US Pat. No. 9,273,344

INSTRUMENT FOR CASSETTE FOR SAMPLE PREPARATION

LUMINEX CORPORATION, Aus...

1. An apparatus comprising:
a rack;
a linear drive shaft;
a plurality of gears;
first and second vertical linear bearings;
a plurality of valve key shafts disposed on a first side of the rack, each of said valve key shafts comprising a magnet at
an end of said valve key shafts distal to the rack;

a linear motor coupled to the plurality of valve key shafts via the linear drive shaft and the plurality of gears, wherein
the linear motor is positioned on either end of the rack;

a vertical engagement driving motor coupled to the rack, wherein:
the vertical engagement driving motor is configured to vertically position the rack, wherein said vertical engagement driving
motor is coupled to the first and second vertical linear bearings; and

the linear motor is configured to horizontally position and rotate the plurality of magnets and the valve key shafts via the
plurality of gears.

US Pat. No. 9,292,938

METHODS AND SYSTEMS FOR IMAGE DATA PROCESSING

Luminex Corporation, Aus...

1. An apparatus, comprising:
at least one processor; and
an imaging subsystem configured to accept a sample that includes a plurality of discrete components, and capture images of
the plurality of discrete components, wherein the plurality of discrete components have fluorescence material associated therewith;

wherein the at least one processor is configured to:
determine locations of selected ones of the plurality of discrete components within a first image of the captured images;
calculate a transform that includes a radial component and a constant component, the radial component being proportional to
a distance between the locations of the selected ones within the first image and a center of the first image; and

determine estimated locations of the selected ones within a second image of the captured images by applying the transform
to the locations of the selected ones within the first image.

US Pat. No. 9,982,291

PROBES FOR IMPROVED MELT DISCRIMINATION AND MULTIPLEXING IN NUCLEIC ACID ASSAYS

LUMINEX CORPORATION, Aus...

1. A method for detecting the presence of a target nucleic acid comprising:(a) contacting a sample with a first cleavable probe, said probe comprising, from 5? to 3?, (i) a first sequence region comprising at least one non-natural nucleotide labeled with a first member of a reporter-quencher pair; (ii) a second sequence region; (iii) a sequence that is the reverse complement of the second sequence region; and (iv) a sequence comprising one or more ribonucleotide base(s) that is complementary to a first region on a first strand of the target nucleic acid;
(b) contacting the cleavable probe with an endoribonuclease, thereby cleaving probe that is hybridized with target nucleic acid to form a truncated cleavable probe;
(c) allowing the truncated cleavable probe to hybridize to itself to form a hairpin probe;
(d) extending the hairpin probe in the presence of a non-natural nucleotide labeled with a second member of a reporter-quencher pair that is capable of base-pairing with the at least one non-natural nucleotide of the first sequence region; and
(e) detecting the target nucleic acid by detecting a change in signal from the label on the cleavable probe and the hairpin probe.

US Pat. No. 9,245,169

APPARATUS, SYSTEM, AND METHOD FOR IMAGE NORMALIZATION USING A GAUSSIAN RESIDUAL OF FIT SELECTION CRITERIA

Luminex Corporation, Aus...

1. A method comprising:
acquiring a two-dimensional image of a plurality of particles, wherein the plurality of particles includes a plurality of
calibration particles having Gaussian intensity profiles based on internal distributions of a first fluorescent material,
and a plurality of non-calibration particles having non-Gaussian intensity profiles based on surface distributions of a second
fluorescent material;

identifying a calibration particle of the plurality of calibration particles by correlating a portion of the image corresponding
to the calibration particle to a Gaussian function;

measuring an intensity of the calibration particle; and
normalizing an intensity of the image based at least in part on the intensity of the calibration particle.

US Pat. No. 9,984,279

APPARATUS, SYSTEM, AND METHOD FOR IMAGE NORMALIZATION USING A GAUSSIAN RESIDUAL OF FIT SELECTION CRITERIA

Luminex Corporation, Aus...

1. A method comprising:a computing system acquiring a two-dimensional image of a plurality of particles in a first channel, wherein the plurality of particles have been exposed to an analyte, wherein the plurality of particles includes a plurality of calibration particles having internal distributions of a first fluorescent material and a plurality of non-calibration particles having surface distributions of a second fluorescent material;
the computing system identifying a calibration particle of the plurality of calibration particles by analyzing first pixel values of first pixels that correspond to the calibration particle in the first channel to correlate intensity values of the first pixels to a Gaussian function;
the computing system identifying a non-calibration particle of the plurality of non-calibration particles by analyzing second pixel values of second pixels that correspond to the non-calibration particle in the first channel to determine that intensity values of the second pixels do not correlate to a Gaussian function;
the computing system measuring an intensity of the calibration particle based on the first pixel values; and
the computing system saving a new version of the two-dimensional image, wherein the new version of the two-dimensional image includes third pixels with third pixel values that are normalized based at least in part on the intensity of the calibration particle.
US Pat. No. 9,193,991

SYSTEMS AND METHODS FOR MULTIPLEX ANALYSIS OF PCR IN REAL TIME

LUMINEX CORPORATION, Aus...

1. A method for multiplexed detection of nucleic acid targets in a sample comprising:
(a) combining in a chamber a sample, a plurality of primer pairs for priming amplification of nucleic acid targets in the
sample, a plurality of first probes immobilized on a plurality of encoded particles such that the identity of each first probe
is known from the encoded particle on which it is immobilized, and a plurality of second probes complementary to the nucleic
acid targets and to the plurality of first probes, wherein the second probes (i) are labeled, and (ii) are not immobilized
on the plurality of encoded particles;

(b) forming amplification products in the chamber for each of the nucleic acid targets amplified with the plurality of primer
pairs;

(c) measuring a signal over time from the encoded particles and a signal over time from the label of the second probes hybridized
to the first probes immobilized on the encoded particles, wherein the encoded particles are immobilized on a surface of the
chamber, and wherein a change in the signal from the label of the second probes hybridized to the first probes immobilized
on the encoded particles indicates the presence of the target nucleic acids; and

(d) detecting the presence or absence of the nucleic acid targets in the sample based on the change in the signal from the
label of the second probes hybridized to the first probes immobilized on the encoded particles.

