公开(公告)号：US20240026348A1

公开(公告)日：2024-01-25

申请号：US18476719

申请日：2023-09-28

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited

Inventor： Susan C. Verity ,  Robert Scott Kuersten ,  Niall Anthony Gormley ,  Andrew B. Kennedy ,  Sarah E. Shultzaberger ,  Andrew Slatter ,  Emma Bell ,  Sebastien Georg Gabriel Ricoult ,  Grace DeSantis ,  Fiona Kaper ,  Han-Yu Chuang ,  Oliver Jon Miller ,  Jason Richard Betley ,  Stephen M. Gross ,  Mats Ekstrand

IPC: C12N15/10

CPC classification number: C12N15/1065 ,  C12N15/1068

Abstract: Materials and methods for preparing nucleic acid libraries for next-generation sequencing are described herein. A variety of approaches are described relating to the use of unique molecular identifiers with transposon-based technology in the preparation of sequencing libraries. Also described herein are sequencing materials and methods for identifying and correcting amplification and sequencing errors.

公开(公告)号：US11685946B2

公开(公告)日：2023-06-27

申请号：US16739739

申请日：2020-01-10

Applicant: ILLUMINA CAMBRIDGE LIMITED

Inventor： Andrew Slatter ,  Esther Musgrave-Brown ,  Susan C. Verity ,  Niall Anthony Gormley

IPC: C12Q1/68 ,  C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6869

CPC classification number: C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6869

Abstract: The present disclosure relates to methods, compositions, and kits for generating a library of tagged nucleic acid fragments without using PCR amplification, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes immobilized on solid support.

公开(公告)号：US20220002783A1

公开(公告)日：2022-01-06

申请号：US17447794

申请日：2021-09-15

Applicant: Illumina Cambridge Limited

Inventor： Louise Fraser ,  Paula Kokko-Gonzales ,  Andrew Slatter

IPC: C12Q1/6806 ,  C12P19/34 ,  C12N15/10 ,  C12Q1/6844

Abstract: Presented are methods and compositions for preparing samples for amplification and sequencing. Particular embodiments relate to methods of preparing nucleic acid-containing cellular samples for library amplification, wherein the methods include lysing cells of the sample to form a lysate, amplifying the nucleic acids from the lysed samples, exposing the amplified nucleic acids to a solid surface, and clonallyr amplifying the amplified nucleic acids to generate clusters.

公开(公告)号：US10774367B2

公开(公告)日：2020-09-15

申请号：US16163005

申请日：2018-10-17

Applicant: Illumina Cambridge Limited

Inventor： Louise Fraser ,  Paula Kokko-Gonzales ,  Andrew Slatter

IPC: C12P19/34 ,  C12Q1/6806 ,  C12N15/10 ,  C12Q1/6844

Abstract: Presented are methods and compositions for preparing samples for amplification and sequencing. Particular embodiments relate to methods of preparing nucleic acid-containing cellular samples for library amplification, wherein the methods include providing nucleic acid containing-cellular samples from blood or FFPE samples, lysing cells of the sample to liberate nucleic acids, and performing tagmentation without purifying the liberated nucleic acids.

公开(公告)号：US20240287504A1

公开(公告)日：2024-08-29

申请号：US18549344

申请日：2022-03-08

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited

Inventor： Andrew Kennedy ,  Sarah Shultzaberger ,  Emma Bell ,  Oliver Miller ,  Kim Schneider ,  Esther Musgrave-Brown ,  Niall Gormley ,  Andrew Slatter ,  Feng Chen

IPC: C12N15/10

CPC classification number: C12N15/1065

Abstract: Genomic library preparation using Cas-gRNA RNPs, and targeted epigenetic assays, are provided herein. Some compositions include, from a first species, substantially only single-stranded polynucleotides; from a second species, substantially only double-stranded polynucleotides; and amplification primers ligated to ends of the second double-stranded polynucleotides and substantially not ligated to any ends of the first double-stranded polynucleotides. Some compositions include first and second molecules of a target polynucleotide having a sequence, the first molecule having a first end at a first subsequence, the second molecule having a first end at a second subsequence, wherein the first subsequence only partially overlaps with the second subsequence. Some examples provide a composition that includes a target polynucleotide and a first fusion protein including a Cas-gRNA RNP coupled to a transposase having an amplification adapter coupled thereto. The Cas-gRNA RNP may be hybridized to a subsequence in the target polynucleotide.

