公开(公告)号：US11760772B2

公开(公告)日：2023-09-19

申请号：US17330853

申请日：2021-05-26

申请人： Illumina, Inc.

发明人： Frank J. Steemers ,  Kevin L. Gunderson ,  Kerri York ,  Ryan Christopher Smith

IPC分类号： C07H1/06 ,  C12Q1/6811 ,  C07H21/00 ,  C12N15/10 ,  C07D495/04 ,  C07H1/00

CPC分类号： C07H1/06 ,  C07D495/04 ,  C07H21/00 ,  C12N15/1003 ,  C12Q1/6811 ,  C07H1/00

摘要： Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags.

公开(公告)号：US20220333157A1

公开(公告)日：2022-10-20

申请号：US17663485

申请日：2022-05-16

申请人： ILLUMINA, INC.

发明人： Frank J. Steemers ,  Ramesh Ramji ,  Steven Norberg ,  Lena Christiansen ,  Dmitry K. Pokholok ,  Fan Zhang

IPC分类号： C12Q1/6806 ,  A61K47/58 ,  A61K47/69 ,  C12M1/12 ,  C12N5/00 ,  C12N5/16

摘要： Embodiments of systems, methods, and compositions provided herein relate to hollow beads encapsulating single cells. Some embodiments include performing multiple co-assays on a single cell encapsulated within a hollow bead, including nucleic acid sequencing, preparing nucleic acid libraries, determining methylation status, identifying genomic variants, or protein analysis.

公开(公告)号：US20220195507A1

公开(公告)日：2022-06-23

申请号：US17250846

申请日：2019-12-13

申请人： ILLUMINA, INC.

发明人： Frank J. Steemers ,  Dmitry K. Pokholok ,  Lena Christiansen

IPC分类号： C12Q1/6848 ,  C12N15/10 ,  C12Q1/6874 ,  C12Q1/6876

摘要： Embodiments of systems, methods, and compositions provided herein relate to assays for selectively controlling enzymatic reactions. Some embodiments relate to methods of inhibiting, reducing, or eliminating secondary DNA (such as mitochondrial DNA) sequencing reads from open chromatic sequencing, whole genome sequencing, or targeted sequencing.

公开(公告)号：US11319534B2

公开(公告)日：2022-05-03

申请号：US16735348

申请日：2020-01-06

申请人： ILLUMINA, INC.

发明人： Frank J. Steemers ,  Sasan Amini ,  Kevin L. Gunderson ,  Natasha Pignatelli ,  Igor Goryshin

IPC分类号： C12N15/10 ,  C12Q1/6806 ,  C12Q1/6869

摘要： Embodiments of the present invention relate to sequencing nucleic acids. In particular, embodiments of the methods and compositions provided herein relate to preparing nucleic acid templates and obtaining sequence data therefrom.

公开(公告)号：US20220033805A1

公开(公告)日：2022-02-03

申请号：US17276667

申请日：2020-03-02

申请人： Sanjay SRIVATSAN ,  Jose MCFALINE-FIGUEROA ,  Vijay RAMANI ,  Junyue CAO ,  Gregory BOOTH ,  Jay SHENDURE ,  Cole TRAPNELL ,  Frank STEEMERS ,  ILLUMINA, INC. ,  UNIVERSITY OF WASHINGTON

发明人： Sanjay Srivatsan ,  Jose McFaline-Figueroa ,  Vijay Ramani ,  Junyue Cao ,  Gregory Booth ,  Jay Shendure ,  Cole Trapnell ,  Frank J. Steemers

IPC分类号： C12N15/10

摘要： Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the method includes nuclear or cellular hashing which permits increased sample throughput and increased doublet detection at high collision rates. In one embodiment, the method includes normalization hashing which aids in estimating and removing technical noise in cell to cell variation and increases sensitivity and specificity.

公开(公告)号：US20210108262A1

公开(公告)日：2021-04-15

申请号：US17076715

申请日：2020-10-21

申请人： Illumina, Inc.

发明人： Sante Gnerre ,  Byoungsok Jung ,  Emrah Kostem ,  Alex Aravanis ,  Alex So ,  Xuyu Cai ,  Zhihong Zhang ,  Frank J. Steemers

IPC分类号： C12Q1/6869 ,  G16B30/00 ,  C12Q1/6806 ,  C12N15/10 ,  C12Q1/6855

摘要： The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

公开(公告)号：US10968448B2

公开(公告)日：2021-04-06

申请号：US16736043

申请日：2020-01-07

申请人： Illumina, Inc.

发明人： Frank J. Steemers ,  Jeffrey S. Fisher ,  Kevin L. Gunderson ,  Sasan Amini ,  Christian Gloeckner

IPC分类号： C12N15/10 ,  C12Q1/6806 ,  C12N9/22

摘要： Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid using one-sided transposition, sequencing the template library, and capturing the contiguity information.

公开(公告)号：US20200370103A1

公开(公告)日：2020-11-26

申请号：US16986066

申请日：2020-08-05

申请人： Illumina, Inc.

发明人： Kevin L. Gunderson ,  Frank J. Steemers

IPC分类号： C12Q1/6827 ,  C12Q1/6837 ,  C12Q1/6848

摘要： This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.

公开(公告)号：US10457969B2

公开(公告)日：2019-10-29

申请号：US14804068

申请日：2015-07-20

申请人： Illumina, Inc.

发明人： Gordon M. Cann ,  Jeffrey G. Mandell ,  Alex Aravanis ,  Steven Norberg ,  Dmitry K. Pokholok ,  Frank J. Steemers ,  Farnaz Absalan ,  Leila Bazargan

IPC分类号： C12P19/34 ,  C12N15/10 ,  C12Q1/6816 ,  C12Q1/683 ,  C12Q1/6869

摘要： A method for enriching a target nucleic acid comprising providing an endonuclease system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid; contacting the target nucleic acid with the endonuclease system to form a complex; and separating the complex and thereby enriching for the target nucleic acid.

公开(公告)号：US10246746B2

公开(公告)日：2019-04-02

申请号：US14572556

申请日：2014-12-16

申请人： ILLUMINA, INC.

发明人： Jeffrey S. Fisher ,  Frank J. Steemers ,  Sasan Amini ,  Kevin L. Gunderson

IPC分类号： C12Q1/68 ,  C12Q1/6874

摘要： A method of sequencing a target nucleic acid polymer by (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer; (b) producing fragments of the modified nucleic acid polymer, wherein the fragments are attached to locations on a solid support surface (c) determining nucleotide sequences from the fragments at the locations; and (d) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the relative distances between the locations on the solid support surface.