公开(公告)号：US20210130885A1

公开(公告)日：2021-05-06

申请号：US17145846

申请日：2021-01-11

Applicant: ILLUMINA, INC.

Inventor： Alex So ,  Li Liu ,  Min-Jui Richard Shen ,  Neeraj Salathia ,  Kathryn M. Stephens ,  Anne Jager ,  Timothy Wilson ,  Justin Fullerton ,  Sean M. Ramirez ,  Shannon Kaplan ,  Rigo Pantoja ,  Bala Murali Venkatesan ,  Steven Modiano

IPC: C12Q1/6837 ,  C12Q1/6874 ,  C12Q1/6816 ,  C12Q1/6855

Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.

公开(公告)号：US20150080230A1

公开(公告)日：2015-03-19

申请号：US14512693

申请日：2014-10-13

Applicant: ILLUMINA, INC.

Inventor： Min-Jui Richard Shen ,  Jonathan Mark Boutell ,  Kathryn M. Stephens ,  Mostafa Ronaghi ,  Kevin Gunderson ,  Bala Murali Venkatesan ,  M. Shane Bowen ,  Kandaswamy Vijayan

IPC: C12Q1/68 ,  B01J19/00

CPC classification number: C12Q1/6848 ,  B01J19/0046 ,  B01J2219/00585 ,  B01J2219/00587 ,  B01J2219/00608 ,  B01J2219/00621 ,  B01J2219/00637 ,  B01J2219/00653 ,  B01J2219/00675 ,  B01J2219/00722 ,  C12Q1/6844 ,  C12Q1/6874 ,  C12Q2521/507 ,  C12Q2527/101 ,  C12Q2527/113 ,  C12Q2535/122 ,  C12Q2565/513 ,  C12Q2565/537

Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

Abstract translation: 一种方法，包括（a）提供包含位点阵列的扩增试剂和具有不同靶核酸的溶液; 和（b）使扩增试剂反应以产生每个具有来自溶液的靶核酸的扩增子的克隆群的扩增位点。 反应可以包括以平均传输速率同时将核酸输送到位点，以及以平均扩增速率扩增转运到位点的核酸，其中平均扩增速率超过平均传输速率。 该反应可以包括从转运到每个位点的核酸产生第一扩增子，并产生来自核酸或第一扩增子的后续扩增子，其中后续扩增子产生的平均速率超过在 其中生成第一个扩增子。

公开(公告)号：US20220243261A1

公开(公告)日：2022-08-04

申请号：US17575279

申请日：2022-01-13

Applicant: Illumina, Inc.

Inventor： Min-Jui Richard Shen ,  Jonathan Mark Boutell ,  Kathryn M. Stephens ,  Mostafa Ronaghi ,  Kevin L. Gunderson ,  Bala Murali Venkatesan ,  M. Shane Bowen ,  Kandaswamy Vijayan

IPC: C12Q1/6848 ,  B01J19/00 ,  C12Q1/6844 ,  C12Q1/6874

Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

公开(公告)号：US10913975B2

公开(公告)日：2021-02-09

申请号：US15747670

申请日：2016-07-21

Applicant: ILLUMINA, INC.

Inventor： Alex So ,  Li Liu ,  Min-Jui Richard Shen ,  Neeraj Salathia ,  Kathryn M. Stephens ,  Anne Jager ,  Timothy Wilson ,  Justin Fullerton ,  Sean M. Ramirez ,  Shannon Kaplan ,  Rigo Pantoja ,  Bala Murali Venkatesan ,  Steven Modiano

IPC: C12Q1/68 ,  C12Q1/6837 ,  C12Q1/6874 ,  C12Q1/6816 ,  C12Q1/6855

Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.

公开(公告)号：US10385384B2

公开(公告)日：2019-08-20

申请号：US15672161

申请日：2017-08-08

Applicant: Illumina, Inc.

Inventor： Min-Jui Richard Shen ,  Jonathan Mark Boutell ,  Kathryn M. Stephens ,  Mostafa Ronaghi ,  Kevin L. Gunderson ,  Bala Murali Venkatesan ,  M. Shane Bowen ,  Kandaswamy Vijayan

IPC: C12Q1/68 ,  B01J19/00 ,  C12Q1/6848 ,  C12Q1/6844 ,  C12Q1/6874

Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

公开(公告)号：US11254976B2

公开(公告)日：2022-02-22

申请号：US16544670

申请日：2019-08-19

Applicant: Illumina, Inc.

