with the local instrument, the analyte polynucleotide and the internal calibrator polynucleotide of the adjustment calibrator, wherein the local instrument comprises or is linked to a memory, and amplifies nucleic acid and monitors amplicon synthesis as amplification is occurring, and wherein the first and second calibration curves are stored in the memory;
(d) determining indicia of amplification for each of the analyte polynucleotide and the internal calibrator polynucleotide of the adjustment calibrator that co-amplified in the nucleic acid amplification reaction using the local instrument;
(e) normalizing the determined indicia of amplification for the analyte polynucleotide to the determined indicia of amplification for the internal calibrator polynucleotide of the adjustment calibrator using the local instrument;
(f) determining a relative relationship between
the difference between the normalized value determined for the adjustment calibrator and one of the first and second calibration curves at the amount of the analyte polynucleotide of the adjustment calibrator and,
the difference between the first and second calibration curves at the amount of the analyte polynucleotide of the adjustment calibrator; and
(g) establishing a calibration plot that maintains said relative relationship to the first and second calibration curves at all values of analyte polynucleotide standard, thereby establishing the adjusted calibration curve for the assay on the local instrument, and wherein the calibration plot is stored in the memory;
(h) amplifying the analyte polynucleotide of the sample using the local instrument;
(i) determining indicia of amplification for the analyte polynucleotide amplified in step (h) using the local instrument; and
(j) determining the quantity of the analyte polynucleotide in the sample from the calibration plot and the indicia of amplification of the analyte polynucleotide using the local instrument.
US Pat. No. 9,863,010

COMPOSITIONS, METHODS AND KITS TO DETECT ADENOVIRUS NUCLEIC ACIDS

GEN-PROBE INCORPORATED

1. A method for detecting an Adenovirus nucleic acid comprising the steps of:
(a) contacting a test sample comprising nucleic acid with at least one hybridization assay probe having a nucleotide sequence
consisting of a sequence selected from the group consisting of SEQ ID NOs: 10, 19, 21, 23, 24, 29, 36, and 37 or a combination
of two or more thereof; and

(b) determining if a probe:target duplex has formed under stringent hybridization conditions in the test sample,
wherein the presence of the probe:target duplex is an indication of the presence of Adenovirus nucleic acid in the test sample.

US Pat. No. 9,817,011

METHOD OF USING A MULTI-WELL TRAY

GEN-PROBE INCORPORATED, ...

1. A method for reconstituting a lyophilized reagent in an automated instrument, the method comprising:
(A) moving an automated pipettor over an unused pipette tip and lowering the automated pipettor into engagement with the pipette
tip;

(B) simultaneously with, prior to, or after step (A), moving a multi-well tray into a dispensing position, wherein the multi-well
tray comprises:

wherein the base of the multi-well tray further comprises
(1) an elongated base having a first end and a second end, said base comprising a top surface, opposed side walls extending
from the top surface to a bottom surface, a first end wall extending between said side walls, and an arm extending outwardly
from the first end of the base and configured to be engaged by a transport mechanism, wherein the arm comprises a bridge and
a post having one end attached to the bridge and an opposite end that is not attached to the bridge and wherein the post extends
from the bridge so as to define a gap between the opposite end of the post and the first end wall;

(2) a plurality of wells depending from the top surface, each well having an opening at the top surface, wherein the wells
are arranged in at least one row extending between the first end and the second end of the base;

(3) a lyophilized reagent contained within one or more of the wells; and
(4) snap fingers disposed at the second end of the base and configured to grasp an element of the instrument for securing
the tray to the element;
and wherein the moving step comprises engaging the post of the multi-well tray with an automated transport mechanism and effecting
movement of the multi-well tray with movement of the transport mechanism;
(C) engaging the snap fingers of the multi-well tray with the element;
(D) lowering the pipette tip with the automated pipettor into a container of diluent and drawing a predetermined amount of
diluent from the container into the pipette tip;

(E) moving the pipette tip with the automated pipettor over the multi-well tray in the dispensing position and positioning
the pipette tip over the well containing the lyophilized reagent;

(F) dispensing the diluent drawn into the pipette tip into the well containing the lyophilized reagent to thereby reconstitute
the lyophilized reagent; and

(G) after a sufficient period of time for the lyophilized reagent to be reconstituted by the diluent, drawing the reconstituted
reagent from the well.

US Pat. No. 9,765,407

DETECTION OF NUCLEIC ACIDS FROM MULTIPLE TYPES OF HUMAN PAPILLOMAVIRUS

GEN-PROBE INCORPORATED, ...

13. A method of detecting human papillomavirus (HPV) nucleic acid present in a biological sample, comprising the steps of:
contacting nucleic acid in a biological sample containing RNA of at least one of HPV types 16, 18, 31, 33, 35, 39, 45, 51,
52, 56, 58, 59 and 68 with a mixture of amplification oligomers that amplify a HPV sequence in an E6/E7 target region sequence;

amplifying a HPV sequence from the target region sequence in at least one HPV type by using the amplification oligomers and
a nucleic acid polymerase in vitro to produce an HPV amplified product; and

detecting the amplified product by using at the mixture of oligomers of claim 1.

US Pat. No. 10,132,821

AUTOMATED METHOD FOR DETERMINING THE PRESENCE OF A MUCOID STRAND

GEN-PROBE INCORPORATED, ...

1. An automated method for determining whether a mucoid strand is suspended from a pipette tip operably positioned on a pipettor, the method comprising the steps of:(a) activating the pipettor to move the pipette tip into a fluid within a container;
(b) aspirating an amount of the fluid into the pipette tip with the pipettor;
(c) activating the pipettor to raise the pipette tip to a position above the fluid; and
(d) while the pipette tip is positioned above the fluid, determining whether a mucoid strand is suspended from the pipette tip with a reverse capacitive liquid level detection system.
US Pat. No. 10,093,989

RED BLOOD CELL LYSIS SOLUTION

GEN-PROBE INCORPORATED, ...

1. A method of analyzing a target RNA from red blood cells comprising:(a) contacting red blood cells with a reagent comprising ammonium chloride at a concentration of 200-300 mM and lithium lauryl sulfate (LLS) at a concentration of 4% to 15% (w/v), the reagent being effective to lyse the red blood cells and inhibit degradation of target RNA released from the red blood cells; and
(b) analyzing the target RNA released from the red blood cells, wherein said analyzing comprises performing an amplification reaction to amplify the target RNA.
US Pat. No. 9,938,590

CAPTURE PROBES IMMOBILIZABLE VIA L-NUCLEOTIDE TAIL

GEN-PROBE INCORPORATED, ...