US Pat. No. 9,249,455

METHODS FOR DETECTION AND QUANTIFICATION OF SMALL RNA

LUMINEX CORPORATION, Aus...

1. A method comprising:
(a) contacting a sample to be tested for the presence or absence of a target small RNA with:
(i) a linear first primer comprising a target binding region and a tail region, wherein the target binding region comprises
about 12 or fewer nucleotides that are complementary to the small RNA;

(ii) a linear second primer comprising a target binding region and a tail region, wherein the target binding region comprises
about 12 or fewer nucleotides that are complementary to the reverse complement of the small RNA,

wherein the tail regions of the first primer, the second primer, or both the first primer and the second primer comprise a
first label and a first non-natural base;

(b) extending the first primer under conditions suitable to produce a first reaction product of the small RNA, if present
in the sample;

(c) amplifying the first reaction product with the first primer and the second primer under conditions suitable to produce
an amplification product, wherein a second non-natural base conjugated to a second label is incorporated into the amplification
product opposite the first non-natural base, and wherein the first non-natural base is iso-C or iso-G and the second non-natural
base is the other of iso-C or iso-G; and

(d) detecting the amplification products produced in step (c) by observing a signal from the first label, the second label,
or both the first label and the second label to determine the presence or absence of the target small RNA in the sample.

US Pat. No. 9,074,250

APPARATUS AND METHODS FOR INTEGRATED SAMPLE PREPARATION, REACTION AND DETECTION

Luminex Corporation, Aus...

1. A method comprising:
(a) providing a composition comprising nucleic acids bound to magnetic particles in a first chamber of a cassette comprising
the first chamber and a reaction chamber;

(b) eluting the nucleic acids from the particles in the first chamber to obtain an eluted nucleic acid sample;
(c) magnetically attracting the magnetic particles to a cavity of a valve member movably disposed within a valve housing,
wherein the valve housing is at least partially disposed between the first chamber and a second chamber and comprises a first
opening in fluid communication with the first chamber and a second opening in fluid communication with the second chamber;

(d) transferring at least a portion of the eluted nucleic acid sample to the reaction chamber in fluid communication with
the first chamber;

(e) amplifying one or more target nucleic acid sequences in the eluted nucleic acid sample by combining the eluted nucleic
acid sample and PCR reagents in the reaction chamber under conditions suitable for PCR.

US Pat. No. 9,810,707

CHIP-BASED FLOW CYTOMETER TYPE SYSTEMS FOR ANALYZING FLUORESCENTLY TAGGED PARTICLES

LUMINEX CORPORATION, Aus...

1. A portable system for processing and analyzing biological or environmental samples, comprising:
an automated assay preparation module configured to process a sample into a fluid assay with fluorescently tagged particles;
and

a microfluidic analysis module coupled to the automated assay preparation module, wherein the microfluidic analysis module
comprises a chip-based flow cytometer having:

a first input conduit for receiving the fluid assay;
a second distinct conduit for receiving a sheath fluid;
a fluid flow chamber coupled to the first and second input conduits, wherein the fluid flow chamber is configured to generate
a fluid stream with the fluid assay confined within the sheath fluid;

a channel coupled to the fluid flow chamber for routing the fluid stream through the flow cytometer;
an illumination subsystem comprising a light source system and an optical system collectively configured to direct light toward
an interrogation region of the channel;

a measurement subsystem comprising:
a collection system comprising collection optics configured to gather fluorescence emitted from the fluorescently tagged particles;
and

an examination system for analyzing the collected fluorescence;
wherein the first conduit, second conduit, fluid flow chamber, channel, and at least some collection optics of the collection
system are fixedly arranged within a substrate, and

wherein the light source system is configured such that individual light sources within the light source system direct light
at different spots within the interrogation region, and wherein the collection system is configured such that the fluorescent
light emitted from the fluorescently tagged particles at each of the different spots is collected by a different detector
of the collection system.

US Pat. No. 9,856,517

INSTRUMENT FOR CASSETTE FOR SAMPLE PREPARATION

LUMINEX CORPORATION, Aus...

1. A system comprising:
a plurality of stackable enclosures stacked one on top of the other, wherein each stackable enclosure of the plurality of
stackable enclosures comprises:

(i) at least one opening configured to receive at least one cassette, the cassette comprising a first plunger disposed within
a chamber;

(ii) a plunger assembly comprising a second plunger configured to engage the first plunger disposed within the chamber of
the cassette when the cassette is present in the stackable enclosure, wherein the first and second plungers are aligned vertically
and horizontally with the chamber of the cassette; and

(iii) at least one sub-system computer;
a system controller module comprising:
(i) a single, touch-panel display; and
(ii) a main computer configured to communicate with the single, touch-panel display and the sub-system computer in the plurality
of stackable enclosures.

US Pat. No. 9,597,685

FLUID RETENTION PLATES AND ANALYSIS CARTRIDGES

LUMINEX CORPORATION, Aus...

1. A system comprising:
a first plate comprising:
a first side;
a second side;
a first reservoir coupled to the first side of the first plate;
a protrusion extending from the second side of the first plate;
a first channel extending from the first side of the first plate through the protrusion on the second side of the first plate;
a fluid displacement mechanism in fluid communication with the first reservoir and the first channel; and
a pierceable seal coupled to the protrusion extending from the second side of the first plate and covering the first channel;
and

a second plate coupleable to the first plate, the second plate comprising:
a first side;
a second side;
a protrusion extending from the first side of the second plate and configured to mate with the protrusion on the second side
of the first plate;

a piercing element associated with the protrusion extending from the first side of the second plate, wherein the piercing
element is configured to extend through the pierceable seal when the protrusion on the second side of the first plate is mated
with the protrusion extending from the first side of the second plate; and

a second channel in fluid communication with the protrusion extending from the first side of the second plate.