Inventor： Min-Jui Richard Shen ,  Jonathan Mark Boutell ,  Kathryn M. Stephens ,  Mostafa Ronaghi ,  Kevin L. Gunderson ,  Bala Murali Venkatesan ,  M. Shane Bowen ,  Kandaswamy Vijayan

IPC: C12Q1/6848 ,  C12Q1/6844 ,  C12Q1/6874 ,  B01J19/00

Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

公开(公告)号：US20150232929A1

公开(公告)日：2015-08-20

申请号：US14622632

申请日：2015-02-13

Applicant: ILLUMINA, INC.

Inventor： Kathryn M. Stephens ,  Cydne Holt ,  Carey Davis ,  Anne Jager ,  Paulina Walichiewicz ,  Yonmee Han ,  David Silva ,  Min-Jui Richard Shen ,  Sasan Amini ,  Frank J. Steemers

IPC: C12Q1/68

Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.

Abstract translation: 本文公开的实施方案提供了用于构建DNA谱的方法，其包括：提供核酸样品，用多个引物扩增核酸样品，多个引物与至少一个包含SNP的靶序列和至少一个包含串联重复序列的靶序列特异性杂交 ，并确定扩增产物中至少一个SNP的基因型和至少一个串联重复序列，从而构建核酸样品的DNA谱。 本文公开的实施方案还提供了与核酸样品中的至少一个短靶序列和至少一个长靶序列特异性杂交的多个引物，其中在单个反应中使用多个引物扩增核酸样品导致 短扩增产物和长扩增产物，其中多个引物中的每一个包含一个或多个标签序列。

公开(公告)号：US08895249B2

公开(公告)日：2014-11-25

申请号：US13783043

申请日：2013-03-01

Applicant: Illumina, Inc.

Inventor： Min-Jui Richard Shen ,  Jonathan Mark Boutell ,  Kathryn M. Stephens ,  Mostafa Ronaghi ,  Kevin Gunderson ,  Bala Murali Venkatesan ,  M. Shane Bowen ,  Kandaswamy Vijayan

IPC: C12Q1/68 ,  C12P19/34 ,  B01J19/00

CPC classification number: C12Q1/6848 ,  B01J19/0046 ,  B01J2219/00585 ,  B01J2219/00587 ,  B01J2219/00608 ,  B01J2219/00621 ,  B01J2219/00637 ,  B01J2219/00653 ,  B01J2219/00675 ,  B01J2219/00722 ,  C12Q1/6844 ,  C12Q1/6874 ,  C12Q2521/507 ,  C12Q2527/101 ,  C12Q2527/113 ,  C12Q2535/122 ,  C12Q2565/513 ,  C12Q2565/537

Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

Abstract translation: 一种方法，包括（a）提供包含位点阵列的扩增试剂和具有不同靶核酸的溶液; 和（b）使扩增试剂反应以产生每个具有来自溶液的靶核酸的扩增子的克隆群的扩增位点。 反应可以包括以平均传输速率同时将核酸输送到位点，以及以平均扩增速率扩增转运到位点的核酸，其中平均扩增速率超过平均传输速率。 该反应可以包括从转运到每个位点的核酸产生第一扩增子，并产生来自核酸或第一扩增子的后续扩增子，其中后续扩增子产生的平均速率超过在 其中生成第一个扩增子。

公开(公告)号：US11530446B2

公开(公告)日：2022-12-20

申请号：US16576583

申请日：2019-09-19

Applicant: Illumina, Inc.

Inventor： Kathryn M. Stephens ,  Cydne Holt ,  Carey Davis ,  Anne Jager ,  Paulina Walichiewicz ,  Yonmee Han ,  David Silva ,  Min-Jui Richard Shen ,  Sasan Amini ,  Frank J. Steemers

IPC: C12Q1/6876 ,  C12Q1/6827 ,  C12Q1/6858 ,  C12Q1/686 ,  C12Q1/6853 ,  C12Q1/6869

Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.

公开(公告)号：US20200224268A1

公开(公告)日：2020-07-16

申请号：US16576583

申请日：2019-09-19

Applicant: Illumina, Inc.

Inventor： Kathryn M. Stephens ,  Cydne Holt ,  Carey Davis ,  Anne Jager ,  Paulina Walichiewicz ,  Yonmee Han ,  David Silva ,  Min-Jui Richard Shen ,  Sasan Amini ,  Frank J. Steemers

IPC: C12Q1/6876 ,  C12Q1/6827 ,  C12Q1/6858 ,  C12Q1/6853 ,  C12Q1/6869

Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.