1. A method of capturing a target nucleic acid, comprising:contacting a target nucleic acid in a sample with a capture probe and an immobilized probe, the capture probe comprising a first segment that binds to the target nucleic acid and a second segment that binds to the immobilized probe, wherein the second segment of the capture probe and the immobilized probe comprise complementary homopolymeric L-nucleic acids that can hybridize to one another, wherein the homopolymeric L-nucleic acids are polyA and polyT, wherein the target nucleic acid binds to the first segment of the capture probe, and the second segment of the capture probe binds to the immobilized probe, thereby capturing the target nucleic acid, wherein the sample includes mRNA or a nucleic acid derived therefrom, wherein the copy number of the target nucleic acid in the sample is up to 33 copies per reaction.
US Pat. No. 9,863,004

MOLECULAR ASSAY REAGENTS AND METHODS

GEN-PROBE INCORPORATED, ...

1. A method for evaluating the quality of a biological sample, comprising:
(a) contacting a nucleic acid molecule obtained from a tissue sample with a control amplification reagent to form a reaction
mixture, wherein the nucleic acid molecule comprises a control nucleic acid, wherein the control nucleic acid comprises medium
chain acyl-coenzyme A dehydrogenase (MCAD);

(b) subjecting the reaction mixture to amplification conditions to produce an amplification mixture, whereby two or more portions
of the control nucleic acid are amplified to produce two or more detectably distinguishable control amplicons, each having
a different length, wherein the two or more different length control amplicons form a size control ladder comprised of amplicons
of increasing length; and

(c) evaluating the amplification mixture to detect the length and amount of each control amplicon, wherein the biological
sample is determined to contain degraded nucleic acid molecules that may adversely impact molecular analysis of the biological
sample if:

(1) the amount detected of each the two or more control amplicons is smaller than the amount detected of each the two or more
control amplicons in a comparative control sample;

(2) the amount detected of each of the two or more control amplicons in the size control ladder decreases as the length of
each control amplicon in the size control ladder increases; or

(3) one or more of the control amplicons are undetectable after production of the amplification mixture.

US Pat. No. 9,856,527

METHODS FOR QUANTITATIVE AMPLIFICATION AND DETECTION OVER A WIDE DYNAMIC RANGE

GEN-PROBE INCORPORATED, ...

1. A method of detecting a target nucleic acid in a sample comprising the steps of:
a. providing a sample suspected of containing a target nucleic acid;
b. generating from said target nucleic acid, a pre-defined ratio of at least two differentiable amplicon species, wherein
said generating step is performed in a single vessel; and

c. detecting the presence and amount of each generated amplicon species, wherein a first amplicon species is detectable in
a first linear range representing a first concentration of target nucleic acid in said sample to a second concentration of
target nucleic acid in said sample and a second amplicon species is detectable in a second linear range representing a third
concentration of target nucleic acid in said sample to a fourth concentration of target nucleic acid in said sample, and wherein:
said first concentration < said third concentration < said second concentration < said fourth concentration such that said
first and second linear ranges overlap and provide an extended dynamic range for determining the presence and amount of said
target nucleic acid in said sample, and wherein said detecting step is performed in a single vessel.

US Pat. No. 9,724,948

METHOD AND APPARATUS FOR PRINTING ON AN OBJECT HAVING A CURVED SURFACE

GEN-PROBE INCORPORATED, ...

14. A method for printing on a curved surface of an article with a printing module, the method comprising:
configuring the printing module in an open configuration to receive an article having a curved surface on which information
is to be printed;

placing an article into the printing module;
configuring the printing module in a printing configuration and securing the article so that the curved surface is in an operative
position with respect to a print head of the printing module;

activating the print head and effecting relative movement between the curved surface and the print head while the print head
is activated and while maintaining the curved surface in the operative position with respect to the print head;

after printing an image onto the curved surface, configuring the printing module into an open configuration enabling the article
to be removed from the printing module; and

removing the article from the printing module.
US Pat. No. 10,006,092

METHOD TO DETECT PROSTATE CANCER IN A SAMPLE

Gen-Probe Incorporated, ...

1. A composition comprising:(a) a urine sample from a subject having or suspected of having prostate cancer, said urine sample comprising at least one prostate cell or nucleic acid extract thereof;
(b) a first oligonucleotide or first primer pair for performing an RNA hybridization and/or amplification reaction on mRNA contained in said urine sample, said first oligonucleotide or first primer pair being specific for a prostate cancer associated PCA3 mRNA molecule which is:
(i) a polynucleotide molecule comprising the sequence of SEQ ID NO: 9, 10 or 13;
(ii) a polynucleotide molecule that hybridizes under high stringency conditions to (i), wherein said high stringency conditions comprise a hybridization at 65° C. in 6×SSC or 5×SSPE, 5×Denhardt's solution, 0.5% SDS and 100 ?g/ml denatured carrier DNA and a washing at 65° C. in 0.2×SSC/0.1% SDS; or
(iii) a polynucleotide molecule fully complementary to (i) or (ii); and
(c) a second oligonucleotide or second primer pair for performing a second RNA hybridization and/or amplification reaction on mRNA contained in said urine sample, said second oligonucleotide or second primer pair being specific for a prostate-specific mRNA molecule,
wherein at least one oligonucleotide in the composition is a labeled oligonucleotide, and the at least one labeled oligonucleotide includes at least one of (i) the first oligonucleotide, (ii) a primer of the first primer pair, (iii) the second oligonucleotide, or (iv) a primer of the second primer pair.
US Pat. No. 9,976,175

CALIBRATION METHOD, APPARATUS AND COMPUTER PROGRAM PRODUCT

Gen-Probe Incorporated, ...

1. A method of quantifying an analyte polynucleotide in a sample with an adjusted calibration curve using a local instrument, said method comprising the steps of:(a) obtaining a pair of coordinates for a fixed-point on a calibration curve specific for a quantitative assay,
wherein the pair of coordinates specify an amount of an analyte polynucleotide and a normalized indicia of amplification value, and wherein the fixed-point was not determined using the local instrument, or was previously determined and stored for later use;
(b) obtaining an adjustment calibrator that comprises a fixed amount of an internal calibrator and a known amount of the analyte polynucleotide;
(c) co-amplifying the analyte polynucleotide and the internal calibrator of the adjustment calibrator using the local instrument, wherein the local instrument comprises a memory, and amplifies nucleic acid and monitors amplicon synthesis as amplification is occurring, and wherein the fixed-point is stored in the memory of the local instrument;
(d) determining indicia of amplification for each of the analyte polynucleotide and the internal calibrator that co-amplified in step (c) using the local instrument;
(e) normalizing the indicia of amplification determined for the analyte polynucleotide to the indicia of amplification determined for the internal calibrator using the local instrument;
(f) establishing the adjusted calibration curve by preparing a calibration plot that comprises a first point and a second point using the local instrument,
wherein the first point comprises coordinates for the known amount of the analyte polynucleotide of the adjustment calibrator and the normalized indicia of amplification for the analyte polynucleotide determined in step (d),
wherein the second point comprises the pair of coordinates, obtained in step (a), for the fixed-point, and wherein the adjusted calibration curve is stored in the memory of the instrument;
(g) amplifying the analyte polynucleotide of the sample using the local instrument;
(h) determining indicia of amplification for the analyte polynucleotide amplified in step (g) using the local instrument; and
(i) determining the quantity of the analyte polynucleotide in the sample from the adjusted calibration curve and the indicia of amplification of the analyte polynucleotide using the local instrument.