公开(公告)号：US20230409629A1

公开(公告)日：2023-12-21

申请号：US18204256

申请日：2023-05-31

Applicant: ILLUMINA CAMBRIDGE LIMITED

Inventor： Natalie Morrell ,  Andrew Slatter ,  Vicki Thomson

IPC: G06F16/58 ,  G06V10/26 ,  B01L3/00 ,  B01L7/00 ,  C12Q1/6844 ,  G06T5/50

CPC classification number: G06F16/58 ,  G06V10/26 ,  B01L3/502761 ,  B01L7/52 ,  C12Q1/6844 ,  G06T5/50 ,  B01L2300/0816 ,  B01L2300/0819 ,  B01L2300/0877 ,  B01L2300/0893 ,  C12Q2304/10 ,  C12Q1/6855

Abstract: In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.

公开(公告)号：US11714848B2

公开(公告)日：2023-08-01

申请号：US17600499

申请日：2020-12-01

Applicant: ILLUMINA CAMBRIDGE LIMITED

Inventor： Natalie Morrell ,  Andrew Slatter ,  Vicki Thomson

IPC: G06F16/58 ,  G06V10/26 ,  B01L3/00 ,  B01L7/00 ,  C12Q1/6844 ,  G06T5/50 ,  C12Q1/6855 ,  C12Q1/6853

CPC classification number: G06F16/58 ,  B01L3/502761 ,  B01L7/52 ,  C12Q1/6844 ,  G06T5/50 ,  G06V10/26 ,  B01L2300/0816 ,  B01L2300/0819 ,  B01L2300/0877 ,  B01L2300/0893 ,  C12Q1/6853 ,  C12Q1/6855 ,  C12Q2304/10 ,  C12Q2304/12 ,  C12Q2304/13

Abstract: In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.

公开(公告)号：US11708573B2

公开(公告)日：2023-07-25

申请号：US17140434

申请日：2021-01-04

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited

Inventor： Grace DeSantis ,  Stephen M. Gross ,  Jian-Sen Li ,  Natalie Morrell ,  Andrew Slatter ,  Kevin Shen ,  Samantha Snow

IPC: C12N15/10 ,  C12N11/06 ,  C12Q1/6869 ,  C12Q1/6806

CPC classification number: C12N15/1065 ,  C12N11/06 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Y207/07 ,  C12Q1/6806 ,  C12Q2521/301 ,  C12Q2525/151 ,  C12Q2525/191

Abstract: The present disclosure relates to methods, compositions, and kits for treating target nucleic acids, including methods and compositions for fragmenting and tagging nucleic acid (e.g., DNA) using transposome complexes bound to a solid support.

公开(公告)号：US20210262028A1

公开(公告)日：2021-08-26

申请号：US17185730

申请日：2021-02-25

Applicant: ILLUMINA CAMBRIDGE LIMITED ,  ILLUMINA, INC.

Inventor： Andrew Slatter ,  Eric Hans Vermaas

IPC: C12Q1/6876 ,  C12Q1/6869

Abstract: An example of a kit includes a flow cell and a genotyping probe fluid. The flow cell includes a substrate, and first and second capture primers attached to the substrate. The genotyping probe fluid includes a liquid carrier, and a genotyping oligonucleotide in the liquid carrier. The genotyping oligonucleotide includes a first primer sequence; a probe sequence that is representative of a target genotyping locus; a restriction endonuclease site; and a second primer sequence that is at least partially complementary to the second capture primer.

公开(公告)号：US20210139887A1

公开(公告)日：2021-05-13

申请号：US17140434

申请日：2021-01-04

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited

Inventor： Grace DeSantis ,  Stephen M. Gross ,  Jian-Sen Li ,  Natalie Morrell ,  Andrew Slatter ,  Kevin Shen ,  Samantha Snow

IPC: C12N15/10 ,  C12N11/06 ,  C12Q1/6869 ,  C12Q1/6806

Abstract: The present disclosure relates to methods, compositions, and kits for treating target nucleic acids, including methods and compositions for fragmenting and tagging nucleic acid (e.g., DNA) using transposome complexes bound to a solid support.