US Pat. No. 9,376,568

DYES FOR LABELLING MOLECULAR LIGANDS

Illumina Cambridge Limite...

1. A compound of formula 1-P or mesomer thereof:

wherein:
CI is a charge balancing counterion and p is an integer from 0 to 7;
n=0, 1, 2, or 3;
Xm and each incidence of X1 and X2 are independently H, unsubstituted alkyl, substituted alkyl, unsubstituted aryl, substituted aryl, arylalkyl, heteroarylalkyl,
alkyl substituted heteroatom, or aryl substituted heteroatom;

R1 is unsubstituted alkyl, unsubstituted aryl, substituted aryl, arylalkyl, or heteroarylalkyl;

each of R2, R3, R4, R5, R6, R7, R8, R9, R10, and R11 is independently H, unsubstituted alkyl, substituted alkyl, unsubstituted aryl, substituted aryl, arylalkyl, heteroarylalkyl,
or a group selected from SO3?, SO3H, COO?, COOH, halide, unsubstituted amino, substituted amino, nitro, and azido;

wherein at least one of R1 to R11 is or contains a functional group selected from SO3?, SO3H, COO?, COOH, halide, unsubstituted amino, substituted amino, nitro, and azido.

US Pat. No. 9,469,872

AMPLIFICATION METHODS TO MINIMISE SEQUENCE SPECIFIC BIAS

ILLUMINA CAMBRIDGE LIMITE...

1. A method for amplifying nucleic acid templates of different sequences comprising
(a) a first round comprising one or more cycles of amplification, wherein the cycles of amplification comprise amplifying
nucleic acid templates in an ensemble under conditions favoring copying AT rich templates over GC rich templates such that
the efficiency of amplification of AT rich templates is not reduced or inhibited relative to non-AT rich templates; and

(b) a second round comprising one or more cycles of amplification, wherein the cycles of amplification comprise amplifying
the nucleic acid templates in the ensemble under conditions favoring copying GC rich templates over AT rich templates such
that the efficiency of amplification of AT rich templates is not reduced or inhibited relative to non-AT rich templates;

wherein the nucleic acid templates are immobilized on a solid support, and
wherein steps (a) and (b) are repeated one or more times.

US Pat. No. 9,156,987

POLYMETHINE COMPOUNDS AND THEIR USE AS FLUORESCENT LABELS

Illumina Cambridge Limite...

1. A compound of formula (I) or mesomeric forms thereof:

wherein mCat+ or mAn? is an organic or inorganic positively/negatively charged counterion and m is an integer 0-3;
each of Ra1 and Ra2 is independently H, SO3?, sulfonamide, halogen, or a further ring fused to an adjacent carbon atom;

Rb is optionally substituted aryl or optionally substituted alkyl;
each of Rc1 and Rc2 is independently alkyl or substituted alkyl; and

either Rb or one of Rc1 or Rc2 contains a linking moiety for further attachment or is linked to a further molecule;

wherein one of the Ra groups is a further fused ring forming a structure of formula (II):

wherein Ra3 is H, SO3?, sulphonamide or halogen; and

Rc1 is alkyl or substituted alkyl.

US Pat. No. 9,222,131

RHODAMINE COMPOUNDS AND THEIR USE AS FLUORESCENT LABELS

Illumina Cambridge Limite...

1. A nucleotide or oligonucleotide labelled with a compound of formula (I) or a mesomer thereof:

Wherein M+/? is a common counter ion,

k is an integer of from 0 to 6,
q is an integer of from 1 to 6,
R1 is H or an alkyl, aryl or substituted alkyl or substituted aryl group,

R2 is H, alkyl or substituted alkyl group, halogen, carboxy, carboxamide, hydroxy- or alkoxy group, or R2 together with R1 or R5 is a carbon or heterosubstituted chain forming a ring,

R3 is H, alkyl or substituted alkyl group, halogen, carboxy, carboxamide, hydroxy- or alkoxy group or R3 together with R4 or R6 is a carbon or heterosubstituted chain forming a ring,

R4 is H or an alkyl, aryl or substituted alkyl or substituted aryl group,

R5 and R6 are H, alkyl or substituted alkyl group, halogen, hydroxy- or alkoxy group,

R8 is H, halogen, hydroxy- or alkoxy group, alkyl or substituted alkyl group or together with R1 is a carbon or heterosubstituted carbon chain forming a ring,

R9 is H, halogen, hydroxy- or alkoxy group, alkyl or substituted alkyl group or together with R4 is a carbon or heterosubstituted carbon chain forming a ring,

R7 is OR11 or NR11R12 where R11 and R12 are independently H, alkyl or a substituted alkyl,

R13 is OR14 or NR14R15 where R14 and R15 are independently H, alkyl or a substituted alkyl; aryl or a substituted aryl, and

R16 and R17 are independently H or an alkyl, aryl or substituted alkyl or substituted aryl group.

US Pat. No. 9,388,463

LABELLED NUCLEOTIDES

Illumina Cambridge Limite...

1. A method for controlling the incorporation of nucleotides into a polynucleotide strand, comprising the steps of:
(a) providing a nucleotide having a ribose or deoxyribose sugar moiety, wherein an enzymatically removable protecting group
is attached to the 3? or the 2? oxygen atom of the ribose or deoxyribose sugar moiety of the nucleotide;

(b) providing a first enzyme to incorporate the nucleotide into the strand, whereby the protecting group prevents incorporation
of another nucleotide into the strand, and detecting the incorporated nucleotide; and

(c) providing a second enzyme to remove the protecting group to expose a 3?-OH group on the first nucleotide, thereby allowing
incorporation of another nucleotide into the strand;

(d) repeating steps (a) to (c) at least once;thereby controlling the incorporation of nucleotides into the strand;
wherein the protecting group comprises a disulfide.
US Pat. No. 9,273,352

POLYMERASES

Illumina Cambridge Limite...

1. A polymerase having amino acid sequence SEQ ID NO:22, having a substitution mutation at position Arg743 to a nonpolar amino
acid or a substitution mutation at position Lys 705 to a nonpolar amino acid, whereby the polymerase has a reduced affinity
for DNA.
US Pat. No. 9,388,464

MODIFIED NUCLEOTIDES

Illumina Cambridge Limite...

1. A method of controlling the incorporation of a nucleotide having a ribose or deoxyribose sugar moiety, and said nucleotide
is complementary to a second nucleotide in a target single-stranded polynucleotide in a synthesis or sequencing reaction,
comprising
incorporating into the growing complementary polynucleotide said nucleotide, the incorporation of said nucleotide preventing
or blocking introduction of subsequent nucleoside or nucleotide molecules into said growing complementary polynucleotide;
wherein a protecting group is attached to the 3? or the 2? oxygen atom of the ribose or deoxyribose sugar moiety of said nucleotide;
and said nucleotide comprises a detectable label linked by a linker; and

reacting the nucleotide with a water-soluble phosphine to cleave the linker;
wherein said detectable label is a fluorophore; and
wherein said water-soluble phosphine also cleaves said protecting group.

US Pat. No. 9,267,173

METHOD FOR PAIRWISE SEQUENCING OF TARGET POLYNUCLEOTIDES

Illumina Cambridge Limite...