US Pat. No. 9,248,422

APPARATUS AND METHODS FOR INTEGRATED SAMPLE PREPARATION, REACTION AND DETECTION

LUMINEX CORPORATION, Aus...

1. An apparatus, comprising:
a housing defining a first flow path and a second flow path, the housing having a flow cell portion defining a detection volume,
wherein the flow cell portion is located within an extension of the housing;

a reaction vial coupled to the housing, the reaction vial defining a reaction volume, the reaction volume in fluid communication
with the detection volume via the first flow path; and

a transfer mechanism in fluid communication with the detection volume via the second flow path, the transfer mechanism configured
to transfer a sample from the reaction volume to the detection volume when the transfer mechanism is actuated;

an optics module interfaced with the extension, wherein:
the apparatus is configured to allow the sample to flow within the first flow path in a first direction into the detection
volume while a second portion of the sample flows within the second flow path in a second direction opposite the first direction;

the optics module comprises a magnet.

US Pat. No. 9,434,939

INSTRUMENT FOR CASSETTE FOR SAMPLE PREPARATION

LUMINEX CORPORATION, Aus...

1. A system comprising:
a network; and
a plurality of instruments, wherein:
each instrument in the plurality of instruments is configured to receive a plurality of cassettes;
each instrument in the plurality of instruments comprises a particle transfer system including a plurality of valve shafts
and a first actuator assembly;

each instrument in the plurality of instruments comprises a computer; and
each instrument in the plurality of instruments comprises a communication device, wherein the communication device is configured
to couple the instrument to the network;

wherein the first actuator assembly is configured to move the plurality of valve shafts between a first position and a second
position; and

the first actuator assembly is configured to rotate each valve shaft from the plurality of valve shafts when the plurality
of valve shafts is in the second position.

US Pat. No. 9,376,613

MAGNETIC MICROSPHERES FOR USE IN FLUORESCENCE-BASED APPLICATIONS

LUMINEX CORPORATION, Aus...

1. A microsphere, comprising:
a core microsphere;
a magnetic material coupled to a surface of the core microsphere; and
a polymer layer surrounding the magnetic material and the core microsphere, wherein the microsphere contains greater than
2% by weight of the magnetic material, and the magnetic material covers 50% or less of the surface of the core microsphere.

US Pat. No. 9,611,509

MATERIALS AND METHODS FOR DETECTION OF NUCLEIC ACIDS

LUMINEX CORPORATION, Aus...

1. A method for differentiating between an intended amplification product and a non-specific amplification product in a polymerase
chain reaction (PCR) comprising:
(a) amplifying a target nucleic acid using a first primer comprising a sequence complementary to a first portion of the target
nucleic acid, a second primer comprising a first region and a second region, the first region comprising a sequence complementary
to a second portion of the target nucleic acid and the second region comprising a labeled nucleotide having a non-natural
base, in the presence of a labeled reporter to generate an amplification product, wherein the labeled reporter comprises a
non-natural base that is incorporated into the amplification product opposite the non-natural base present in the second region
of the second oligonucleotide primer;

(b) observing a signal from the labeled reporter at a first temperature that is below a predicted melting temperature of the
intended amplification product;

(c) determining a melting temperature of the amplification product by observing a change in the signal from the labeled reporter
while increasing the temperature above the first temperature; and

(d) determining that the amplification product is the intended amplification product if the determined melting temperature
corresponds to the predicted melting temperature or determining that the amplification is not the intended amplification product
if the determined melting temperature does not correspond to the predicted melting temperature.

US Pat. No. 9,587,270

CHIMERIC PRIMERS WITH HAIRPIN CONFORMATIONS AND METHODS OF USING SAME

LUMINEX CORPORATION, Aus...

1. A nucleic acid molecule comprising:
(a) a target-specific primer sequence;
(b) an anti-tag sequence 5? of the target-specific primer sequence;
(c) a tag sequence 5? of the anti-tag sequence; and
(d) a blocker between the anti-tag sequence and the tag sequence.
US Pat. No. 9,539,577

APPARATUS AND METHODS FOR INTEGRATED SAMPLE PREPARATION, REACTION AND DETECTION

LUMINEX CORPORATION, Aus...

1. An apparatus, comprising:
(a) an instrument enclosure configured to contain a cassette, the cassette comprising:
(i) a lysis chamber,
(ii) an elution chamber, and
(iii) a reaction chamber;
(b) a heater assembly disposed within the instrument enclosure, the heater assembly comprising a first heater module comprising
a first lumen and a second lumen and configured to receive at least a portion of the reaction chamber;

(c) an optics assembly disposed within the instrument enclosure, the optics assembly comprising an excitation module, a detection
module, a first optical member, and a second optical member, wherein the first optical member is configured to convey electromagnetic
energy from the excitation module to the reaction chamber via the first lumen, and wherein the second optical member is configured
to convey electromagnetic energy from the reaction chamber to the detection module via the second lumen.

US Pat. No. 9,286,504

METHODS AND SYSTEMS FOR IMAGE DATA PROCESSING

Luminex Corporation, Aus...

1. A method, comprising:
a computing system receiving a first normalization set of one or more images of an imaging region containing first particles
having a first known concentration of fluorescence material associated therewith;

the computing system receiving a second normalization set of one or more images of the imaging region containing second particles
having a second known concentration of fluorescence material associated therewith;

the computing system determining, based on the received first and second normalization sets, normalization parameters for
selected portions of the imaging region;

the computing system receiving a data set of one or more images of the imaging region containing particles having an unknown
concentration of fluorescence material associated therewith; and

the computing system normalizing the data set based on the normalization parameters.

US Pat. No. 9,745,438

METHOD AND SYSTEM FOR MANUFACTURE AND USE OF MACROPOROUS BEADS IN A MULTIPLEX ASSAY

LUMINEX CORPORATION, Aus...

