公开(公告)号：US12084474B2

公开(公告)日：2024-09-10

申请号：US16411913

申请日：2019-05-14

申请人： Illumina, Inc. ,  Illumina Cambridge Limited

发明人： Xiaolin Wu ,  Randall Smith ,  Peyton Shieh ,  John M. Beierle ,  Wayne N. George ,  Elliot John Lawrence ,  Jie Mao ,  Xiaohai Liu

IPC分类号： C07H21/04 ,  C12Q1/6806 ,  C12Q1/6876

CPC分类号： C07H21/04 ,  C12Q1/6806 ,  C12Q1/6876 ,  C12Q1/6806 ,  C12Q2523/107 ,  C12Q2525/113 ,  C12Q2565/543

摘要： Embodiments of the present disclosure relate to methods of preparation of templates for polynucleotide sequencing. In particular, the disclosure relates to linearization of clustered polynucleotides in preparation for sequencing by cleavage of one or more first strands of double-stranded polynucleotides immobilized on a solid support by a transition metal complex, for example, a palladium complex or a nickel complex. Further disclosure relate to linearization of clustered polynucleotides by cleaving one or more second strands of double double-stranded polynucleotides immobilized on a solid support comprising azobenzene linker by Na2S2O4. Nucleotides and oligonucleotides comprising a 3′ phosphate moiety blocking group, and methods of removing the same using a fluoride reagent are also disclosed.

公开(公告)号：US20230212667A1

公开(公告)日：2023-07-06

申请号：US18089867

申请日：2022-12-28

申请人： ILLUMINA CAMBRIDGE LIMITED ,  ILLUMINA, INC.

发明人： Jonathan Mark Boutell ,  Eli M. Carrami ,  Pietro Gatti Lafranconi ,  Philip Balding ,  Oliver Jon Miller ,  Kay Klausing ,  Justin Robbins ,  Xiaolin Wu

IPC分类号： C12Q1/6874

CPC分类号： C12Q1/6874 ,  C12Q1/6806

摘要： Polynucleotide sequencing methods for sequencing one or more polynucleotide templates use primers bound to a surface as sequencing primers. The surface primers may include at least a portion of a surface oligonucleotide used during cluster formation. The sequencing methods may be used for single stranded sequencing or double stranded sequencing. Double stranded sequencing methods may employ an enzyme that has nick-translation activity. A kit includes all the reagents needed for sequencing does not include sequencing primers. The kit may be used to accomplish the sequencing methods of the present disclosure.

公开(公告)号：US20230383342A1

公开(公告)日：2023-11-30

申请号：US18325610

申请日：2023-05-30

申请人： Illumina Cambridge Limited ,  Illumina Singapore Pte. Ltd. ,  Illumina, Inc. ,  Illumina Software, Inc.

发明人： Xiaolin Wu ,  Patrick McCauley ,  Madushani Dharmarwardana ,  Saurabh Nirantar ,  Misha Golynskiy ,  Xiangyuan Yang ,  Ramesh Neelakandan ,  Benedict Mackworth ,  Carole Anastasi ,  Aathavan Karunakaran ,  Gery M. Vessere ,  David Bracher

IPC分类号： C12Q1/6869 ,  G01N21/64

CPC分类号： C12Q1/6869 ,  G01N2021/6439 ,  G01N2021/6419 ,  G01N21/6428

摘要： Embodiments of the present disclosure relate to kits, compositions, and methods for nucleic acid sequencing, for example, two-channel nucleic acid sequencing by synthesis using blue and green light excitation. In particular, unlabeled nucleotides for incorporation may be used in conjunction with affinity reagents containing detectable labels excitable by blue and/or green lights, for specific binding to each type of nucleotides incorporated.

公开(公告)号：US20230042267A1

公开(公告)日：2023-02-09

申请号：US17855325

申请日：2022-06-30

申请人： ILLUMINA, INC. ,  ILLUMINA CAMBRIDGE LIMITED

发明人： Jonathan Mark Boutell ,  Wayne N. George ,  Xiaoyu Ma ,  Xiaolin Wu ,  Weixian Xi

IPC分类号： C08G63/685 ,  C08G63/82 ,  C08G63/91

摘要： An example of a kit includes a flow cell, a primer fluid, and a cleaving fluid. The flow cell includes at least one surface functionalized with a polymeric hydrogel including azide functional groups or amine functional groups. The primer fluid includes a plurality of alkyne-containing primers, each alkyne-containing primer having an amino cleavable group attaching a primer sequence of the alkyne-containing primer to an alkyne-containing moiety of the alkyne-containing primer. The cleaving fluid includes a substance that is reactive with the amino cleavable group.