1. A method of pairwise sequencing, the method comprising:
(a) providing a solid support having immobilised thereon a plurality of first template polynucleotides linked to the solid
support at their 5? ends, the solid support further comprising a plurality of 5?-end immobilized amplification primers;

(b) obtaining sequence data from a first region of the first template polynucleotides;
(c) hybridizing one or more extension oligonucleotides to the amplification primers, each extension oligonucleotide comprising
a first portion complementary to an immobilized amplification primer, and a second portion whose sequence is the same sequence
as a selected region of the first template polynucleotide;

(d) performing an extension reaction to extend hybridized immobilized amplification primers to produce a population of extended
primers;

(e) de-hybridizing the extension oligonucleotides, hybridizing the selected regions of the templates to the extended primers
and further extending the extended primers to copy the first template polynucleotides to generate a plurality of second immobilised
template polynucleotides;

(f) obtaining sequence data for a second region of each of the second immobilised template polynucleotides, wherein determining
the sequences of the first and second regions of the first and second template polynucleotides achieves pairwise sequencing
of said first and second regions of said target polynucleotides.

US Pat. No. 9,085,698

DYES FOR LABELLING MOLECULAR LIGANDS

Illumina Cambridge Limite...

1. A compound of formula I or mesomers thereof:

wherein
CI is a charge balancing counterion and p is an integer from 1-7;
m is 1, 3, 5, 7, or 9;
each incidence of X is independently hydrogen, halogen, alkyl- or aryloxy, alkyl- or arylthio, amino- or substituted amino,
aryl or alkyl, any of which may be optionally substituted with a substituent selected from carboxyl, sulfonate, sulfinate,
sulfonamide, hydroxyl, amino, alkyl- or aryl- amino, dialkyl(aryl)amino, alkoxy, aryloxy, alkyl- or arylthio and halogen;
optionally, one or more X groups are combined to form a cyclic ring;

Y is independently selected from O, NRa, S, Se, CRb?CRc or CR2R3;

Z is independently selected from O, NRa, S, Se, CRb?CRc or CR4R5;

wherein Ra, Rb, Rc, R2, R3, R4, and R5 are independently selected from hydrogen, halogen, alkyl- or aryloxy, alkyl- or arylthio, amino- or substituted amino, alkyl,
aryl or substituted alkyl, or substituted aryl;

R1 is selected from aryl or alkyl, any of which may be optionally substituted with at least one substituent selected from carboxyl,
sulfonate, sulfinate, sulfonamide or substituted sulfonamide, hydroxyl, amino, alkyl(aryl)amino, dialkyl(aryl)amino, alkoxy,
halogen, succinimidyl ester, ester, and amide or substituted amide;

R6, R7, R8, R9, R10, R11, R12, R13, R14, R15, R16, R17, and R18 are independently selected from carboxyl, sulfonate, sulfinate, sulfoxide, sulfone, sulfonamide, hydroxyl, amino, alkylamino,
dialkylamino, alkoxy, halogen, alkyl succinimidyl ester, ester, amide, or any ortho-disposed pair of R6, R7, R8, R9, R10, R11, R12, R13, R14, R15, R16, R17, and R18 is combined to form a further fused aromatic or heterocyclic ring that is optionally substituted; wherein at least one of
R14, R15, R16, R17, or R18 is sulfonate or a further fused ring derived from R14, R15, R16, R17, or R18 comprises at least one sulfonate substituent; with the proviso that none of R14, R15, R16, R17, and R18 are carboxyl and wherein provided that Y is CR2R3 or Z is CR4R5.

US Pat. No. 9,079,148

USING POPULATIONS OF BEADS FOR THE FABRICATION OF ARRAYS ON SURFACES

Illumina Cambridge Limite...

1. An array comprising spatially discrete nucleic acid features on a surface, wherein each spatially discrete feature comprises
two or more different amplification primers each having a different sequence attached to the surface, and wherein each spatially
discrete feature is separated from any other discrete feature by a space which does not carry amplification primers, wherein
the array of spatially discrete features comprises an average center-to-center distance that is less than two times the diameter
of a feature.
US Pat. No. 9,328,378

METHOD OF LIBRARY PREPARATION AVOIDING THE FORMATION OF ADAPTOR DIMERS

Illumina Cambridge Limite...

1. A method for generating a library of template polynucleotide molecules from one or more primary polynucleotide molecules,
said method comprising:
(a) providing blunt end target polynucleotide duplexes; and performing a tailing reaction to attach a single nucleotide overhang
to the 3? ends of the blunt end target polynucleotide duplexes;

(b) ligating an adaptor polynucleotide construct to both ends of the target polynucleotide duplexes to generate combined ligated
adaptor-target-adaptor sequences;

(c) preparing an amplification reaction comprising said combined ligated adaptor-target-adaptor sequences and at least two
different primer oligonucleotides, wherein each of said at least two different primer oligonucleotides is complementary to
at least a part of the adaptor polynucleotide construct sequence of the combined ligated adaptor-target-adaptor sequences,
and complementary to the single nucleotide overhang attached to the target polynucleotide duplex, not extending beyond the
single nucleotide overhang, and wherein a first primer of the two primer oligonucleotides is between 21-100 nucleotides in
length and comprises a 5? sequence having the sequence of nucleotides 1-21 of SEQ ID NO: 6; and

(d) performing an amplification reaction wherein said at least two different primer oligonucleotides anneal to complementary
parts of the adaptor-target-adaptor sequences and are extended by sequential addition of nucleotides to generate a plurality
of amplification products complementary to at least one strand of the combined ligated adaptor-target-adaptor sequences, wherein
each of said plurality of amplification products has a first common sequence at its 5? end and a second common sequence at
its 3? end, and wherein said plurality of amplification products comprises a library of template polynucleotide molecules.

US Pat. No. 9,121,060

MODIFIED NUCLEOTIDES

Illumina Cambridge Limite...

1. A method of controlling the incorporation of a nucleotide having a ribose or deoxyribose sugar moiety, and said nucleotide
is complementary to a second nucleotide in a target single-stranded polynucleotide in a synthesis or sequencing reaction,
comprising incorporating into the growing complementary polynucleotide said nucleotide, the incorporation of said nucleotide
preventing or blocking introduction of subsequent nucleoside or nucleotide molecules into said growing complementary polynucleotide
and said nucleotide comprises a detectable label linked by a linker; and reacting the nucleotide with a water-soluble phosphine
to cleave the linker.

US Pat. No. 9,410,199

LABELLED NUCLEOTIDES

Illumina Cambridge Limite...

1. A method for determining the identity of a nucleotide in a target single-stranded polynucleotide, comprising:
(a) providing one or more of the nucleotides A, G, C and T or U in which each of said nucleotides has a base that is attached
to a distinct detectable label via a linker, said linker being cleavable with a water-soluble phosphine and said cleavable
linker comprising an azido group; and a nascent polynucleotide complementary to the target polynucleotide, one of said provided
nucleotides being suitable for incorporation into said nascent polynucleotide;

(b) incorporating the nucleotide suitable for incorporation into said nascent polynucleotide;
(c) detecting the detectable label of the incorporated nucleotide to identify the incorporated nucleotide; and
(d) cleaving the azido linker of the incorporated nucleotide with a water-soluble phosphine.

US Pat. No. 9,376,678

METHOD OF PREPARING LIBRARIES OF TEMPLATE POLYNUCLEOTIDES

Illumina Cambridge Limite...

1. A library of different target nucleic acids comprising a plurality of different polynucleotide duplexes having polynucleotide
adapters at each end;
wherein polynucleotide adapters are forked adapters formed by annealing of partially complementary first and second polynucleotide
strands;

wherein the first polynucleotide strand comprises the sequence set forth in SEQ ID NO: 1; and
wherein the second polynucleotide strand comprises the sequence set forth in SEQ ID NO: 2.