1. A method of manufacturing macroporous particles comprising:
(a) providing seed particles having multiple polymer chains;
(b) mixing the seed particles with a solution comprising a monomer, a co-monomer, and a crosslinking agent, wherein the amount
of crosslinking agent in the solution is less than 25%;

(c) swelling the seed particles;
(d) initiating polymerization of the swelled particles;
(e) modifying an active group of the co-monomer on an exterior surface of the swelled particles to form a modified active
group;

(f) washing the swelled particles in solvent to remove the seed particles and expose macropores, wherein the macropores have
a diameter greater than 20 nm, and further wherein the exterior surface within the macropores has the active group and the
exterior surface outside the macropores has the modified active group; and

(g) conjugating a first analytical species to the active group within the macropores and conjugating a second analytical species
to the modified active group outside the macropores.

US Pat. No. 9,562,261

METHODS FOR DETECTION AND TYPING OF NUCLEIC ACIDS

LUMINEX CORPORATION, Aus...

1. A composition comprising a primer pair for the amplification of a target nucleic acid sequence, each primer of said primer
pair having a 5? end and a 3? end, and at least one non-natural base selected from the group consisting of iso-G and iso-C
internal to said 5? and 3? ends to create one or more mismatches with the target nucleic acid sequence, wherein at least one
primer of said primer pair comprises a labeled iso-G or a labeled iso-C at its 5? end.

US Pat. No. 9,063,088

METHODS AND SYSTEMS FOR IMAGE DATA PROCESSING

Luminex Corporation, Aus...

1. An apparatus, comprising:
at least one processor; and
an imaging subsystem configured to accept a plurality of particles in an imaging region of the apparatus, supply light to
the imaging region, and capture images of the plurality of particles, wherein the particles have fluorescence material associated
therewith;

wherein the at least one processor is configured to:
determine locations of selected particles of the plurality of particles within a first one of the captured images;
calculate a transform that includes a radial component and a constant component, the radial component being proportional to
a distance between the locations of the selected particles within the first image and a center of the first image; and

determine estimated locations of the selected particles within a second one of the captured images by applying the transform
to the locations of the particles within the first image.

US Pat. No. 9,745,615

INSTRUMENT FOR CASSETTE FOR SAMPLE PREPARATION

LUMINEX CORPORATION, Aus...

1. A system comprising:
a plurality of stackable enclosures stacked one on top of the other, wherein each stackable enclosure of the plurality of
stackable enclosures comprises:

(i) at least one opening configured to receive one or more cassettes,
(ii) at least one actuator assembly, said actuator assembly comprising a plurality of plungers configured to be movable between
a first position and a second position such that the plurality of plungers are configured to engage a surface of the one or
more cassettes when the plurality of plungers are moved from the first position to the second position; and

(iii) at least one sub-system computer;
a system controller module comprising a single, touch-panel display and a main computer configured to communicate with the
single, touch-panel display and the sub-system computer in the plurality of stackable enclosures.

US Pat. No. 9,745,620

SYSTEMS AND METHODS FOR MULTIPLEX ANALYSIS OF PCR IN REAL TIME

LUMINEX CORPORATION, Aus...

1. A method of detecting a target molecule in a sample comprising:
(a) forming a capture sandwich complex by binding a target molecule, if present in a sample, with (i) a capture antibody,
and (ii) a detection antibody, wherein the capture antibody is linked to a magnetic particle and the detection antibody is
linked to a detection nucleic acid sequence;

(b) applying a magnetic field to a surface of a chamber containing the capture antibody linked to the magnetic particle to
draw the magnetic particle to the surface in order to immobilize the capture sandwich complex on the surface of the chamber,
wherein the magnetic field is applied before or after the capture sandwich complex is formed;

(c) while the capture sandwich complex is immobilized on the surface of the chamber, washing the chamber to remove excess
detection antibody from the chamber;

(d) introducing into the chamber a primer pair for priming amplification of the detection nucleic acid sequence, a labeling
agent, and a probe complementary to an amplification product of the primer pair and the detection nucleic acid sequence, wherein
the probe is immobilized on an encoded magnetic bead such that the identity of the probe is known from the encoded magnetic
bead on which it is immobilized;

(e) performing an amplification cycle to form a labeled amplification product of the detection nucleic acid sequence amplified
with the primer pair;

(f) hybridizing the labeled amplification product to the probe immobilized on the encoded magnetic bead; and
(g) detecting the target molecule, if present in the sample, by detecting a signal from the encoded magnetic bead and a signal
from the labeled amplification product.

US Pat. No. 9,719,855

EVALUATION OF FOCUSING PERFORMANCE IN AN ASSAY ANALYSIS SYSTEM

Luminex Corporation, Aus...

1. A method, comprising:
performing an automated routine to adjust a focal position of a photosensitive detection subsystem of an assay analysis system;
subsequent to performing the automated routine, imaging particles arranged within an imaging chamber of the assay analysis
system to create an image;

generating a frequency spectrum of the image via a discrete Fourier transform; and
comparing a width of a primary lobe of the frequency spectrum at a selected brightness value to a benchmark to evaluate a
performance of the automated routine to adjust the focal position of the photosensitive detection subsystem.

US Pat. No. 9,657,332

PROBES FOR IMPROVED MELT DISCRIMINATION AND MULTIPLEXING IN NUCLEIC ACID ASSAYS

LUMINEX CORPORATION, Aus...

1. An in vitro method for detecting the presence of a target nucleic acid comprising:
(a) contacting the sample with a first set of probes, said set of probes comprising an upstream probe comprising, from 5?
to 3?, (i) at least one non-natural nucleotide labeled with a first member of a reporter-quencher pair; (ii) a tag sequence;
and (iii) a sequence complementary to a first region on a first strand of the target nucleic acid; and a downstream probe
comprising, from 5? to 3?, (i) a mirrored tag sequence having the same sequence as the tag sequence of the upstream probe;
and (ii) a sequence complementary to a second region on a first strand of the target nucleic acid downstream of the first
region, wherein the upstream probe comprises a 3? sequence of 3 or more bases complementary to the downstream probe such that
when hybridized to the target nucleic acid the set of probes form a T-junction;

(b) extending the upstream probe to synthesize sequences complementary to the mirrored tag sequence on the downstream probe
to form an extended upstream probe;

(c) allowing the extended upstream probe to hybridize to itself to form a hairpin probe;
(d) extending the hairpin probe in the presence of a non-natural nucleotide labeled with a second member of a reporter-quencher
pair that is capable of base-pairing with the at least one non-natural nucleotide in the upstream probe; and

(e) detecting the target nucleic acid by detecting a change in signal from the label on the upstream probe and the hairpin
probe.