US Pat. No. 9,744,506

INSTRUMENTS FOR MIXING THE CONTENTS OF A DETECTION CHAMBER

GEN-PROBE INCORPORATED, ...

1. An instrument for processing a sample in a receptacle having a plurality of interconnected chambers, the instrument comprising:
a receptacle-receiving area for receiving the receptacle;
a detector having components positioned to detect a light signal from the contents of a detection chamber of the receptacle
when the receptacle is placed in an operative position in said receptacle-receiving area, said components comprising a light
source and a signal detecting element disposed on the same side of the receptacle-receiving area;

at least one movable compression element disposed to be adjacent the detection chamber and situated between the receptacle
and said light source and said signal detecting element of said detector when the receptacle is placed in the operative position
in said receptacle-receiving area,

wherein said compression element is configured to transmit light from said light source to said detection chamber and to transmit
light signals from said detection chamber to said signal detecting element, and

wherein the compression element is a fixed element of the detector, so that the light source and the signal detecting element
move with the compression element when the compression element engages the flexible portion of the detection chamber;

a translating mounting platform, adapted to move back and forth in a reciprocal manner, on which the detector is mounted so
as to be moveable with the mounting platform, wherein the translating mounting platform includes a base having two longitudinal
slots formed therein configured to slidably receive two pins extending upwardly from a surface supporting the mounting platform
for movement of the mounting platform in a direction transverse to longitudinal axes of the two pins;

an actuator coupled to the mounting platform; and
a controller programmed to move said compression element into engagement with a flexible portion of the detection chamber
to thereby depress the flexible portion to agitate the contents of the detection chamber or to move the contents of the detection
chamber into an adjacently connected chamber of the receptacle, wherein the controller is programmed to control the actuator
to selectively move the mounting platform back and forth, thereby moving the compression element, which is fixed with respect
to the detector, back and forth between a retracted position and an extended position engaged with the detection chamber.

US Pat. No. 9,771,572

METHOD OF ISOLATING NUCLEIC ACID FROM SPECIMENS IN LIQUID-BASED CYTOLOGY PRESERVATIVES CONTAINING FORMALDEHYDE

GEN-PROBE INCORPORATED, ...

1. A method of isolating a nucleic acid from processing a specimen that includes a clinical sample disposed in a liquid-based
cytology preservative that comprises formaldehyde, the method comprising the steps of:
(a) combining the specimen with a protease enzyme and a formaldehyde scavenger that is 2-imidazolidone to create a reaction
mixture;

(b) incubating the reaction mixture at an elevated temperature for a period of time sufficient to reverse chemical modifications
of nucleic acid that may be contained in the specimen by formaldehyde in the liquid-based cytology preservative; and

(c) isolating a nucleic acid from the reaction mixture after the incubating step.
US Pat. No. 9,752,201

COMPOSITIONS AND METHOD FOR DETECTING HUMAN PARVOVIRUS NUCLEIC ACID AND FOR DETECTING HEPATITIS A VIRUS NUCLEIC ACIDS IN SINGLE-PLEX OR MULTIPLEX ASSAYS

GEN-PROBE INCORPORATED, ...

1. A method for detecting a human parvovirus target nucleic acid in a sample, said method comprising:
(A) providing a sample, wherein said sample is suspected of containing at least one of human parvovirus;
(B) contacting said sample with an oligomer combination for amplifying a human parvovirus nucleic acid target region and an
HAV nucleic acid target region, said oligomer combination comprising

(a) a first parvovirus amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:80, and wherein
the first parvovirus amplification oligomer does not comprise an additional target-hybridizing sequence; and

(b) a second parvovirus amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:111 or SEQ
ID NO:112 attached at its 5? end to a promoter sequence, and wherein the second parvovirus amplification oligomer does not
comprise an additional target-hybridizing sequence;

(C) performing an in vitro nucleic acid amplification reaction, wherein any parvovirus target nucleic acid present in said
sample is used as a template for generating a parvovirus amplification product; and

(D) detecting the presence or absence of the parvovirus amplification product, thereby indicating the presence or absence
of parvovirus in said sample.

US Pat. No. 9,718,059

MULTI-WELL TRAY AND RACK THEREFOR

GEN-PROBE INCORPORATED, ...

20. An assembly for use in an automated process comprising:
a rack comprising:
a chassis having a top surface and first and second opposing ends, the chassis including locking members;
a plurality of machine readable indicia including data disposed on the chassis; and
a handle disposed on the first end surface of the chassis;
two or more multi-well trays supported on the chassis of the rack, each multi-well tray comprising:
a base including locking features;
a card insert removably securable to the base; and
one or more sets of wells, wherein each set comprises:
a receptacle cap well formed in the base and configured to receive a receptacle cap;
a receptacle well formed in the base and configured to receive a receptacle; and
a reagent well formed in the card insert and containing a lyophilized reagent;
wherein the locking members of the rack are operatively engaged with the locking features of the each multi-well tray to secure
the multi-well tray to the chassis of the rack;

a receptacle disposed in at least one of the receptacle wells;
a cap disposed in at least one of the receptacle cap wells, wherein the cap is configured for locking attachment to the receptacle;
and

a fluid cartridge comprising:
a liquid chamber and a liquid reservoir in fluid communication with the liquid chamber, the liquid chamber and the liquid
reservoir containing a reconstitution solution for reconstituting the lyophilized reagent, and

a frangible seal covering the liquid chamber and the liquid reservoir of the fluid cartridge.

US Pat. No. 10,120,136

INDEXING SIGNAL DETECTION MODULE

GEN-PROBE INCORPORATED, ...

1. An apparatus for transmitting an optical signal emission from the contents of each of a plurality of receptacles, said apparatus comprising:a processing module configured to hold the plurality of receptacles;
a plurality of signal transmission conduits, each signal transmission conduit comprising an optical fiber coupled to the processing module to transmit an optical signal emitted by the contents of an associated one of the plurality of receptacles between a first end and a second end thereof, wherein each of the plurality of signal transmission conduits transmits both an excitation and an emission signal; and
a conduit reformatter constructed and arranged to secure the first ends of the respective signal transmission conduits in a first spatial arrangement corresponding to a spatial arrangement of the plurality of receptacles held within the processing module, such that the first end of each signal transmission conduit is positioned to receive an emission signal emitted by the contents of the associated receptacle, and to secure the second ends of the respective signal transmission conduits in a second spatial arrangement different from the first spatial arrangement.