US Pat. No. 9,309,409

POLYMETHINE COMPOUNDS AND THEIR USE AS FLUORESCENT LABELS

Illumina Cambridge Limite...

1. A compound of formula (I) or mesomeric forms thereof:
wherein mCat+ or mAn? is an organic or inorganic positively/negatively charged counterion and
m is an integer 0-3;
n is an integer 1-5;
Rf represents OH or O?; or an ester or amine conjugate linked to a substrate moiety;

each of Ra1 and Ra2 is independently H, SO3?, sulfonamide, halogen, or a further ring fused to an adjacent carbon atom; wherein either Ra1 or Ra2 is sulphonamide or SO3?; and

each of Rc1 and Rc2 is independently alkyl or substituted alkyl;

wherein when Ra1 or Ra2 is SO3?, either i) Rc1 or Rc2 is an alkyl sulfonic acid group, or ii) Ra1 or Ra2 is a sulphonamide.

US Pat. No. 9,217,178

METHOD OF NUCLEOTIDE DETECTION

Illumina Cambridge Limite...

1. A method of inhibiting light-induced degradation of nucleic acids during a detection step of a nucleic acid sequencing
reaction comprising the steps of:
a. incorporating one or more fluorescently labelled nucleotides into a strand of nucleic acid complementary to a template
nucleic acid immobilized to a solid support;

b. irradiating said template nucleic acid in the presence of a detection buffer comprising ascorbic acid, or a salt thereof,
and determining the identity of one or more of the incorporated nucleotides;

c. removing the fluorescent label from the incorporated nucleotide(s) using a chemical treatment; and
d. washing said solid support;
wherein steps a-d are repeated at least 10 times.

US Pat. No. 9,512,478

METHODS FOR INDEXING SAMPLES AND SEQUENCING MULTIPLE POLYNUCLEOTIDE TEMPLATES

ILLUMINA CAMBRIDGE LIMITE...

1. A method for sequencing nucleic acid sequences and identifying subsets of nucleic acid sequences, each subset of nucleic
acid sequences isolated from a different source, the method comprising the steps of:
a) providing at least two different samples comprising nucleic acid target sequences and amplifying the target sequences with
two or more sample specific amplification primers to generate amplified adaptor-target-adaptors, wherein one of said amplification
primers comprises a sample specific tag sequence, and wherein said sample specific tag sequence differentiates amplified adaptor-target-adaptors
originating from different samples;

b) pooling the amplified adaptor-target-adaptors of the at least two different samples;
c) immobilizing the pooled adaptor-target-adaptors on a surface;
d) sequencing the immobilized adaptor-target-adaptors on the surface to determine a sequence read of each immobilized adaptor-target-adaptor
by hybridizing a first sequencing primer to the immobilized adaptor-target-adaptors, performing a first sequencing read and
removing the first sequencing primer;

e) sequencing the sample specific tag sequence of each immobilized adaptor-target-adaptor by hybridizing a second sequencing
primer to the immobilized adaptor-target-adaptors and performing a second sequencing read, wherein steps d) and e) determine
nucleic acid sequences of the immobilized adaptor-target-adaptors and identify each of the immobilized adaptor-target-adaptors
as a member of a subset of nucleic acid sequences.

US Pat. No. 9,441,272

COMPOSITIONS AND METHODS FOR SEQUENCING NUCLEIC ACIDS

ILLUMINA CAMBRIDGE LIMITE...

1. A nucleic acid sequencing method comprising:
providing a substrate having a surface, said surface comprising a site having a plurality of primers attached thereto;
contacting said plurality of primers with a plurality of template nucleic acids;
extending the primers in the presence of a first modified nucleotide such that said first modified nucleotide is incorporated
in a plurality of extended strands;

synthesizing complements of the extended strands using a polymerase that incorporates a second modified nucleotide complementary
to said first modified nucleotide; and

initiating a sequencing read from the point of incorporation of said first modified nucleotide, thereby producing nucleic
acid sequence information.

US Pat. No. 9,410,200

LABELLED NUCLEOTIDES

Illumina Cambridge Limite...

1. A method of labeling a nucleic acid molecule, the method comprising:
incorporating into the nucleic acid molecule a nucleotide molecule using a polymerase, wherein the nucleotide molecule has
a base that is linked to a fluorophore via a cleavable linker and the nucleotide molecule has a deoxyribose sugar moiety,

wherein the deoxyribose sugar moiety comprises a protecting group attached via the 3? oxygen atom, and said protecting group
can be modified or removed to expose a 3? OH group, the protecting group comprising an azido group.

US Pat. No. 9,297,043

METHOD FOR SEQUENCING A POLYNUCLEOTIDE TEMPLATE

Illumina Cambridge Limite...

1. A method for pairwise sequencing of first and second strands of target polynucleotides, wherein the first and second strands
of each target polynucleotide have complementary sequences to each other, the method comprising:
(a) forming a plurality of nucleic acid colonies by solid phase nucleic acid amplification on a solid support, wherein each
of the nucleic acid colonies comprises multiple copies of a first strand and a complementary second strand formed by amplification
of a single originating target polynucleotide;

(b) forming a single-stranded region in first strands of the colonies and hybridizing first sequencing primers to the single-stranded
region;

(c) carrying out a first sequencing reaction by sequential addition of nucleotides to the first sequencing primers to determine
sequences from the first strands; whereby after said sequencing reaction, the colonies comprise a plurality of intact duplexes
on the solid support, the intact duplexes comprising a portion of the multiple copies of the first strand and a complementary
second strand;

(d) cleaving the first strands;
(e) removing at least a portion of the first strands from the colonies, whereby a single-stranded region is formed in each
of the complementary second strands;

(f) carrying out a second sequencing reaction by sequential addition of nucleotides to determine sequences from the complementary
second strands, wherein the first sequencing reaction and the second sequencing reaction permit pairwise sequencing of the
target polynucleotides.

US Pat. No. 9,121,062

LABELLED NUCLEOTIDES

Illumina Cambridge Limite...

1. A nucleoside or nucleotide comprising a base attached to a detectable label via a cleavable linker, wherein the cleavable
linker comprises a disulfide group and further comprises an azido group, and wherein the nucleoside or nucleotide further
comprises a ribose or deoxyribose moiety which comprises a hydroxyl protecting group attached to the 2? or 3? oxygen atom,
and wherein the base is connected to the cleavable linker via a propargylamido or propargylamido moiety.
US Pat. No. 9,447,389

MODIFIED POLYMERASES FOR IMPROVED INCORPORATION OF NUCLEOTIDE ANALOGUES

Illumina Cambridge Limite...

1. An altered Vent DNA polymerase, wherein the second amino acid of the motif A region is mutated to alanine (A); and the
third amino acid of the motif A region is mutated to an amino acid selected from the group consisting of serine (S), alanine
(A), glycine (G), and the amino acids having beta-branched side chains, whereby the altered Vent DNA polymerase is capable
of incorporating a 3? O-azidomethyl-modified nucleotide.
US Pat. No. 9,085,802

PREPARATION OF TEMPLATES FOR NUCLEIC ACID SEQUENCING

Illumina Cambridge Limite...

