公开(公告)号：US20180044732A1

公开(公告)日：2018-02-15

申请号：US15722500

申请日：2017-10-02

Applicant: ILLUMINA, INC.

Inventor： Mostafa Ronaghi ,  Helmy A. Eltoukhy

IPC: C12Q1/68

CPC classification number: C12Q1/6874 ,  C12Q1/6837 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2565/543

Abstract: The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to methods for obtaining long lengths of sequencing data.

公开(公告)号：US09416415B2

公开(公告)日：2016-08-16

申请号：US14641054

申请日：2015-03-06

Applicant: ILLUMINA, INC.

Inventor： Mostafa Ronaghi ,  Helmy A. Eltoukhy

IPC: C12P19/34 ,  C12Q1/68

CPC classification number: C12Q1/6874 ,  C12Q1/6837 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2565/543

Abstract: A method of sequencing nucleic acids, which can include steps of (a) providing a substrate having a surface having a repeating pattern of features, wherein the features are spatially separated from each other on the surface of the substrate; (b) contacting the repeating pattern of features with a solution of different target nucleic acids to seed a subset of the features that contact the solution, wherein no more than the subset of the features that contact the solution is seeded with the target nucleic acids; (c) amplifying the target nucleic acids at the subset of features; (d) repeating steps (b) and (c) to increase the number of features that are seeded with a nucleic acid, thereby making an array of different nucleic acid colonies; and (e) detecting sequencing reactions at the different nucleic acid colonies on the surface.

Abstract translation: 一种测序核酸的方法，其可以包括以下步骤：（a）提供具有具有重复特征图案的表面的基底，其中所述特征在所述基底的表面上彼此空间上分离; （b）将特征的重复模式与不同靶核酸的溶液接触以接种与所述溶液接触的特征的子集，其中不超过所述接触所述溶液的特征子集与所述靶核酸接种; （c）在特征子集上扩增靶核酸; （d）重复步骤（b）和（c）以增加用核酸接种的特征数，从而制成不同核酸集落的阵列; 和（e）检测表面上不同核酸集落处的测序反应。

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：US12297498B2

公开(公告)日：2025-05-13

申请号：US18129747

申请日：2023-03-31

Applicant: Illumina, Inc.

Inventor： Molly He ,  Cheng-Yao Chen ,  Eric Kool ,  Mostafa Ronaghi ,  Michael Previte ,  Rigo Pantoja

IPC: C12Q1/68 ,  C12Q1/6806 ,  C12Q1/6818 ,  C12Q1/6874

Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.

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：US20220106588A1

公开(公告)日：2022-04-07

申请号：US17451771

申请日：2021-10-21

Applicant: Illumina, Inc.

Inventor： Yir-Shyuan Wu ,  Filiz Gorpe-Yasar ,  Tarun Kumar Khurana ,  Victoria Popic ,  Erich B. Jaeger ,  Mostafa Ronaghi

IPC: C12N15/10 ,  C12Q1/6806 ,  B01L3/00 ,  B01L7/00 ,  C12Q1/6834

Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating long DNA fragments for high-throughput spatial indexing. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.

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：US10233493B2

公开(公告)日：2019-03-19

申请号：US15853118

申请日：2017-12-22

Applicant: Illumina, Inc.

Inventor： Molly He ,  Cheng-Yao Chen ,  Eric Kool ,  Mostafa Ronaghi ,  Michael Previte ,  Rigo Pantoja

IPC: C12P19/34 ,  C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6818

Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.

公开(公告)号：US09777326B2

公开(公告)日：2017-10-03

申请号：US15237480

申请日：2016-08-15

Applicant: ILLUMINA, INC.

Inventor： Mostafa Ronaghi ,  Helmy A. Eltoukhy

IPC: C12P19/34 ,  C12Q1/68

CPC classification number: C12Q1/6874 ,  C12Q1/6837 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2565/543

Abstract: A method of sequencing nucleic acids, which can include steps of (a) providing a substrate comprising a surface having a repeating pattern of features, wherein the features are spatially separated from each other on the surface of the substrate; (b) contacting the repeating pattern of features with a solution of different nucleic acids to seed a subset of the features that contact the solution, wherein each feature in the subset is seeded with a single nucleic acid from the solution, and a plurality of the features that contact the solution are not seeded with a nucleic acid from the solution; (c) amplifying the nucleic acids to form a nucleic acid colony at each of the features in the seeded subset; (d) repeating steps (b) and (c) to increase the number of features that are seeded with a nucleic acid, thereby making an array of different nucleic acid colonies; and (e) detecting sequencing reactions at the different nucleic acid colonies on the surface.

公开(公告)号：US08709729B2

公开(公告)日：2014-04-29

申请号：US13905003

申请日：2013-05-29

Applicant: Illumina, Inc.

Inventor： Mostafa Ronaghi ,  Helmy Eltoukhy

IPC: C12Q1/68 ,  C12P19/34

CPC classification number: C12Q1/6874 ,  C12Q1/6837 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2565/543

Abstract: A method of making an array of nucleic acid colonies, including the steps of (a) providing a substrate having a patterned surface of features, wherein the features are spatially organized in a repeating pattern on the surface of the substrate; (b) contacting the substrate with a solution of different target nucleic acids to seed no more than a subset of the features that contact the solution; (c) amplifying the nucleic acids on the subset of features; and (d) repeating steps (b) and (c) to increase the number of features that are seeded with a nucleic acid, thereby making an array of nucleic acid colonies.

Abstract translation: 一种制备核酸集落阵列的方法，包括以下步骤：（a）提供具有图案化特征表面的基底，其中所述特征在空间上以基底表面上的重复图案组织; （b）使底物与不同靶核酸的溶液接触不超过接触溶液的特征的一部分; （c）扩增特征子集上的核酸; 和（d）重复步骤（b）和（c）以增加用核酸接种的特征的数量，由此形成核酸集落阵列。