US Pat. No. 10,119,163

METHODS AND COMPOSITIONS FOR NUCLEIC ACID AMPLIFICATION

GEN-PROBE INCORPORATED, ...

1. A target capture reaction mixture, wherein the reaction mixture comprises at least one target nucleic acid, at least one target capture oligonucleotide and at least one amplification oligomer complex, wherein each of said amplification oligomer complexes comprises a first amplification oligomer member having a first target specific sequence that is joined to a second amplification oligomer member having a second target specific sequence, wherein the first amplification oligomer member is a non-promoter primer and the second amplification oligomer member is a promoter primer, and wherein each of said target capture oligomers and each of said amplification oligomer complexes specifically hybridizes to a different target nucleic acid sequence.
US Pat. No. 9,890,433

COMPOSITIONS AND METHODS FOR DETECTING HUMAN PAPILLOMAVIRUS NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

1. An oligomer combination for detecting a human papillomavirus type 33 (HPV33) target nucleic acid and a human papillomavirus
type 31 (HPV31) in a sample suspected of containing HPV33 and/or HPV31 and at least one of HPV types 52, and 58, said oligomer
combination comprising:
first and second amplification oligomers for specifically amplifying an HPV33 nucleic acid target region, wherein
(a) the first HPV33 amplification oligomer comprises a first target-hybridizing sequence that is from 15 to 27 contiguous
nucleotides in length and is contained in the sequence of SEQ ID NO:66 and that includes the sequence of SEQ ID NO:67 or SEQ
ID NO:69; and

(b) the second HPV33 amplification oligomer is a promoter primer or a promoter provider comprising (i) a second target-hybridizing
sequence, wherein the second target hybridizing sequence is from 15 to 27 contiguous nucleotides in length and is contained
in the sequence of SEQ ID NO:70 and includes the sequence of SEQ ID NO:72 or SEQ ID NO:73; and (ii) a promoter sequence joined
to 5? end of the second target-hybridizing sequence; and

first and second amplification oligomers for specifically amplifying an HPV type 31 (HPV31) nucleic acid target region, wherein
(c) the first HPV31 amplification comprises a first target-hybridizing sequence that is from 15 to 27 contiguous nucleotides
in length and is contained in the sequence of SEQ ID NO:74 and that includes at least the sequence of SEQ ID NO:75, SEQ ID
NO:76, or SEQ ID NO:77; and

(d) the second HPV31 amplification oligomer is a promoter primer or a promoter provider comprising (i) a second target-hybridizing
sequence, wherein the second target hybridizing sequence is from 15 to 30 contiguous nucleotides in length and is contained
in the sequence of SEQ ID NO:78 and includes at least the sequence of SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81; and (ii)
a promoter sequence joined to 5? end of the second target-hybridizing sequence.

US Pat. No. 9,670,554

CAPTURE PROBES FOR USE IN DETECTING THE PRESENCE OF TRICHOMONAS VAGINALIS IN A SAMPLE

GEN-PROBE INCORPORATED, ...

1. A set of capture probes comprising:
a first capture probe consisting of: (i) a target-complementary sequence, the base sequence of which is selected from the
group consisting of the base sequences of SEQ ID NO: 90 and SEQ ID NO: 91; and (ii) a non-complementary sequence comprising
a homopolymer tail, wherein the non-complementary sequence does not stably bind to a target nucleic acid derived from Trichomonas vaginalis when the target-complementary sequence is stably hybridized to the target nucleic acid; and

a second capture probe consisting of: (i) a target-complementary sequence, the base sequence of which is selected from the
group consisting of SEQ ID NO: 55 and SEQ ID NO: 56; and (ii) a non-complementary sequence comprising a homopolymer tail,
wherein the non-complementary sequence does not stably bind to a target nucleic acid derived from Trichomonas vaginalis when the target-complementary sequence is stably hybridized to the target nucleic acid.

US Pat. No. 10,138,525

COMPOSITIONS AND METHODS TO DETECT ATOPOBIUM VAGINAE NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

1. A method for detecting in a sample a 16S rRNA of A. vaginae or a gene encoding a 16S rRNA of A. vaginae, comprising the steps of:a. providing a sample, wherein said sample is suspected of containing an Atopobium vaginae bacterium;
b. contacting said sample with at least two amplification oligomers, each being from 15 to 25 nucleotides in length and configured to generate from a 16S rRNA of A. vaginae or a gene encoding a 16S rRNA of A. vaginae, an amplicon comprising a nucleotide sequence that is SEQ ID NO:43, wherein said at least two amplification oligomers specifically hybridize to A. vaginae target nucleic acid in the presence of one or more of G. vaginalis, Prevotella sp, anaerobic gram positive cocci, Mobiluncus sp, Mycoplasma hominis, Eggerthella hongkongensis, Megasphaera sp, and/or Leptotrichia sanguinegens;
c. performing an in vitro nucleic acid amplification reaction wherein any target nucleic acid present in said sample is used as a template for generating an amplification product; and
d. performing a detection reaction to determine the presence or absence of the amplification product.
US Pat. No. 9,994,921

COMPOSITIONS, METHODS AND KITS TO DETECT HERPES SIMPLEX VIRUS NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

9. A composition for use in a HSV-2 target nucleic acid amplification assay comprising at least two amplification oligomers capable of stably hybridizing to a HSV US8.5 target nucleic acid, wherein a first amplification oligomer comprises a target hybridizing sequence at least 15 nucleotides in length and configured to target a sequence in a region of the HSV US 8.5 corresponding tonucleotides 113 to 144 of SEQ ID NO:2;
and wherein a second amplification oligomer comprises a target hybridizing sequence at least 15 nucleotides in length and configured to target a sequence in a region of the HSV US8.5 ORF corresponding to
nucleotides 172 to 200 of SEQ ID NO:2, and further comprising joined at its 5? end a T7 promoter sequence.

US Pat. No. 10,094,847

AUTOMATED SAMPLE PROCESSING INSTRUMENTS, SYSTEMS, PROCESSES, AND METHODS

GEN-PROBE INCORPORATED, ...