1. A method of preparing single-stranded templates for a nucleic acid sequencing reaction comprising,
(i) providing a solid support comprising a plurality amplification primers, wherein a subset of said plurality of amplification
primers comprises a cleavage site;

(ii) amplifying a template using the subset of primers on the support to produce a plurality of double-stranded nucleic acid
molecules, wherein both strands of each double-stranded nucleic acid molecule are attached to the solid support at their 5?
ends, whereby the cleavage site is positioned in a double-stranded region of each double-stranded molecule;

(iii) cleaving only one strand of the double stranded molecules at the cleavage site, the cleavage not comprising cleavage
with a restriction endonuclease or a nicking endonuclease;

(iv) subjecting the cleaved strand to denaturing conditions to remove the portion of the cleaved strand not attached to the
solid support, followed by re-annealing the cleaved strand to the opposite strand, thereby generating immobilized partially
or substantially single-stranded templates; and

(v) hybridizing a sequencing primer to the immobilized partially or substantially single-stranded templates, thereby preparing
single-stranded templates for a nucleic acid sequencing reaction.

US Pat. No. 9,303,290

METHOD OF NUCLEOTIDE DETECTION

Illumina Cambridge Limite...

1. A method of sequencing at least two nucleotides of a template nucleic acid comprising repeating the steps of:
a) incorporating one or more fluorescently labelled nucleotides into a strand of nucleic acid complementary to said template
nucleic acid; and

b) determining the identity of one or more of the incorporated nucleotide(s) wherein the steps of determining the identity
of the incorporated nucleotide(s) is carried out in a buffer which comprises ascorbic acid, or a salt thereof;

wherein at least 10 nucleotides are incorporated and the identity of the base present in each of the incorporated nucleotides
is determined.

US Pat. No. 9,498,763

PREPARATION OF TEMPLATES FOR NUCLEIC ACID SEQUENCING

Illumina Cambridge Limite...

1. A method of preparing single-stranded templates for a nucleic acid sequencing reaction comprising,
(i) providing a solid support comprising a plurality of amplification primers, wherein a subset of said plurality of amplification
primers comprises a cleavage site;

(ii) amplifying a template using subset of the primers on the support to produce a plurality of double-stranded nucleic acid
molecules, wherein both strands of each double-stranded nucleic acid molecule are attached to the solid support at their 5?
ends, whereby the cleavage site is positioned in a double-stranded region of each double-stranded molecule;

(iii) cleaving only one strand of the double stranded molecules at the cleavage site;
(iv) subjecting the cleaved strand to denaturing conditions to remove the portion of the cleaved strand not attached to the
solid support, followed by re-annealing the cleaved strand to the opposite strand, thereby generating immobilized partially
or substantially single-stranded templates; and

(v) hybridizing a sequencing primer to the immobilized partially or substantially single-stranded templates, thereby preparing
single-stranded templates for a nucleic acid sequencing reaction.

US Pat. No. 9,593,373

MODIFIED NUCLEOSIDES OR NUCLEOTIDES

Illumina Cambridge Limite...

1. A modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety
having a removable 3?-hydroxy protecting group forming a structure —O—C(R)2N3 covalently attached to the 3?-carbon atom, wherein
R is independently selected from the group consisting of hydrogen, —C(R1)m(R2)n, —C(?O)OR3, —C(?O)NR4R5, —C(R6)2O(CH2)pNR7R8 and —C(R9)2O-Ph-C(?O)NR10R11;

R1 is selected from hydrogen, or optionally substituted alkyl;

R2 is halogen;

R3 is selected from hydrogen or optionally substituted alkyl;

each R4 and R5 is independently selected from hydrogen, optionally substituted alkyl, optionally substituted aryl, optionally substituted
heteroaryl, or optionally substituted aralkyl;

each R6 and R9 is selected from hydrogen, optionally substituted alkyl or halogen;

each R7, R8, R10 and R11 is independently selected from hydrogen, optionally substituted alkyl, optionally substituted aryl, optionally substituted
heteroaryl, or optionally substituted aralkyl;

m is an integer of 0 to 3;
n is an integer of 0 to 3; provided that the total of m+n equals to 3; and
p is an integer of 0 to 6; provided that
at least one R is not hydrogen.

US Pat. No. 9,637,786

METHOD FOR SEQUENCING A POLYNUCLEOTIDE TEMPLATE

Illumina Cambridge Limite...

1. A method for pairwise sequencing of first and second regions of a target double-stranded polynucleotide, wherein said first
and second regions are in complementary strands of the target polynucleotide, the method comprising:
(a) providing a solid support having immobilised thereon a plurality of template polynucleotide duplexes each comprising the
double-stranded target polynucleotide, wherein each template duplex is formed from complementary first and second template
strands linked to the solid support at their 5? ends;

(b) cleaving the second template strands of a sub-fraction of the template polynucleotide duplexes to remove all or a portion
of said second template strands, thereby generating single-stranded regions on the complementary first template strands;

(c) hybridising first sequencing primers to the single-stranded regions of the first template strands generated in part (b);
(d) carrying out a first sequencing reaction by sequential addition of nucleotides to the first sequencing primer to determine
the sequence of a first region of the target polynucleotide in the first template strand;

(e) cleaving the first template strands of substantially all intact template polynucleotide duplexes not cleaved in part (b)
to remove all or a portion of said first template strands, thereby generating single-stranded regions on the second template
strands that were not cleaved in part (b);

(f) hybridising a second sequencing primer to the single stranded regions of the second template strands generated in part
(e); and

(g) carrying out a second sequencing reaction by sequential addition of nucleotides to second sequencing primer to determine
the sequence of a second region of the target polynucleotide in the second template strand.

US Pat. No. 9,127,314

LABELLED NUCLEOTIDES

Illumina Cambridge Limite...

1. A method for determining the identity of a nucleotide in a target single-stranded polynucleotide, comprising:
(a) providing one or more of the nucleotides A, G, C and T or U in which each of said nucleotides has a base that is attached
to a distinct detectable label via a linker, said linker being cleavable with a water-soluble phosphine and said cleavable
linker comprising a disulfide; and a nascent polynucleotide complementary to the target polynucleotide, one of said provided
nucleotides being suitable for incorporation into said nascent polynucleotide;

(b) incorporating the nucleotide suitable for incorporation into said nascent polynucleotide;
(c) detecting the detectable label of the incorporated nucleotide to identify the incorporated nucleotide; and
(d) cleaving the disulfide linker of the incorporated nucleotide with a water-soluble phosphine.
US Pat. No. 9,605,310

LABELLED NUCLEOTIDES

Illumina Cambridge Limite...

1. A method for determining the sequence of a target single-stranded polynucleotide, comprising monitoring the sequential
incorporation of complementary nucleotides,
wherein the nucleotides each have a base that is linked to a detectable label vial a cleavable linker comprising an azido
group, wherein each of the nucleotides has a ribose or deoxyribose sugar moiety and the ribose or deoxyribose sugar moiety
comprises an azido protecting group attached via the 2? or 3? oxygen atom, and

wherein the identity of each nucleotide incorporated is determined by detection of the label linked to the base, and subsequent
removal of the label and the protecting group under a single set of conditions.

US Pat. No. 9,902,994

METHOD FOR RETAINING EVEN COVERAGE OF SHORT INSERT LIBRARIES

ILLUMINA CAMBRIDGE LIMITE...