US Pat. No. 9,636,689

ROTATING MAGNETIC ACTUATOR

LUMINEX CORPORATION, Aus...

1. A magnetic actuator configured to isolate particles in a fluid assay, the magnetic actuator comprising:
a first magnet magnetized in a first direction, a second magnet magnetized in a second direction, a third magnet magnetized
in a third direction, and a fourth magnet magnetized in a fourth direction, wherein the directions are not identical and each
direction is either parallel or orthogonal to the other directions such that a Halbach effect is induced on one side of the
magnets;

a motor configured to rotate at least two of the first, second, third and fourth magnets;
a lateral support member configured to support the motor, the first magnet, the second magnet; the third magnet, and the fourth
magnet; and

a first linear magnet array comprising the first magnet, the second magnet, the third magnet, and the fourth magnet, where
each of the first, second, third and fourth magnets is adjacent to at least one other of the first, second, third and fourth
magnets;

wherein the motor is configured to rotate at least two of the first, second, third and fourth magnets in the linear magnet
array approximately 180 degrees about an axis through the first magnet, the second magnet, the third magnet, and the fourth
magnet.

US Pat. No. 9,170,198

CROSSTALK REDUCTION

Luminex Corporation, Aus...

1. A method, comprising:
illuminating a sample with a light source, wherein the sample includes a plurality of fluorescent species, and wherein illuminating
the sample with the light source excites at least two of the plurality of fluorescent species;

measuring at least two fluorescence signals from the sample, wherein the at least two fluorescence signals include component
signals from the at least two of the plurality of fluorescent species; and

determining, by an assaying device, an amount of crosstalk between the at least two fluorescence signals, wherein the determined
amount of crosstalk is based on a correlation between respective time derivatives of the at least two fluorescence signals.

US Pat. No. 9,970,050

HYDROLYSIS PROBES

LUMINEX CORPORATION, Aus...

1. A method for detecting a target nucleic acid in a sample, comprising:(a) contacting the sample with a first target-specific primer complementary to a first region on a first strand of the target nucleic acid, and a target-specific probe complementary to a second region on the first strand of the target nucleic acid downstream of the first region under stringent conditions for hybridization of the target nucleic acid with the first target-specific primer and the target-specific probe, wherein the target-specific probe comprises a tag at its 5? or 3? end and a reporter;
(b) cleaving the hybridized target-specific probe with a nucleic acid polymerase having exonuclease activity to release the reporter from the tag;
(c) hybridizing the tag to a complementary anti-tag immobilized on a solid support; and
(d) detecting the target nucleic acid by detecting a decrease in signal from the reporter on the solid support, wherein the decrease in signal from the reporter is determined by comparison to a reference signal from a reporter on a non-hybridizing probe attached to a solid or to a signal from the reporter on the solid support prior to the cleaving of the hybridized target-specific probe.

US Pat. No. 9,828,598

CASSETTE FOR SAMPLE PREPARATION

LUMINEX CORPORATION, Aus...

1. An apparatus comprising:
(a) a reaction chamber;
(b) a removable lid configured to provide access to an opening in a first surface of the reaction chamber;
(c) a plurality of holding chambers disposed along a second surface of the reaction chamber, wherein each holding chamber
of the plurality of holding chambers comprises a valve assembly configured to selectively place the plurality of holding chambers
in fluid communication with the reaction chamber via a plurality of openings in the second surface of the reaction chamber;

(d) a particle chamber comprising a first opening and a second opening, wherein the particle chamber and the reaction chamber
are in fluid communication with the reaction chamber via the first opening;

(e) a waste chamber comprising an opening, wherein the waste chamber is movable from a first position in which the opening
of the waste chamber is aligned with the second opening of the particle chamber and a second position in which the opening
of the waste chamber is not aligned with the second opening of the particle chamber; and

(f) an elution chamber comprising an opening, wherein the elution chamber is movable from a first position in which the opening
of the elution chamber is aligned with the second opening of the particle chamber and a second position in which the opening
of the elution chamber is not aligned with the second opening of the particle chamber.

US Pat. No. 9,500,644

PARTICLE POPULATIONS AND ASSAYS HAVING VARYING AMOUNTS OF MAGNETIC MATERIAL AND PARTICLE CONCENTRATIONS AMONG DIFFERENT SUBSETS OF PARTICLES AND METHODS FOR PROCESSING ASSAYS HAVING SUCH PARTICLE POPULATIONS

LUMINEX CORPORATION, Aus...

1. A method, comprising:
introducing an assay into a static imaging optical analysis system, wherein the assay comprises (i) one or more analytes of
interest, and (ii) at least two discrete particle sets distinguishable at least by their distinct concentrations of particles
within the assay and the discrete ranges of magnetic material coupled to the particles of the respective particle sets;

routing the assay in proximity to an, imaging plane within the static imaging optical analysis system;
generating a magnetic field in proximity to the imaging plane that is sufficient to attract and immobilize a ratio of particles
from the at least two discrete particle sets that is different from the ratio of particles comprising the at least two discrete
particle sets in the assay as the assay is introduced into the static imaging optical analysis system;

imaging the particles immobilized on the imaging plane; and
analyzing one or more images produced from the step of imaging to determine the presence, absence and/or concentrations of
the one or more analytes of interest within the assay.

US Pat. No. 9,406,144

REAL-TIME TRACKING AND CORRELATION OF MICROSPHERES

LUMINEX CORPORATION, Aus...