1. An automated instrument for processing a sample, the instrument comprising:a movable first rack configured to hold a sample containing receptacle, the first rack defining a first recess;
a movable second rack configured to hold a processing receptacle, the second rack defining a second recess;
a first lock comprising a first locking pin configured to be received in the first recess, the first lock configured to move between a locked configuration and an unlocked configuration, wherein the first lock is configured to be engaged with the first rack in the locked configuration of the first lock to secure the first rack within the automated instrument, and wherein the first lock is disengaged from the first rack in the unlocked configuration of the first lock to allow movement of the first rack within the automated instrument;
a second lock comprising a second locking pin configured to be received in the second recess, the second lock configured to move between a locked configuration and an unlocked configuration, wherein the second lock is configured to be engaged with the second rack in the locked configuration of the second lock to secure the second rack within the automated instrument, and wherein the second lock is configured to be disengaged from the second rack in the unlocked configuration of the second lock to allow movement of the second rack within the automated instrument;
a robotic arm movable within the automated instrument; and
a controller configured to control the robotic arm to:
(i) engage and move the first lock to the locked configuration of the first lock,
(ii) engage and move the first lock to the unlocked configuration of the first lock,
(iii) engage and move the second lock to the locked configuration of the second lock,
(iv) engage and move the second lock to the unlocked configuration of the second lock, and
(v) pick-and-place the sample containing receptacle, the processing receptacle, or both within the automated instrument.
US Pat. No. 10,190,180

COMPOSITIONS AND METHODS FOR AMPLIFYING AND CHARACTERIZING HCV NUCLEIC ACID

GEN-PROBE INCORPORATED, ...

1. A method for determining at least partial genotype information for hepatitis C virus type la (HCV-la) in a sample, the method comprising:(1) contacting a sample, said sample suspected of containing HCV-la, with
at least two amplification oligomers for amplifying at least one target region of an HCV-la target nucleic acid, wherein said at least one HCV-la target region is selected from the group consisting of
(a) a first target region comprising nucleotide positions 8522 to 9372 of SEQ ID NO:155 or the complement thereof, wherein if the first target region is amplified, then the at least two amplification oligomers comprise (i) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs:65, 43, and 34; and (ii) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs:69, 38, and 41;
(b) a second target region comprising nucleotide positions 7788 to 8838 of SEQ ID NO:155 or the complement thereof, wherein if the second target region is amplified, then the at least two amplification oligomers comprise (i) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 57, 63, and 28; and (ii) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 40, 35, and 42;
(c) a third target region comprising nucleotide positions 6966 to 7970 of SEQ ID NO:155 or the complement thereof, wherein if the third target region is amplified, then the at least two amplification oligomers comprise (i) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 60, 58, and 36; and (ii) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 31, 73, and 62;
(d) a fourth target region comprising nucleotide positions 6076 to 7117 of SEQ ID NO:155 or the complement thereof, wherein if the fourth target region is amplified, then the at least two amplification oligomers comprise (i) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 55, 70, and 29; and (ii) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs:46, 45, and 61;
(e) a fifth target region comprising nucleotide positions 5094 to 6304 of SEQ ID NO:155 or the complement thereof, wherein if the fifth target region is amplified, then the at least two amplification oligomers comprise (i) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 39, 44, and 68; and (ii) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 47, 51, and 59;
(f) a sixth target region comprising nucleotide positions 4258 to 5297 of SEQ ID NO:155 or the complement thereof, wherein if the sixth target region is amplified, then the at least two amplification oligomers comprise (i) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 52, 49, and 72; and (ii) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 37, 75, and 53; and
(g) a seventh target region comprising nucleotide positions 3434 to 4482 of SEQ ID NO:155 or the complement thereof, wherein if the seventh target region is amplified, then the at least two amplification oligomers comprise (i) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 77, 79, and 81; and (ii) at least one oligomer comprising a target-hybridizing sequence comprising a nucleotide sequence selected from SEQ ID NOs: 78, 80, and 71;
(2) performing at least one in vitro nucleic acid amplification reaction, wherein any HCV-la target nucleic acid present in said sample is used as a template for generating at least one amplification product corresponding to at least one of the first through seventh target regions; and
(3) detecting the nucleobase at one or more nucleotide positions within the at least one amplification product, thereby determining at least partial genotype information for the HCV-la in said sample.
US Pat. No. 10,184,147

CLOSED NUCLEIC ACID STRUCTURES

GEN-PROBE INCORPORATED, ...

1. A method of forming a closed nucleic acid structure from target nucleic acid, comprising a method selected from the group consisting of:(1) (a) denaturing a target nucleic acid; (b) annealing a primer pair to opposing strands of the denatured target nucleic acid, each of the primers having a 5? phosphate group, each of the primers having a 3? segment and a 5? segment, the 3? segments of the primers being target-binding segments; (c) extending the primers with a nucleic acid polymerase to obtain primer extended target nucleic acids, some of which have a strand with an overhanging 5? segment from the first primer and others of which have an opposing strand with an overhanging 5? segment from the second primer, wherein extension blocker oligonucleotides hybridizing to regions of the strands of the target nucleic acid 5? to the regions hybridizing to the primers are used to align the 3? ends of extended target nucleic acids with the 5? nucleobase of the 3? segments of the primers; (d) denaturing the primer-extended target nucleic acids; (e) annealing a first adaptor and a second adaptor, both having a 5? region and a 3? region, to the denatured primer-extended target nucleic acids to form an adaptor-capped nucleic acid having one strand comprising the 5? segment from the first primer and an opposing strand comprising the 5?segment from the second primer, and adaptors annealed to the 5? segments of the primers at both ends of the adaptor-capped nucleic acid; wherein the 3? region of the adaptor comprises a stem-loop structure, the 5? region of the adaptor having a 5? phosphate group, and the 5? region of the first adaptor is complementary to the 5? segment of the first primer and the 5? region of the second adaptor is complementary to the 5? segment of the second primer; and (f) contacting the adaptor-capped nucleic acid with a ligase which seals a nick in the adaptor-capped nucleic acid, thereby forming a closed nucleic acid structure;
(2) (a) denaturing a target nucleic acid; (b) annealing a primer pair to opposing strands of the denatured target nucleic acid, each of the primers having a 3? segment and a 5? segment, the 3? segments of the primers being target-binding segments, the 5? segments being complementary in opposing orientations, a first of the primers having a 5? phosphate group and the second of the primers lacking a 5? phosphate and/or having a shorter 5? segment than the first primer; (c) extending the primers with a nucleic acid polymerase to obtain primer-extended target nucleic acids, some of which have a strand with an overhanging 5? segment from the first primer and others of which have an opposing strand with an overhanging 5? segment from the second primer; (d) denaturing the primer-extended target nucleic acids; (e) annealing strands of the denatured primer-extended target nucleic acids having overhanging 5? segments, wherein strands and opposing strands anneal to one another and circularize by annealing of the 5? segments thereby forming a closed nucleic acid structure; and
(f) contacting the closed nucleic acid structure with a ligase which seals a nick between the 5? phosphate group of the first primer and an adjacent 3? hydroxyl group leaving the closed nucleic acid structure with a single nick or gap between the 5? segment of the second primer and a 3? hydroxyl of an adjacent nucleotide;
(3) (a) contacting a target nucleic acid with a primer pair under amplification conditions, each of the primers having a 5? phosphate group, each of the primers having a 3? segment and a 5? segment, the 3? segments of the primers being target-binding segments; the first 3? to 5? nucleobase unit in the 5? segment is an extension blocker; wherein the extension blocker blocks nucleobase unit extension by a nucleic acid polymerase when the 5? segment serves as a template for nucleobase unit extension; thereby forming an amplified target nucleic acid having a strand comprising an overhanging 5? segment from the first primer and an opposing strand comprising an overhanging 5?segment from the second primer; (b) annealing a first adaptor and a second adaptor, both having a 5? region and a 3? region, to the amplified target nucleic acids to form an adaptor-capped nucleic acid, wherein the 3? region of the adaptor comprises a stem-loop structure, the 5? region of the adaptor having a 5? phosphate group, and the 5? region of the first adaptor is complementary to the 5? segment of the first primer and the 5? region of the second adaptor is complementary to the 5? segment of the second primer; and (c) contacting the adaptor-capped nucleic acid with a ligase which seals a nick in the adaptor-capped nucleic acid thereby forming a closed nucleic acid structure; and
(4) (a) contacting a target nucleic acid with a primer pair under amplification conditions, each of the primers having a 3? segment and a 5? segment, the 3? segments of the primers being target-binding segments, the 5? segments being complementary in opposing orientations, a first of the primers having a 5? phosphate group and the second of the primers lacking a 5? phosphate group and/or having a shorter 5? segment than the first primer; the first 3? to 5? nucleobase unit in the 5? segment is an extension blocker; wherein the extension blocker blocks nucleobase unit extension by a nucleic acid polymerase when the 5? segment serves as a template for nucleobase unit extension, thereby forming an amplified target nucleic acids having a strand comprising an overhanging 5? segment from the first primer and an opposing strand comprising an overhanging 5? segment from the second primer (b) annealing an overhanging 5? segment from the first primer of one strand of the amplified target nucleic acid and an overhanging 5? segment from the second primer of the opposing strand of the same amplified target nucleic acid thereby forming an annealed target nucleic acid; and (c) contacting the annealed target nucleic acid with a ligase which seals a nick between the 5? phosphate group of the first primer and an adjacent 3? hydroxyl group leaving the closed nucleic acid structure with a single nick or gap between the 5? segment of the second primer and a 3? hydroxyl of an adjacent nucleotide.