1. A method of solid-phase nucleic acid amplification of template polynucleotide molecules, the method comprising:
(a) preparing a library of template polynucleotide molecules with common sequences as their 5? ends and common sequences at
their 3? ends by:

(1) providing a plurality of target polynucleotide duplex fragments having a distribution of sequences, and having an average
fragment length of less than 150 base pairs;

(2) treating the plurality of target polynucleotide duplex fragments to phosphorylate the 5? ends of each of the plurality
of target polynucleotide duplex fragments and to incorporate a single nucleotide overhang at each of the 3? ends of each of
the plurality of short target polynucleotide duplex fragments, wherein the treating produces a plurality of modified target
polynucleotide duplex fragments,

wherein all steps in step (2) are performed at a temperature of less than 65° C.; and
(3) ligating adaptor polynucleotides to both ends of each of the plurality of modified target polynucleotide duplex fragments
to produce a library of template polynucleotide molecules;

wherein the distribution of sequences in the library of template polynucleotide molecules is essentially equal to the distribution
of sequences of the short target polynucleotide duplex fragments; and

(b) amplifying by solid-phase amplification reaction the template polynucleotide molecules.
US Pat. No. 10,006,081

END MODIFICATION TO PREVENT OVER-REPRESENTATION OF FRAGMENTS

ILLUMINA CAMBRIDGE LIMITE...

1. A method of reducing representation of the ends of a primary polynucleotide sequence in a library of fragments generated from said primary polynucleotide sequence, the method comprising:a) performing an amplification reaction with one or more modified amplification primers, said modified amplification primers comprising a modification configured to prevent fragments originating from the ends of the primary polynucleotide from ligating to an adapter, thereby forming a modified primary polynucleotide sequence;
b) fragmenting the modified primary polynucleotide sequence such that the 5? terminal fragment and the 3? terminal fragment each comprise the modification and the internal fragments do not comprise the modification;
c) ligating an adapter to the internal fragments generated in step b), thereby forming a library of ligated internal fragments generated from said primary polynucleotide sequence; and
d) optionally purifying the ligated internal fragments by removing the unligated terminal fragments.

US Pat. No. 9,944,924

POLYNUCLEOTIDE MODIFICATION ON SOLID SUPPORT

ILLUMINA, INC., San Dieg...

1. A method of performing size selection of a template library comprising:a. contacting a plurality of template polynucleotides with immobilized capture primers under conditions sufficient for hybridization to produce a plurality of hybridized template polynucleotides, wherein the plurality of template polynucleotides comprises template polynucleotides having different sizes;
b. extending immobilized capture primers that are hybridized to a template polynucleotide to produce double-stranded immobilized templates; and
c. subjecting the double-stranded immobilized templates to selectively denaturing conditions, whereby a first subset of the immobilized double-stranded templates is selectively denatured to become single-stranded, and a second subset of the immobilized double-stranded templates is not denatured, thereby providing a first subset of single-stranded, extended immobilized capture primers and the second subset of immobilized double-stranded templates.
US Pat. No. 9,977,861

METHODS AND SYSTEMS FOR DETERMINING HAPLOTYPES AND PHASING OF HAPLOTYPES

Illumina Cambridge Limite...

1. A method for determining the sequence of a nucleic acid sample comprising:a) providing a first plurality of nucleic acid fragments having a first length,
wherein said plurality comprises parental chromosome fragments of maternally and paternally inherited chromosomes from a diploid, triploid or polyploid organism,
wherein individual fragments in said first plurality comprise naturally occurring polymorphisms that form a haplotype and a plurality of synthetic polymorphisms, the plurality of synthetic polymorphisms forming different patterns on individual fragments of maternally inherited chromosomes relative to corresponding paternally inherited chromosomes and to other corresponding fragments of the maternally inherited chromosomes, such that individual fragments from an individual maternally inherited chromosome having an individual pattern of the different patterns are distinguishable from individual fragments of a corresponding individual paternally inherited chromosome and from the other corresponding fragments of the maternally inherited chromosomes that do not have the individual pattern and wherein the plurality of synthetic polymorphisms forming the different patterns are formed by modifying the nucleic acids by partial and incomplete bisulfate conversion of cytosines in the plurality of nucleic acid fragments;
b) preparing a nucleic acid library from said first plurality of nucleic acid fragments, wherein said nucleic acid library comprises a second plurality of nucleic acid fragments of a second length less than that of said first length,
wherein naturally occurring polymorphisms of a haplotype are separated on different nucleic acid fragments of said second plurality,
wherein each of said nucleic acid fragments of said second plurality has a first pattern of said plurality of synthetic polymorphisms that is the same as a second pattern of said plurality of synthetic polymorphisms present in another nucleic acid fragment of said second plurality of nucleic acid fragments, wherein the first pattern and the second pattern are from only one of the individual maternally inherited chromosome or the corresponding individual paternally inherited chromosome and the different patterns comprise the first pattern and the second pattern,
c) sequencing nucleic acid fragments of said nucleic acid library,
d) aligning the plurality of synthetic polymorphisms among the nucleic acid fragments that are sequenced using said first pattern and said second pattern to determine the sequence of the nucleic acid sample, wherein said sequence comprises said naturally occurring polymorphisms of said haplotype, and
(e) determining that the sequence includes the naturally occurring polymorphisms of said haplotype on one of the individual maternally inherited chromosome or the corresponding individual paternally inherited chromosome.

US Pat. No. 9,929,746

METHODS AND SYSTEMS FOR DATA ANALYSIS AND COMPRESSION

Illumina Cambridge Limite...

1. A nucleic acid sequencing system for compressing sequencing data, comprising:a) a processor; and
b) a memory coupled with the processor and having instructions that when executed by the processor perform a method comprising:
i) receiving a collection of data strings corresponding to a first set of nucleotide data for a first nucleic acid fragment being sequenced in the system;
ii) identifying a first character representing a first nucleotide in each of the data strings in the collection;
iii) generating a first Burrows Wheeler transform index for a compressed data string containing the first characters corresponding to a first nucleotide of each data string;
iv) identifying an additional character representing an additional nucleotide in each of the data strings; and
v) updating the first Burrows Wheeler transform index with the additional characters corresponding to each additional nucleotide of the received collection of data strings to form compressed sequencing data.
US Pat. No. 9,902,951

METHOD OF NUCLEIC ACID AMPLIFICATION

Illumina, Inc., San Dieg...

1. A process that can be used to identify in a nucleic acid sample the presence or absence of nucleic acid sequence differences,
wherein each said difference is with respect to one or more reference sequences, the process comprising:
a) fragmenting nucleic acids in said sample;
b) linking adapter sequences to the nucleic acid fragments generated in step a);
c) binding said nucleic acid fragments to a solid support to form bound nucleic acid fragments, and amplifying said bound
nucleic acid fragments; and

d) identifying nucleic acid sequences within said amplified nucleic acid fragments.
US Pat. No. 9,828,627

REDUCING DNA DAMAGE DURING SAMPLE PREPARATION AND SEQUENCING USING SIDEROPHORE CHELATORS

Illumina Cambridge Limite...

1. A composition for nucleic acid preparation comprising:
a reagent for nucleic acid preparation comprising a siderophore and a buffer, wherein the siderophore is present in the reagent
at a concentration of 0.01 mM to 1 mM;

a plurality of oligonucleotides covalently bound to a solid support;
a plurality of nucleic acid molecules from a sample, wherein the plurality of nucleic acid molecules are hybridized to the
plurality of oligonucleotides covalently bound to the solid support; and

an isolated enzyme selected from the group consisting of a DNA polymerase and a ligase;
wherein the composition does not contain EDTA, EGTA or DTPA.

US Pat. No. 9,738,786

DYES FOR LABELLING MOLECULAR LIGANDS

Illumina Cambridge Limite...

1. A compound or a mesomer thereof, wherein the compound is:

US Pat. No. 9,758,825

CENTROID MARKERS FOR IMAGE ANALYSIS OF HIGH DENSITY CLUSTERS IN COMPLEX POLYNUCLEOTIDE SEQUENCING

ILLUMINA CAMBRIDGE LIMITE...