1. A method, comprising:
capturing, using an optical detector, a first and a second image of one or more particles;
capturing, using a video detector, a plurality of video frames of the one or more particles;
time stamping the first and second images captured using the optical detector;
time stamping the plurality of video frames captured using the video detector;
identifying, using the processor, a first image position of a particle in the first image of the one or more particles;
correlating, using the time stamps and a processor, the first image position of the particle in the first image to a second
image position of the particle in the second image using the plurality of video frames;

transforming the identified first image position of the particle in the first image from a position in an image coordinate
system to a position in a video frame coordinate system to identify a first video frame position;

identifying a first video frame of the plurality of video frames with a time stamp that is closest to a time stamp of the
first image;

identifying a particle with a position in the identified first video frame that is closest to the first video frame position;
tracking the movement of the particle from the first video frame to a second video frame to locate a second video frame position
of the particle in the second video frame; and

inverse transforming the second video frame position in the video frame coordinate system to a position in the image coordinate
system to identify a second image position of the particle in the second image.

US Pat. No. 10,047,391

INSTRUMENT FOR CASSETTE FOR SAMPLE PREPARATION

LUMINEX CORPORATION, Aus...

1. An apparatus comprising:a rack comprising a first end, a second end, a first side and a second side, wherein the first side is opposed to the second side;
a first vertical linear bearing and a second vertical linear bearing, wherein the first vertical linear bearing and the second vertical linear bearing are coupled to the rack;
a vertical engagement driving motor coupled to the rack, wherein the vertical engagement driving motor is configured to vertically position the rack;
a first plurality of heaters and thermal sensors disposed on the first side of the rack; and
a first plurality of heater and thermal sensor connectors, wherein the first plurality of heater and thermal sensor connectors are aligned with the first plurality of heaters and thermal sensors.

US Pat. No. 9,965,866

REAL-TIME TRACKING AND CORRELATION OF MICROSPHERES

LUMINEX CORPORATION, Aus...

1. A method for correlating a position of a droplet in a first image with a position of the droplet in a second image, comprising:capturing, using an optical detector, a first and a second image of one or more droplets;
capturing, using a video detector, a plurality of video frames of the one or more droplets;
identifying, using a processor, a first image position of a droplet in the first image of the one or more droplets;
transforming the identified first image position of the droplet in the first image from a position in an image coordinate system to a position in a video frame coordinate system to identify a first video frame position of the plurality of video frames;
identifying a droplet with a position in the identified first video frame that is closest to the first video frame position;
tracking the movement of the droplet from the first video frame to a second video frame to locate a second video frame position of the droplet in the second video frame; and
inverse transforming the second video frame position in the video frame coordinate system to a position in the image coordinate system to identify a second image position of the droplet in the second image.
US Pat. No. 9,738,923

METHODS FOR GENERATING STABILIZED LYOPHILIZED MATERIALS

LUMINEX CORPORATION, Aus...

1. A method of making a composition of stabilized, lyophilized PCR reagents comprising:
(a) combining a solid object which may have a diameter or length in its longest dimension of between about 0.5 mm to about
5 mm or between about 1 mm to about 2 mm, one or more lyophilization reagents, and one or more PCR reagents in a receptacle;

(b) lyophilizing the solid object, the one or more lyophilization reagents, and the one or more PCR reagents to form lyophilized
PCR reagents;

(c) adding a solid wax to the lyophilized PCR reagents in a receptacle;
(d) heating both the wax and the lyophilized PCR reagents in the receptacle to melt the wax and impregnate the lyophilized
PCR reagents with the wax; and

(e) re-solidifying the wax to form stabilized, lyophilized PCR reagents.

US Pat. No. 9,752,968

ROTATING SHIELDED MAGNETIC ACTUATOR

LUMINEX CORPORATION, Aus...

1. A system configured to isolate particles in a fluid assay comprising:
a chassis;
a magnetic actuator coupled to the chassis, the magnetic actuator having rotatable shielded magnets, wherein each of the rotatable
shielded magnets comprises:

a top surface;
a bottom surface; and
a shield, wherein the shield covers the bottom surface and is directly coupled to the rotatable shielded magnet;
a tub coupled to the chassis; and
a well plate coupled to the tub and comprising a plurality of wells arranged in columns and rows;
where the tub is configured to support the well plate such that each shielded magnet is adjacent to at least one column of
wells.

US Pat. No. 9,645,142

MAGNETIC MICROSPHERES FOR USE IN FLUORESCENCE-BASED APPLICATIONS

LUMINEX CORPORATION, Aus...

1. A population of magnetically responsive microspheres comprising:
at least a first and a second subset of microspheres, wherein microspheres in the first and second subsets of microspheres
comprise:

a core microsphere;
a magnetic material coupled to a surface of the core microsphere, wherein 50% or less of the surface of the core microsphere
is covered by the magnetic material; and

a polymer layer that surrounds the magnetic material,
and further wherein the first subset of microspheres exhibits different magnetic properties as compared to the second subset
of microspheres such that the microspheres in the first and second subsets of microspheres can be distinguished from each
other based on their magnetic properties.

US Pat. No. 9,624,531

CASSETTE FOR SAMPLE PREPARATION

LUMINEX CORPORATION, Aus...

1. A system comprising:
a plurality of cassettes, each cassette of the plurality of cassettes comprising:
a first chamber comprising an opening configured for receiving a sample into the first chamber, and a removable lid configured
to provide access to the opening;

a second chamber;
a third chamber;
a first valve comprising a valve housing defining a first valve opening in fluid communication with the first chamber and
a second valve opening in fluid communication with the second chamber;

a second valve comprising a valve housing defining a first valve opening in fluid communication with the second chamber and
a second valve opening in fluid communication with the third chamber; and

a plurality of reagent chambers, wherein each of the plurality of reagent chambers comprises a puncturable or sealable member
defining at least a portion of a boundary between the plurality of reagent chambers and the first chamber; and

a magazine configured to receive the plurality of cassettes.
US Pat. No. 10,040,071

APPARATUS AND METHODS FOR INTEGRATED SAMPLE PREPARATION, REACTION AND DETECTION

LUMINEX CORPORATION, Aus...