US Pat. No. 10,146,973

SYSTEMS AND METHODS FOR READING MACHINE-READABLE LABELS ON SAMPLE RECEPTACLES

GEN-PROBE INCORPORATED, ...

1. A method of reading machine-readable labels on sample receptacles, comprising:moving a first sample rack between a first position and a second position along a first lane in a housing, the first sample rack holding a first plurality of sample receptacles, wherein each sample receptacle of the first plurality of sample receptacles has a machine-readable label;
moving a camera to focus the camera at a point along the first lane;
with the camera, reading the machine-readable label of each sample receptacle of the first plurality of sample receptacles held by the first sample rack as the first sample rack moves between the first position and the second position;
moving a second sample rack between a first position and a second position along a second lane different than the first lane in the housing, the second sample rack holding a second plurality of sample receptacles, wherein each sample receptacle of the second plurality of sample receptacles has a machine-readable label;
moving the camera to focus the camera at a point along the second lane; and
with the camera, reading the machine-readable label of each sample receptacle of the second plurality of sample receptacles held by the second sample rack as the second sample rack moves between the first position and the second position.
US Pat. No. 9,914,982

COMPOSITIONS AND METHODS FOR DETECTING HEPATITIS B VIRUS

GEN-PROBE INCORPORATED, ...

1. A method of detecting HBV nucleic acid contained in a test sample comprising nucleic acids, comprising the steps of:
(a) contacting the test sample with at least two amplification oligomers, wherein a first amplification oligomer comprises
a target-hybridizing region having a nucleotide sequence consisting of SEQ ID NO:26;

(b) amplifying any HBV nucleic acid that may be present in the test sample in an in vitro nucleic acid amplification reaction,
whereby there are synthesized HBV amplicons if the test sample contained HBV nucleic acid; and

(c) detecting the HBV amplicons, if present, with at least one hybridization assay probe, thereby detecting HBV nucleic acid
contained in the test sample, wherein the at least one hybridization assay probe is at least 17 contiguous nucleotides contained
within a sequence consisting of SEQ ID NO:67 or the complement thereof, allowing for the presence of RNA equivalents and nucleotide
analogs.

US Pat. No. 10,214,760

METHODS FOR AMPLIFYING NUCLEIC ACID USING TAG-MEDIATED DISPLACEMENT

GEN-PROBE INCORPORATED, ...

1. A method of amplifying a nucleic acid target region, the method comprising:contacting a target nucleic acid comprising the target region with
(1) a first amplification oligomer comprising
(a) a target-binding priming segment (T1) complementary to a 3?-end of the target region;
(b) a first heterologous displacer tag (D1) located 5? to T1; and
(c) an intervening spacer segment (S1) between T1 and D1;
said contacting comprising conditions whereby the target nucleic acid serves as a template for extension from the first amplification oligomer to produce a first amplification product comprising T1 and D1;
(2) a second amplification oligomer comprising a target-binding segment T2 complementary to a region of the first amplicon that is the complement of a 5?-end of the target region, and wherein said contacting further comprises conditions whereby the first amplicon serves as a template to produce a second amplicon comprising segments cT1 and cD1, complementary to T1 and D1, respectively;
(3) a third amplification oligomer comprising target-binding priming segment T1p having a nucleotide sequence complementary to T1, or complementary to the complement of a second amplicon target sequence cT1? near or overlapping with cT1 and situated 5? to cD1; and
(4) a fourth amplification oligomer comprising a displacer priming segment D1p having a nucleotide sequence complementary to D1;
wherein said contacting further comprises conditions whereby the second amplicon serves as a template for extension from both the third and fourth amplification oligomers, wherein extension of T1p from a T1p:cT1/cT1? hybrid produces a third amplicon, and wherein extension of D1p from a D1p:cD1 hybrid produces a fourth amplicon while displacing the third amplicon.

US Pat. No. 10,190,984

SYSTEMS AND METHODS FOR ANALYZING A SAMPLE AND FOR MONITORING THE PERFORMANCE OF AN OPTICAL SIGNAL DETECTOR

GEN-PROBE INCORPORATED, ...