1. A solid support comprising a plurality of fiducial markings, the markings comprising a ring of fluorescently labeled nucleic
acids surrounding a center region lacking fluorescently labeled nucleic acids.

US Pat. No. 9,683,230

SAMPLE PREPARATION ON A SOLID SUPPORT

Illumina Cambridge Limite...

1. A method of preparing an immobilized library of tagged DNA fragments comprising:
(a) providing a solid support having transposome complexes immobilized thereon, wherein said transposome complexes comprise
a transposase bound to a first polynucleotide, said first polynucleotide comprising

(i) a 3? portion comprising a transposon end sequence, and
(ii) a first tag comprising a first tag domain;
(b) providing a sample comprising target DNA, proteins and other cellular components from an in vivo source;
(c) applying said sample to the solid support under conditions wherein said target DNA, proteins and other cellular components
are present at the same proportion as in said in vivo source, whereby the target DNA is fragmented by the transposome complexes,
and the 3? transposon end sequence of the first polynucleotide is transferred to a 5? end of at least one strand of the fragments;
thereby producing an immobilized library of double-stranded fragments wherein at least one strand is 5?-tagged with the first
tag.

US Pat. No. 9,982,244

RECOMBINASE MUTANTS

ILLUMINA CAMBRIDGE LIMITE...

1. A UvsX recombinase polypeptide comprising an amino acid sequence that is at least 90% identical to SEQ ID NO: 1, which UvsX recombinase polypeptide comprises an amino acid substitution mutation at the position functionally equivalent to position 256 in the Enterobacteria phage RB49 UvsX of SEQ ID NO: 1, said UvsX recombinase polypeptide having increased recombinase activity compared to a T4 UvsX recombinase polypeptide having SEQ ID NO: 8 or a RB49 UvsX recombinase polypeptide having all of the amino acid sequence of SEQ ID NO:1 except for a His to Ser substitution at amino acid position 63 of SEQ ID NO: 1.
US Pat. No. 9,889,422

METHODS OF LOCALIZING NUCLEIC ACIDS TO ARRAYS

ILLUMINA CAMBRIDGE LIMITE...

1. A population of polynucleotides comprising template nucleic acids having a first end capable of hybridizing to SEQ ID NO:
3, a second end capable of hybridizing to SEQ ID NO: 5 and a remainder polynucleotide disposed between the first end and the
second end, wherein the template nucleic acids are different from each other.

US Pat. No. 10,125,390

LABELLED NUCLEOTIDES

Illumina Cambridge Limite...

1. A nucleotide or nucleoside molecule having a ribose or deoxyribose sugar moiety and a base linked to a detectable label via a cleavable linker, wherein the sugar moiety comprises a protecting group attached via a 3? oxygen atom, and wherein said protecting group comprises an azido group that can be modified or removed to expose a 3? OH group.
US Pat. No. 9,970,055

METHOD OF NUCLEOTIDE DETECTION

ILLUMINA CAMBRIDGE LIMITE...

1. A kit for sequencing a nucleic acid template, the kit comprising:a plurality of fluorescently labelled nucleotides;
an enzyme capable of catalyzing incorporation of the fluorescently labelled nucleotides into a nucleic acid strand complementary to the nucleic acid template to be sequenced; and
a buffer comprising ascorbic acid or a salt thereof, or a supply of ascorbic acid or a salt thereof suitable for preparing the buffer.

US Pat. No. 9,815,916

POLYMERS AND DNA COPOLYMER COATINGS

ILLUMINA CAMBRIDGE LIMITE...

1. A polymer for surface functionalization, comprising a recurring unit of Formula (I) and a recurring unit of Formula (II):

wherein:
each R1a, R2a, R1b and R2b is independently selected from the group consisting of hydrogen, optionally substituted alkyl, and optionally substituted
phenyl;

each R3a and R3b is independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted phenyl,
and optionally substituted C7-14 aralkyl; and

each L1 and L2 is independently selected from the group consisting of an optionally substituted alkylene linker and an optionally substituted
heteroalkylene linker.

US Pat. No. 9,765,391

METHODS FOR SEQUENCING A POLYNUCLEOTIDE TEMPLATE

ILLUMINA CAMBRIDGE LIMITE...

1. A method for sequencing a first region and a second region of a polynucleotide template, the method comprising:
(a) providing a polynucleotide template immobilized on a surface, said polynucleotide template comprising
a single polynucleotide strand having a first region and a second region, said first region and said second region separated
by at least 50 nucleotides, and

a self-complementary hairpin polynucleotide linker comprising a loop region and a stem region, wherein the 5? end of one strand
of the stem region is linked to the 3? end of said polynucleotide strand and the 3? end of the other strand of the stem region
comprises a first free 3?-hydroxyl group used for initiating sequencing of the first region of the polynucleotide strand,

(b) performing a first sequencing-by-synthesis reaction comprising sequential incorporation of different complementary reversibly-terminated
nucleotides into the 3? end of said polynucleotide template, thereby determining the sequence of the first region of the polynucleotide
strand, wherein each of said nucleotides comprises a fluorescent label and a 3? blocking group, the blocking group prevents
any further nucleotide incorporation into the 3? end of said polynucleotide template, and wherein said sequential incorporation
comprises

(i) incorporating one of said nucleotides into the first free 3?-hydroxyl group and detecting a fluorescent signal generated
from the fluorescent label using a CCD camera or other fluorescence detection means, and

(ii) cleaving the fluorescent label and the 3? blocking group from said one of said nucleotides in the 3? end of said polynucleotide
template, thereby yielding a free 3?-hydroxyl group before another of said nucleotides is incorporated into the 3? end of
the polynucleotide template,

(c) adding an unlabeled nucleotide to the free 3?-hydroxyl group in the last nucleotide added in step (b) and performing an
extension reaction in the presence of different unlabeled nucleotides, thereby generating an extension product having a second
free 3? hydroxyl group used for initiating sequencing of the second region of the polynucleotide strand, and

(d) performing a second sequencing-by-synthesis reaction comprising sequential incorporation of different complementary reversibly-terminated
nucleotides into the 3? end of the extension product generated in step (c), thereby determining the sequence of the second
region of the polynucleotide strand, wherein each of said nucleotides comprises a fluorescent label and a 3? blocking group,
the blocking group prevents any further nucleotide incorporation into the 3? end of said polynucleotide template, and wherein
said sequential incorporation after step (c) comprises

i) incorporating one of said nucleotides into the second free 3?-hydroxyl group and detecting a fluorescent signal generated
from the fluorescent label using a CCD camera or other fluorescence detection means, and

(ii) cleaving the fluorescent label and the 3? blocking group from said one of said nucleotides in the 3? end of said extension
product, thereby yielding a free 3? hydroxyl group before another of said nucleotides is incorporated into the 3? end of said
extension product;

wherein said polynucleotide strand ranges in length from 100 nucleotides to 1 kb.
US Pat. No. 9,999,866

PREPARATION OF TEMPLATES FOR NUCLEIC ACID SEQUENCING

ILLUMINA CAMBRIDGE LIMITE...

1. A method of preparing single-stranded templates for a nucleic acid sequencing reaction comprising,(i) providing a solid support comprising a plurality of amplification primers, wherein a subset of said plurality of amplification primers comprises a cleavage site;
(ii) amplifying a template using the subset of the amplification primers on the solid support to produce a plurality of double-stranded nucleic acid molecules, wherein both strands of each double-stranded nucleic acid molecule are attached to the solid support at their 5? ends, whereby the cleavage site is positioned in a double-stranded region of each double-stranded molecule;
(iii) cleaving only one strand of the double stranded molecules at the cleavage site;
(iv) subjecting the cleaved strand to denaturing conditions to remove the portion of the cleaved strand not attached to the solid support, thereby generating immobilized partially or substantially single-stranded templates; and
(v) hybridizing a sequencing primer to the immobilized partially or substantially single-stranded templates, thereby preparing single-stranded templates for a nucleic acid sequencing reaction.