公开(公告)号：US20220290234A1

公开(公告)日：2022-09-15

申请号：US17694404

申请日：2022-03-14

申请人： ILLUMINA, INC. ,  ILLUMINA CAMBRIDGE LIMITED

发明人： Sarah Shultzaberger ,  Xiaolin Wu ,  Eric Brustad ,  Niall Gormley

IPC分类号： C12Q1/6876 ,  C12Q1/6806 ,  C07H19/16

摘要： Examples provided herein are related to detecting methylcytosine and its derivatives using S-adenosyl-L-methionine analogs (xSAMs). Compositions and methods for performing such detection are disclosed. A target polynucleotide may include cytosine (C) and methylcytosine (mC). The method may include (a) protecting the C in the target polynucleotide from deamination; and (b) after step (a), deaminating the mC in the target polynucleotide to form thymine (T). Protecting the C from deamination may include adding a protective group to the 5 position of the C, e.g., using a methyltransferase enzyme that adds the first protective group from an xSAM.

公开(公告)号：US20190352327A1

公开(公告)日：2019-11-21

申请号：US16411913

申请日：2019-05-14

申请人： Illumina, Inc. ,  Illumina Cambridge Limited

发明人： Xiaolin Wu ,  Randall Smith ,  Peyton Shieh ,  John M. Beierle ,  Wayne N. George ,  Elliot John Lawrence ,  Jie Mao ,  Xiaohai Liu

IPC分类号： C07H21/04 ,  C12Q1/6876

摘要： Embodiments of the present disclosure relate to methods of preparation of templates for polynucleotide sequencing. In particular, the disclosure relates to linearization of clustered polynucleotides in preparation for sequencing by cleavage of one or more first strands of double-stranded polynucleotides immobilized on a solid support by a transition metal complex, for example, a palladium complex or a nickel complex. Further disclosure relate to linearization of clustered polynucleotides by cleaving one or more second strands of double double-stranded polynucleotides immobilized on a solid support comprising azobenzene linker by Na2S2O4. Nucleotides and oligonucleotides comprising a 3′ phosphate moiety blocking group, and methods of removing the same using a fluoride reagent are also disclosed.

公开(公告)号：US11773438B2

公开(公告)日：2023-10-03

申请号：US17562510

申请日：2021-12-27

申请人： Illumina Cambridge Limited

发明人： Xiaolin Wu ,  Xiaohai Liu

IPC分类号： C12Q1/68 ,  C07H19/14 ,  C12Q1/6869

CPC分类号： C12Q1/6869 ,  C07H19/14

摘要： Some embodiments of the present application relate to novel modified nucleotide linkers for increasing the efficiency of nucleotide incorporation in Sequencing by Synthesis applications. Methods of preparing these modified nucleotide linkers are also provided herewith.

公开(公告)号：US11597969B2

公开(公告)日：2023-03-07

申请号：US17103169

申请日：2020-11-24

申请人： Illumina Cambridge Limited

发明人： Xiaolin Wu ,  Xiaohai Liu ,  Nikolai Nikolaevich Romanov ,  Antoine Francais ,  Patrick McCauley ,  Michael Callingham ,  Carole Anastasi

IPC分类号： C12Q1/68 ,  C09B57/02 ,  C12Q1/6869

摘要： Embodiments of the present disclosure relate to cyclooctatetraene containing dyes and their uses as fluorescent labels. Also provided are composition containing cyclooctatetraene. The dyes and compositions may be used in various biological applications, such as nucleic acid sequencing.

公开(公告)号：US10239909B2

公开(公告)日：2019-03-26

申请号：US15575743

申请日：2016-05-23

申请人： ILLUMINA CAMBRIDGE LIMITED

发明人： Nikolai Romanov ,  Xiaolin Wu

IPC分类号： C07H19/10 ,  C09B23/06 ,  C09K11/06 ,  C07H19/14 ,  C09B69/10 ,  C12Q1/6876 ,  C07D401/06

摘要： The present disclosure relates to new compounds and their use as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications. The labels are advantageous due to their long Stokes shifts.

公开(公告)号：US09498763B2

公开(公告)日：2016-11-22

申请号：US14738591

申请日：2015-06-12

申请人： Illumina Cambridge Limited

发明人： Xiaohai Liu ,  John Milton ,  Geoffrey Paul Smith ,  Colin Lloyd Barnes ,  Isabelle Rasolonjatovo ,  Roberto Rigatti ,  Xiaolin Wu ,  Tobias William Barr Ost ,  Graham John Worsley ,  David James Earnshaw ,  Gerardo Turcatti ,  Anthony Romieu

IPC分类号： C12Q1/68 ,  B01J19/00

CPC分类号： B01J19/0046 ,  B01J2219/00596 ,  B01J2219/00608 ,  B01J2219/00675 ,  B01J2219/00722 ,  C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6874 ,  C12Q2565/543 ,  C12Q2535/101 ,  C12Q2523/113 ,  C12Q2523/107 ,  C12Q2521/331 ,  C12Q2521/307

摘要： The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: providing at least one double-stranded nucleic acid molecule, wherein both strands of the double-stranded nucleic acid molecule are attached to a solid support at the 5′ end, cleaving one or both strands of the double-stranded nucleic acid molecule, and subjecting the cleaved strand(s) to denaturing conditions to remove the portion of the cleaved strand(s) not attached to the solid support, thereby generating a partially or substantially single-stranded template for a nucleic acid sequencing reaction.