1. An assay instrument comprising:a first fluorometer comprising a first detection channel having a first light source and a first sensor, the first detection channel being configured to emit and focus light generated by the first light source at a first detection zone, and to receive and focus light on the first sensor;
a carrier comprising a first non-fluorescent surface portion, defining a recess, and configured to support a first receptacle, wherein the carrier and the first fluorometer are movable relative to each other among at least (i) a first position at which a portion of the first receptacle is in the first detection zone, (ii) a second position at which the first non-fluorescent surface portion of the carrier is in the first detection zone, and (iii) a third position at which the recess is in the first detection zone; and
a controller operatively coupled to the first fluorometer and configured to:
determine a characteristic of a sample contained within the first receptacle based on a first measured intensity of light focused on the first sensor while the carrier is at the first position, and
determine an operational performance status of the first fluorometer based on at least one of (i) a second measured intensity of light focused on the first sensor while the carrier is at the second position and (ii) a third measured intensity of light focused on the first sensor while the carrier is at the third position.

US Pat. No. 10,159,981

PLASTIC BODY CONFIGURED FOR ENGAGEMENT WITH AN AUTOMATED RECEPTACLE TRANSPORT MECHANISM

GEN-PROBE INCORPORATED, ...

1. A plastic body comprising:a generally cylindrical upper portion having an open end configured for engagement with an automated pipettor;
a plurality of longitudinally oriented ribs disposed on an inner surface of the open end of the upper portion; and
a plurality of concave recesses disposed on an outer surface of the upper portion, each of the recesses being disposed directly opposite an associated one of the ribs, and each of the recesses extending along at least part of the length of the associated one of the ribs,
wherein the recesses are configured to flex or expand radially outwardly relative to an axial center of the upper portion when a force is applied to the ribs.

US Pat. No. 10,167,500

TAGGED OLIGONUCLEOTIDES AND THEIR USE IN NUCLEIC ACID AMPLIFICATION METHODS

GEN-PROBE INCORPORATED, ...

1. A method for the selective amplification and detection of at least one target nucleic acid sequence from a nucleic acid sample, said method comprising the steps of:(a) treating a nucleic acid sample comprising a target nucleic acid sequence with a tagged oligonucleotide comprising first and second regions, said first region comprising a target hybridizing sequence which hybridizes to a 3?-end of said target nucleic acid sequence and said second region comprising a tag sequence situated 5? to said target hybridizing sequence, wherein said second region does not stably hybridize to a target nucleic acid containing said target nucleic acid sequence;
(b) reducing in said nucleic acid sample the effective concentration of unhybridized tagged oligonucleotide having an active form in which a target hybridizing sequence of said unhybridized tagged oligonucleotide is available for hybridization to said target nucleic acid sequence;
(c) after step (b), initiating a nucleic acid polymerase dependent primer extension reaction from the 3? end of the tagged oligonucleotide hybridized to the target nucleic acid, thereby producing an extension product;
(d) separating the primer extension product from the target nucleic acid; and
(e) producing amplification products in an isothermal nucleic acid amplification reaction using first and second oligonucleotides, wherein said first oligonucleotide comprises a hybridizing sequence which hybridizes to a 3?-end of the complement of said target nucleic acid sequence and said second oligonucleotide comprises a hybridizing sequence which hybridizes to the complement of said tag sequence, wherein said second oligonucleotide does stably hybridize to said target nucleic acid, and wherein each of said amplification products comprises a base sequence which is substantially identical or complementary to the base sequence of said target nucleic acid sequence and further comprises a base sequence which is substantially identical or complementary to all or a portion of said tag sequence; and
(f) detecting the amplification products generated in step (e), wherein detecting the amplification products comprises exposing the amplification products to a probe having a hybridizing sequence which hybridizes to the amplification product.
US Pat. No. 10,316,352

METHODS OF CAPTURING A TARGET NUCLEIC ACID FOR AMPLIFICATION AND DETECTION USING AN INACTIVATABLE TARGET CAPTURE OLIGOMER

GEN-PROBE INCORPORATED, ...

1. A method for the specific hybridization and capture of a target nucleic acid strand, said method comprising the steps of:a. treating a nucleic acid sample with an inactivatable target capture oligomer,
wherein said inactivatable target capture oligomer comprises a target hybridizing region, a binding pair member and a tag-closing region,
wherein said target hybridizing region stably hybridizes to said target nucleic acid strand under a first set of conditions,
wherein said tag-closing region is from 3 contiguous nucleobases in length to 20 contiguous nucleobases in length, does not stably hybridize to said target hybridizing region under said first set of conditions, is substantially complementary to a portion of said target hybridizing region such that the tag-closing region and target hybridizing region will stably hybridize under a second set of conditions less stringent than the first set of conditions, and does not stably hybridize to said target nucleic acid strand under the first or second set of conditions, and
wherein said target hybridizing region, said binding pair member and said tag-closing region are joined as a single molecule;
b. providing said first set of conditions, whereby said target hybridizing region of molecules of said inactivatable target capture oligomer stably hybridizes with said target nucleic acid present in said nucleic acid sample and does not stably hybridize with said tag-closing region;
c. providing said second set of less stringent conditions, thereby allowing molecules of said inactivatable target capture oligomer that are not stably hybridized with said target nucleic acid to form an inactive configuration by stably hybridizing said tag-closing region with said target hybridizing region;
d. performing a capture step wherein a complex comprising said molecules of said inactivatable capture oligomer stably hybridized with said target nucleic acid strand in step b is captured;
e. determining the specific hybridization and capture of said target nucleic acid strand in said nucleic acid sample by performing a reaction following step d, wherein said reaction comprises an amplification reaction and a detection reaction;
wherein stable hybridization of two nucleic acid strands in a reaction mixture means the temperature of a reaction mixture including the strands is at least 2° C. below the melting temperature of the duplex formed by the strands.
US Pat. No. 10,240,185

COMPOSITIONS, KITS AND RELATED METHODS FOR THE DETECTION AND/OR MONITORING OF SALMONELLA

Gen-Probe Incorporated, ...

13. A kit for use in detecting Salmonella in a sample, said kit comprising (i) a molecular torch oligonucleotide comprising the nucleotide sequence consisting essentially of SEQ ID NO: 66, 67, 68, 69, or 70 wherein the molecular torch specifically hybridizes to a sequence within a Salmonella target nucleic acid, (ii) an RNA polymerase, and (iii) a promoter oligonucleotide for isothermally amplifying the Salmonella target nucleic acid.

US Pat. No. 10,196,674

MULTIPHASE NUCLEIC ACID AMPLIFICATION

GEN-PROBE INCORPORATED, ...