US Pat. No. 9,994,896

METHOD FOR SEQUENCING A POLYNUCELOTIDE TEMPLATE

ILLUMINA CAMBRIDGE LIMITE...

1. A method for sequencing, the method comprising:(a) amplifying a template to generate a single-stranded polynucleotide, wherein the single-stranded polynucleotide comprises:
a first region of known sequence;
a first template region;
a second region of known sequence, wherein the first template region is between the first region of known sequence and the second region of known sequence;
a second template region; and
a third region of known sequence, wherein the second template region is between the second region of known sequence and the third region of known sequence;
(b) disposing the single-stranded polynucleotide on a planar support to generate a single-stranded polynucleotide immobilized on the planar support, wherein the single-stranded polynucleotide forms part of a colony comprising identical copies of the single-stranded polynucleotide, the solid support comprising an array of colonies located at discrete sites on the solid support;
(c) hybridizing a first primer to the first region of known sequence in the single-stranded polynucleotide immobilized on the planar support;
(d) extending the first primer to form a first extended primer hybridized to the single-stranded polynucleotide, wherein the first extended primer comprises a fluorescent label;
(e) detecting fluorescence emitted from the fluorescent label in the first extended primer while the first extended primer is hybridized to the single-stranded polynucleotide immobilized on the planar support;
(f) denaturing the first extended primer from the single-stranded polynucleotide;
(g) hybridizing a second primer to the second region of known sequence in the single-stranded polynucleotide immobilized on the planar support, wherein the second primer is hybridized to the single-stranded polynucleotide after denaturing the first extended primer from the single-stranded polynucleotide;
(h) extending the second primer to form a second extended primer hybridized to the single-stranded polynucleotide immobilized on the planar support, wherein the second extended primer comprises a fluorescent label; and
(i) detecting fluorescence emitted from the fluorescent label in the second extended primer while the second extended primer is hybridized to the single-stranded polynucleotide.
US Pat. No. 9,976,174

METHODS, CARRIER ASSEMBLIES, AND SYSTEMS FOR IMAGING SAMPLES FOR BIOLOGICAL OR CHEMICAL ANALYSIS

ILLUMINA CAMBRIDGE LIMITE...

1. A method comprising:positioning a first carrier assembly on a system stage, the first carrier assembly including a support frame having an inner frame edge that defines a window of the support frame, the first carrier assembly including a removable first substrate that is positioned within the window and surrounded by the inner frame edge, the first substrate having a sample thereon that is positioned within an imaging zone of an optical system;
detecting optical signals from the sample of the first substrate using the optical system in accordance with a first imaging protocol;
replacing the first carrier assembly with a second carrier assembly on the system stage, the second carrier assembly having a removable second substrate, the second substrate having a sample thereon that is positioned within the imaging zone of the optical system, wherein the first and second substrates are different types of substrates; and
detecting optical signals from the sample of the second substrate using the optical system in accordance with a second imaging protocol that is different from the first imaging protocol,
wherein each of the first and second carrier assemblies includes apertures that extend into the respective carrier assembly, the apertures receiving corresponding datums when the respective carrier assembly is positioned on the system stage, wherein the first substrate engages the datums and the second substrate does not engage the datums.
US Pat. No. 10,059,928

POLYMERASES

ILLUMINA CAMBRIDGE LIMITE...

1. An altered family B polymerase having a reduced affinity for DNA, wherein the polymerase comprises at least two substitution mutations selected from the positions functionally equivalent to Lys705, Arg713, and Arg743 of the 9° N DNA polymerase amino acid sequence of SEQ ID NO:22.

US Pat. No. 9,982,250

REVERSIBLE SURFACE FUNCTIONALIZATION

Illumina Cambridge Limite...

1. A method for reversibly immobilizing a biological molecule to a surface of a substrate, comprising:providing a biological molecule covalently bonded to a host molecule, said host molecule comprises a hydrophilic portion and a hydrophobic portion, wherein the biological molecule comprises a primer oligonucleotide and wherein said host molecule comprises an optionally substituted cyclodextrin or a derivative thereof;
providing a substrate having a surface comprising functionalized silane covalently attached thereto, wherein the functionalized silane comprises a guest moiety that can form a host-guest complex with the host molecule;
contacting the biological molecule with the functionalized silane such that the biological molecule is immobilized to the surface through the host-guest reversible interaction between the functionalized silane and the host molecule; and
generating a clustered array of polynucleotides from the primer oligonucleotide.

US Pat. No. 10,138,514

MODIFIED NUCLEOSIDES OR NUCLEOTIDES

Illumina Cambridge Limite...

1. A modified nucleotide or nucleoside molecule comprising a ribose or deoxyribose sugar moiety having a removable 3?-hydroxy protecting group forming a structure —O—CH(R)N3 covalently attached to the 3?-carbon atom, whereinR is selected from the group consisting of —C(R1)m(R2)n, —C(?O)OR3, —C(?O)NR4R5, —C(R6)2O(CH2)pNR7R8 and —C(R9)2O-Ph-C(?O)NR10R11;
R1 is hydrogen, or optionally substituted alkyl;
R2 is halogen;
R3 is hydrogen or optionally substituted alkyl;
each of R4 and R5 is independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted aralkyl;
each of R6 and R9 is selected from the group consisting of hydrogen, optionally substituted alkyl and halogen;
each of R7, R8, R10 and R11 is independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted aralkyl;
m is an integer of 1 or 2;
n is an integer of 1 or 2; provided that m+n is equal to 3; and
p is an integer of 0 to 6.

US Pat. No. 10,041,066

SAMPLE PREPARATION ON A SOLID SUPPORT

ILLUMINA CAMBRIDGE LIMITE...

1. A solid support having transposome complexes immobilized thereon, wherein said transposome complexes comprise a transposase bound to a first polynucleotide, wherein the first polynucleotide comprises:(i) a 3? portion comprising a transposon end sequence, and
(ii) a first tag comprising a first tag domain,
wherein the transposome complexes are homodimers, the homodimers comprising a first plurality of homodimers comprising a first polynucleotide of a first sequence and a second plurality of homodimers comprising a first polynucleotide of a second sequence.
US Pat. No. 9,868,982

PREPARATION OF TEMPLATES FOR METHYLATION ANALYSIS

ILLUMINA CAMBRIDGE LIMITE...

1. A method of genome-wide analysis of the methylation status of cytosine bases in a whole genome sample, comprising:
a. providing a whole genome sample and fragmenting the whole genome sample to produce fragmented double stranded nucleic acid
target fragments, wherein the fragments are obtained from said whole genome, and wherein the fragments span across said whole
genome;

b. ligating forked universal adaptors to the fragmented double stranded nucleic acid target fragments to produce adaptor-ligated
double stranded nucleic acid target fragments comprising identical nucleic acid bases at each termini, wherein after said
ligation step, said adaptor-ligated double stranded nucleic acid target fragments comprise a region of double stranded nucleic
acids and at least one region of single stranded nucleic acids and wherein all cytosine bases in said forked universal adaptors
are methylated, and wherein said forked universal adaptors are phosphorylated at the 5? end and said at least one region of
single stranded nucleic acids is capable of hybridizing to SEQ ID NO: 6;

c. treating the adaptor-ligated double stranded nucleic acid target fragments with bisulfite to convert non-methylated cytosine
bases to uracil thereby producing treated adaptor-ligated double stranded nucleic acid target fragments;

d. optionally performing an amplification step to produce amplicons of the treated adapter-ligated double stranded nucleic
acid target fragments;

e. attaching the treated adaptor-ligated double stranded nucleic acid fragments or the amplicons thereof to a solid support;
f. sequencing the treated adaptor-ligated double stranded nucleic acid target fragments or the amplicons thereof to generate
sequences; and

g. analyzing the sequences of step to determine which cytosine bases were converted to uracil bases, thereby determining the
methylation status of the whole genome sample.