1. An apparatus, comprising:(a) a heater assembly comprising a receiving block coupled to a first heating module, wherein the receiving block comprises a reaction volume, a first lumen and a second lumen; and
(b) an optics assembly coupled to the heater assembly, the optics assembly comprising:
a slide assembly comprising a slide block slidably mounted on a slide rail;
a first optical member and a second optical member;
a plurality of excitation modules and a plurality of detection modules coupled to the slide block, wherein the slide assembly is configured to sequentially move each of the plurality of excitation modules relative to the first optical member and to sequentially move each of the plurality of detection modules relative to the second optical member, wherein:
the first optical member is in optical communication with the excitation module and the reaction volume via the first lumen; and
the second optical member is in optical communication with the reaction volume and the detection module via the second lumen.

US Pat. No. 9,931,636

APPARATUS AND METHOD FOR INTEGRATED SAMPLE PREPARATION, REACTION AND DETECTION

LUMINEX CORPORATION, Aus...

1. An apparatus, comprising:a housing defining a linear flow path;
a reaction vial coupled to the housing, the reaction vial defining a reaction volume, the reaction volume in fluid communication with the linear flow path, wherein the reaction vial comprises a lyophilized substance comprising PCR reagents;
a transfer mechanism configured to transfer a sample from the reaction vial into the linear flow path when the transfer mechanism is actuated; and
a plurality of movable members movably coupled to the housing, the plurality of movable members configured to separate the linear flow path into a plurality of PCR volumes, each PCR volume from the plurality of PCR volumes being fluidically isolated from an adjacent PCR volume from the plurality of PCR volumes.

US Pat. No. 9,767,344

METHODS AND SYSTEMS FOR IMAGE DATA PROCESSING

Luminex Corporation, Aus...

1. A system, comprising:
an imaging subsystem comprising at least two light sources that emit light having different wavelength band characteristics,
and wherein the imaging subsystem is configured to image, at different wavelength bands using one or more of the light sources,
particles disposed within the imaging subsystem; and

a data processing subsystem configured to:
store data acquired for multiple images of the particles, wherein the multiple images correspond to different wavelength bands,
and wherein particular images of the multiple images include spots corresponding to the particles;

create a first composite image of the multiple images, wherein the first composite image includes first composite spots corresponding
to the particles, the first composite spots having a first amount of misalignment from the spots in the particular images;
and

modify coordinates of at least one of the multiple images such that a second composite image based on the modified coordinates
includes second composite spots having a second, smaller amount of misalignment from the spots in the multiple images.

US Pat. No. 10,011,861

CLEAVABLE HAIRPIN PRIMERS

LUMINEX CORPORATION, Aus...

1. A method for amplifying a target nucleic acid comprising:(a) contacting a sample with a first nucleic acid construct and a second nucleic acid construct, each of said first and second nucleic acid constructs comprising (i) a target-specific primer region, wherein the target-specific region comprises a target-binding dependent cleavage sequence; (ii) a first stem forming region 5? of the target-specific primer region; and (iii) a second stem forming region 3? of the target-specific primer region, wherein the second stem forming region is complementary to the first stem forming region, wherein the target-specific primer regions of said first and second nucleic acid constructs are configured as a primer pair for amplifying a target nucleic acid;
(b) hybridizing the first and second nucleic acid constructs to the target nucleic acid if present in the sample;
(c) cleaving the first and second nucleic acid constructs with a cleaving agent that recognizes the target-binding dependent cleavage sequences of the first and second nucleic acid constructs to obtain first and second extendable primers; and
(d) extending the first and second extendable primers to amplify the target nucleic acid.

US Pat. No. 10,214,767

INSTRUMENT FOR CASSETTE FOR SAMPLE PREPARATION

LUMINEX CORPORATION, Aus...

1. A method, comprising:(a) disposing a cassette in an instrument enclosure, the cassette comprising:
(i) a first chamber;
(ii) a second chamber;
(iii) a valve comprising a stationary piece and a movable piece, the movable piece defining a cavity within which magnetic particles can be disposed, the valve configured to transfer the magnetic particles between the first chamber and the second chamber while maintaining fluid isolation between the first chamber and the second chamber;
(iv) a third chamber; and
(v) a fourth chamber;
(b) actuating a first plunger disposed within the third chamber of the cassette to transfer a first reagent from the third chamber into the first chamber, wherein the first plunger comprises a first sealing element to prevent leakage of first reagent until the first plunger is moved;
(c) actuating a second plunger disposed within the fourth chamber of the cassette to transfer a second reagent from the fourth chamber into the first chamber, wherein the second plunger comprises a second sealing element to prevent leakage of second reagent until the second plunger is moved;
(d) applying a magnetic force to the valve to attract the magnetic particles into the cavity of the movable piece of the valve; and
(e) moving the movable piece of the valve relative to the stationary piece of the valve such that the magnetic particles are transferred between the first chamber and the second chamber while maintaining fluid isolation between the first chamber and the second chamber.
US Pat. No. 10,144,954

METHODS FOR GENERATING STABILIZED LYOPHILIZED MATERIALS

LUMINEX CORPORATION, Aus...

1. A method of performing PCR comprising:(a) obtaining a receptacle containing a wax-treated lyophilized pellet comprising a DNA polymerase and a sugar, wherein the wax-treated lyophilized pellet is formed by heating the lyophilized pellet to at least 50° C. in the presence of a wax, then solidifying the wax;
(b) adding an aqueous liquid comprising nucleic acids on top of the wax-treated lyophilized pellet;
(c )melting the wax and inverting the wax and the aqueous liquid in the receptacle to form a wax layer and a reaction solution layer in the receptacle; and
(d) performing at least one cycle of PCR.