1. A method of quantifying a target nucleic acid sequence in a sample, comprising the steps of:(a) contacting the sample with a first amplification oligonucleotide, specific for a first portion of the target nucleic acid sequence, under conditions allowing hybridization of the first amplification oligonucleotide to the first portion of the target nucleic acid sequence, thereby generating a pre-amplification hybrid that comprises the first amplification oligonucleotide and the target nucleic acid sequence;
(b) isolating the pre-amplification hybrid by target capture onto a solid support followed by washing to remove any of the first amplification oligonucleotide that did not hybridize to the first portion of the target nucleic acid sequence in step (a);
(c) amplifying, in a first phase amplification reaction mixture, at least a portion of the target nucleic acid sequence of the pre-amplification hybrid isolated in step (b) in a first phase, substantially isothermal, transcription-associated amplification reaction under conditions that support linear amplification thereof, but do not support exponential amplification thereof, thereby resulting in a reaction mixture comprising a first amplification product,
wherein the first phase amplification reaction mixture comprises a second amplification oligonucleotide, the second amplification oligonucleotide being complementary to a portion of an extension product of the first amplification oligonucleotide and wherein the second amplification oligonucleotide is not enzymatically extended in the first phase of isothermal transcription-associated amplification reaction, and
wherein the first amplification product is not a template for nucleic acid synthesis during the first phase, substantially isothermal, transcription-associated amplification reaction;
(d) combining the reaction mixture comprising the first amplification product with at least one component that participates in exponential amplification of the first amplification product, but that is lacking from the reaction mixture comprising the first amplification product, to produce a second phase amplification reaction mixture,
wherein the second phase amplification reaction mixture additionally comprises a sequence-specific hybridization probe;
(e) performing, in a second phase, substantially isothermal, transcription-associated amplification reaction in the second phase amplification reaction mixture, an exponential amplification of the first amplification product, thereby synthesizing a second amplification product;
(f) detecting, with the sequence-specific hybridization probe at regular time intervals, synthesis of the second amplification product in the second phase amplification reaction mixture; and
(g) quantifying the target nucleic acid sequence in the sample using results from step (f).
US Pat. No. 10,344,341

METHOD FOR DETECTING CHIKUNGUNYA VIRUS

GEN-PROBE INCORPORATED, ...

1. A method for detecting a Chikungunya virus (CHIKV) nucleic acid sequence in a test sample, said method comprising the steps of:(a) contacting nucleic acids of the test sample with a set of amplification oligonucleotides,
wherein a first member of said set is up to 100 bases in length and complementary to at least 15 contiguous bases contained within SEQ ID NO:14, and
wherein a second member of said set is up to 100 bases in length and complementary to at least 15 contiguous bases of an extension product of the first member of said set of amplification oligonucleotides when a polynucleotide consisting of SEQ ID NO:14 is the template in a template-dependent primer extension reaction;
(b) performing an in vitro nucleic acid amplification reaction using nucleic acids of the test sample as templates together with said set of amplification oligonucleotides, whereby, if said test sample comprises said CHIKV nucleic acid sequence, there is produced an amplification product; and
(c) detecting any of said amplification product that may have been produced in the in vitro nucleic acid amplification reaction,
wherein detecting said amplification product in an amount greater than a cutoff value indicates that the CHIKV nucleic acid sequence is present in the test sample, and
wherein detecting said amplification product in an amount less than the cutoff value indicates that the CHIKV nucleic acid sequence is absent from the test sample.

US Pat. No. 10,343,127

EVAPORATION-CONTROLLING CONTAINER INSERTS

Gen-Probe Incorporated, ...

1. A method for mixing the fluid contents of a container while retarding evaporation of the fluid contents from the container, the method comprising:inserting a single-piece evaporation-limiting insert into an opening of a neck of the container, the evaporation-limiting insert comprising a hollow tubular body configured to extend into the container from the neck of the container, the tubular body including a plurality of holes formed through a wall of the tubular body and distributed along at least a portion of the length of the tubular body, and wherein the fluid contents comprise solid supports, wherein each of the holes is sized to permit passage of the solid supports therethrough, and wherein agitating the fluid contents of the container is performed to keep the solid supports in suspension; and
agitating the fluid contents of the container to promote mixing of the fluid contents, whereby the holes formed through the wall of the tubular body of the insert permit fluid to flow through a space inside the tubular body.
US Pat. No. 10,323,288

COMPOSITIONS, METHODS AND KITS TO DETECT ADENOVIRUS NUCLEIC ACIDS

GEN-PROBE INCORPORATED, ...

1. A composition for use in an Adenovirus target nucleic acid amplification and detection assay comprising (i) at least two amplification oligomers capable of stably hybridizing to Adenovirus target nucleic acid and (ii) at least one detectably labeled detection probe oligomer capable of stably hybridizing to an amplicon generated by said at least two amplification oligomers,wherein each of said at least two amplification oligomers is from 10 to 50 nucleotides in length and wherein the amplification oligomers are respectively configured to specifically hybridize to regions within a target sequence of Adenovirus selected from the group consisting of from nucleotides 1 to 99 and from nucleotides 83 to 175 of Accession Number AB330090.1 (SEQ ID No. 47) wherein,
at least one of said at least two amplification oligomers is complementary to the targeted Adenovirus nucleic acid within nucleotides 1 to 99 of SEQ ID No. 47 and comprises a target hybridizing sequence as set forth in SEQ ID No: 25 with no mismatches or with 1 or 2 mismatches to the targeted Adenovirus nucleic acid; and
at least one of said at least two amplification oligomers is complementary to the targeted Adenovirus nucleic acid within nucleotides 83 to 175 of SEQ ID No. 47 and comprises a target hybridizing sequence as set forth in SEQ ID No: 27 with no mismatches or with 1 or 2 mismatches to the targeted Adenovirus nucleic acid; and
wherein one of said at least one detection probe oligomer is from 20 to 22 contiguous nucleotides in length and comprises a target hybridizing sequence contained within SEQ ID No. 1 or the complement thereof, with no mismatches or with 1 or 2 mismatches to SEQ ID No. 1.

US Pat. No. 10,279,351

SYSTEM FOR PERFORMING A MAGNETIC SEPARATION PROCEDURE

GEN-PROBE INCORPORATED, ...

1. A system for separating an analyte of interest from other components of a sample contained in a receptacle, the system comprising:a receptacle holding station configured to receive and hold a receptacle delivered to the receptacle holding station, the receptacle holding station comprising:
one or more stationary magnets positioned to apply a magnetic field to the contents of the receptacle held in the receptacle holding station, wherein the receptacle holding station is configured to hold the receptacle stationary relative to the one or more stationary magnets when present in the receptacle holding station; and
a solid, single-piece cover panel positioned to cover an open end of a receptacle held in the receptacle holding station, thereby obstructing access to the contents of the receptacle held in the receptacle holding station; and
a magnetic separation station comprising one or more magnets, the magnetic separation station being constructed and arranged to perform a magnetic separation procedure on the contents of a receptacle transported from the receptacle holding station to the magnetic separation station by an automated receptacle transport by magnetically isolating an analyte immobilized on a magnetically-responsive solid support and removing other components of the sample from the receptacle, wherein the magnetic separation station is configured to provide relative movement between the receptacle and the one or more magnets after the receptacle is transported to the magnetic separation station.