US Pat. No. 10,144,754

LABELLED NUCLEOTIDES

Illumina Cambridge Limite...

1. A nucleoside or nucleotide comprising a base attached to a detectable label via a phosphine-cleavable linker comprising a disulfide, wherein the nucleoside or nucleotide comprises a ribose or deoxyribose moiety with a hydroxyl protecting group attached to the 2? or 3? oxygen atom, and wherein the protecting group is azidomethyl.
US Pat. No. 10,017,750

MODIFIED POLYMERASES FOR IMPROVED INCORPORATION OF NUCLEOTIDE ANALOGUES

ILLUMINA CAMBRIDGE LIMITE...

1. An altered family B archaeal DNA polymerase, wherein the second amino acid of the motif A region is mutated to alanine (A); and the third amino acid of the motif A region is mutated to an amino acid selected from the group consisting of serine (S), alanine (A), glycine (G), and the amino acids having beta-branched side chains, whereby the altered family B archaeal DNA polymerase is capable of incorporating a 3? O-azidomethyl-modified nucleotide.

US Pat. No. 10,214,768

COUMARIN COMPOUNDS AND THEIR USES AS FLUORESCENT LABELS

Illumina Cambridge Limite...

19. A compound of Formula (I), or salts, mesomeric forms thereof:
wherein R1 is

 and wherein R1 is optionally substituted with one or more substituents selected from the group consisting of alkyl, substituted alkyl, alkoxy, alkenyl, alkynyl, haloalkyl, haloalkoxy, alkoxyalkyl, amino, aminoalkyl, halo, cyano, hydroxy, hydroxyalkyl, heteroalkyl, C-carboxy, O-carboxy, C-amido, N-amido, nitro, sulfonyl, sulfo, sulfino, sulfonate, S-sulfonamido, N-sulfonamido, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted cycloalkyl, and optionally substituted heterocyclyl;
each R2, R3, R4, R5, and R9 is independently selected from the group consisting of H, alkyl, substituted alkyl, alkoxy, alkenyl, alkynyl, haloalkyl, haloalkoxy, alkoxyalkyl, amino, aminoalkyl, halo, cyano, hydroxy, hydroxyalkyl, heteroalkyl, C-carboxy, O-carboxy, C-amido, N-amido, nitro, sulfonyl, sulfo, sulfino, sulfonate, S-sulfonamido, N-sulfonamido, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heteroaryl and optionally substituted heterocyclyl;
each R10a, R10b and R10c is independently alkyl substituted with carboxyl, carboxylate, sulfo or sulfonate;
R6 and R7 together with the atoms to which they are attached form an optionally substituted 5-10 membered heterocyclyl;
R8 is selected from the group consisting of H, alkyl, substituted alkyl, alkoxy, alkenyl, alkynyl, haloalkyl, haloalkoxy, alkoxyalkyl, amino, aminoalkyl, halo, cyano, hydroxy, hydroxyalkyl, heteroalkyl, C-carboxy, O-carboxy, C-amido, N-amido, nitro, sulfonyl, sulfo, sulfino, sulfonate, S-sulfonamido, N-sulfonamido, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heteroaryl and optionally substituted heterocyclyl;
the bond represented by a solid and dashed line is selected from the group consisting of a single bond and a double bond, provided that when is a double bond, then R3 is absent.

US Pat. No. 10,190,157

MODIFIED NUCLEOTIDE LINKERS

Illumina Cambridge Limite...

1. A nucleoside or nucleotide covalently attached to a fluorophore through a linker, wherein said linker comprises a structure of formula (I) or (II), or combination of both:
wherein
R1 is optionally substituted C1-6 alkyl;
R2 is hydrogen or optionally substituted C1-6 alkyl;
R3 is optionally substituted C1-6 alkyl, —NR5—C(?O)R6, or —NR7—C(?O)—OR8;
R4 is hydrogen or optionally substituted C1-6 alkyl;
each R5 and R7 is independently hydrogen or optionally substituted C1-6 alkyl;
each R6 and R8 is independently optionally substituted C1-6 alkyl;
each of the methylene repeating unit in

 is optionally substituted;
X is methylene (CH2), oxygen (O), or sulfur (S);
m is an integer of 0 through 20;
n is an integer of 1 through 20; and
p is an integer of 1 through 20.

US Pat. No. 10,144,967

POLYMETHINE COMPOUNDS AND THEIR USE AS FLUORESCENT LABELS

Illumina Cambridge Limite...

1. A nucleotide or oligonucleotide labelled with a compound of formula (I) or mesomeric forms thereof:
wherein mCat+ or mAn? is an organic or inorganic positively/negatively charged counterion and
m is an integer 0-3;
n is an integer 1-5;
Rf is OH or O?;
each of Ra1 and Ra2 is independently H, SO3?, sulfonamide, halogen, or a further optionally substituted aromatic ring fused to adjacent carbon atoms of the corresponding indole's benzene ring; with the proviso that either Ra1 or Ra2 is sulfonamide or SO3?; and
each of Rc1 and Rc2 is independently alkyl or substituted alkyl; wherein when Ra1 or Ra2 is SO3?, either i) Rc1 or Rc2 is an alkyl sulfonic acid group, or ii) Ra1 or Ra2 is a sulfonamide.

US Pat. No. 10,253,359

METHOD OF PREPARING LIBRARIES OF TEMPLATE POLYNUCLEOTIDES

ILLUMINA CAMBRIDGE LIMITE...

1. A forked polynucleotide adapter formed by annealing of partially complementary first and second polynucleotide strands, wherein at least one of the strands comprises a polynucleotide sequence complementary to the sequence of SEQ ID NO: 4.

US Pat. No. 10,239,909

POLYMETHINE COMPOUNDS WITH LONG STOKES SHIFTS AND THEIR USE AS FLUORESCENT LABELS

Illumina Cambridge Limite...

1. A compound of formula (I?) or mesomeric forms thereof:
wherein mCat+ or mAn? is an organic or inorganic positively/negatively charged counterion;
m is an integer 0-3;
x is an integer 0-2;
Ra1 is H, SO3?, sulfonamide, halogen, hydroxy, alkoxy, amino or a further ring fused to an adjacent carbon atom where the ring is optionally substituted with one or more SO3?, sulfonamide, or halogen;
Rb1 is SO3?, sulfonamide, halogen, hydroxy, alkoxy, amino, COOH or an amide or ester thereof;
n is 0-3;
each of Rc1 and Rc2 is independently alkyl or substituted alkyl;
each of Rd1 and Rd2 is independently H, alkyl, aryl, substituted alkyl, or substituted aryl; and
Re1 is alkyl, substituted alkyl, aryl or substituted aryl; wherein either Rc1, Rb1 or Re1 comprises a COOH or COO? or an amide or ester thereof.