US Pat. No. 10,108,844

METHODS AND SYSTEMS FOR IMAGE DATA PROCESSING

Luminex Corporation, Aus...

1. A system, comprising:an imaging subsystem configured to image, at different wavelength bands, particles disposed within the imaging subsystem, wherein the imaging comprises:
selecting a first set of one or more optical filters corresponding to a first wavelength band;
illuminating the particles through the first set of optical filters;
selecting a second set of one or more optical filters corresponding to a second wavelength band; and
illuminating the particles through the second set of optical filters; and
a data processing subsystem configured to:
store data acquired for multiple images of the particles, and wherein particular images of the multiple images include spots corresponding to the particles, wherein a first image of the particular images corresponds to the first set of optical filters, wherein a second image of the particular images corresponds to the second set of optical filters;
create a first composite image of the multiple images, wherein the first composite image includes first composite spots corresponding to the particles, the first composite spots having a first amount of misalignment from the spots in the particular images; and
modify coordinates of at least one of the multiple images such that a second composite image based on the modified coordinates includes second composite spots having a second, smaller amount of misalignment from the spots in the multiple images.

US Pat. No. 10,092,906

DIAGNOSTIC CARTRIDGES HAVING FLEXIBLE SEALS

LUMINEX CORPORATION, Aus...

1. A cartridge for processing a sample, the cartridge comprising:a base, a middle frame, a top frame, and a flexible seal wherein:
the middle frame is located on top of the base such that it is between the base and the top frame;
the flexible seal is located within the middle frame;
the top frame is located on top of the flexible seal;
the base comprises:
a sample well;
a plurality of reagent wells;
a plurality of polymerase chain reaction (PCR) wells;
a perforable seal covering and sealing the reagent wells and the PCR wells;
a hybridization chamber; and
an analysis chamber;
the middle frame comprises a sample well port configured to introduce a sample into the sample well;
a plurality of pipette tips, wherein each pipette tip is positioned in an opening in the flexible seal; and
wherein the flexible seal covers and extends over the top of more than one well and permits movement of the plurality of pipette tips such that each pipette tip can move over more than one well while in the flexible seal.
US Pat. No. 10,253,354

SYSTEMS AND METHODS FOR MULTIPLEX ANALYSIS OF PCR IN REAL TIME

LUMINEX CORPORATION, Aus...

1. A method for multiplexed detection of nucleic acid targets in a sample comprising:(a) combining in a chamber (i) a sample, (ii) a plurality of primer pairs for priming amplification of nucleic acid targets in the sample, wherein at least one primer of each primer pair comprises a label, and (iii) a first plurality of probes complementary to labeled amplification products obtained by amplification of the nucleic acid targets by the primer pairs, wherein the probes are immobilized on a plurality of encoded particles such that the identity of each probe is known from the encoded particle on which it is immobilized;
(b) performing a plurality of amplification cycles to form labeled amplification products for each of the nucleic acid targets amplified with the plurality of primer pairs;
(c) hybridizing the labeled amplification products to the probes immobilized on the encoded particles;
(d) during the plurality of amplification cycles, measuring a signal from the encoded particles and a signal from the labeled amplification products hybridized to the probes immobilized on the encoded particles, wherein the encoded particles are immobilized on a surface of the chamber, and wherein an increase in the signal from the labeled amplification products hybridized to the probes immobilized on the encoded particles during the plurality of amplification cycles indicates the presence of the target nucleic acids; and
(e) detecting the presence or absence of the nucleic acid targets in the sample based on the presence or absence of the signal from the labeled amplification products hybridized to the probes immobilized on the encoded particles.

US Pat. No. 10,240,189

SOLID SUPPORT ASSAY SYSTEMS AND METHODS UTILIZING NON-STANDARD BASES

LUMINEX CORPORATION, Aus...

1. A method for detecting the presence or absence of a target nucleic acid in a sample comprising:(a) producing an amplified target nucleic acid comprising a first non-standard base by amplifying the target nucleic acid using a reaction mixture that comprises a first primer complementary to a first strand of the target nucleic acid and a second primer complementary to a second strand of the target nucleic acid, wherein the second primer further comprises the first non-standard base and wherein the first non-standard base is not complementary with standard bases;
(b) specifically hybridizing a strand of the amplified target nucleic acid comprising the first non-standard base to a capture oligonucleotide on a solid support, thereby forming a hybridized capture oligonucleotide on the solid support;
(c) extending the hybridized capture oligonucleotide in a reaction mixture comprising a labeled nucleotide comprising a second non-standard base that is complementary to the first non-standard base of the amplified target nucleic acid, thereby forming an extended hybridized capture oligonucleotide comprising the labeled nucleotide on the solid support; and
(d) detecting the presence or absence of the target nucleic acid in the sample by determining the presence or absence of the extended hybridized capture oligonucleotide comprising the labeled nucleotide on the solid support.

US Pat. No. 10,179,899

APPARATUS AND METHODS FOR MAGNETIC MIXING

LUMINEX CORPORATION, Aus...

1. An apparatus comprising:a shaft comprising a first end and a second end and a longitudinal axis extending between the first end and the second end;
a motor coupled to the shaft, wherein the motor is configured to rotate the shaft about the longitudinal axis of the shaft;
a plurality of magnets coupled to the shaft, wherein each magnet of the plurality of magnets comprises a first end proximal to the longitudinal axis of the shaft and a second end distal to the longitudinal axis of the shaft; and
a module comprising a plurality of housings arranged along a linear axis, wherein:
each housing of the plurality of housings is configured to receive a chamber,
each magnet of the plurality of magnets is aligned with a corresponding housing of the plurality of housings;
the shaft is configured to move from a first shaft position to a second shaft position;
in the first shaft position, the second end of each magnet of the plurality of magnets is distal from the corresponding housing of the plurality of housings;
in the second shaft position, the second end of each magnet of the plurality of magnets is proximal to the corresponding housing of the plurality of housings; and
the longitudinal axis of the shaft is substantially parallel to the linear axis of the plurality of housings.