公开(公告)号：US20170321271A1

公开(公告)日：2017-11-09

申请号：US15588203

申请日：2017-05-05

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL

IPC: C12Q1/68 ,  B01J19/00 ,  C12N15/10

CPC classification number: C12Q1/6874 ,  B01J19/0046 ,  B01J2219/00547 ,  B01J2219/00572 ,  B01J2219/00722 ,  C12N15/1065 ,  C40B20/04 ,  C40B70/00

Abstract: A kit for use with a nucleic acid sequencing instrument can include a plurality of combinatorial barcodes sequences meeting the following criteria: each of the combinatorial barcode sequences comprise a plurality of iterations of a sequence motif, where the sequence motif comprises a first nucleotide base from a first group of nucleotide bases followed by a second nucleotide base from a second group of nucleotide bases, the first group and the second group differing from each other; and the plurality of combinatorial barcode sequences is at least 1,000,000 different barcode sequences.

公开(公告)号：US20170044602A1

公开(公告)日：2017-02-16

申请号：US15236172

申请日：2016-08-12

Applicant: Life Technologies Corporation

Inventor： Earl HUBBELL ,  Jonathan SCHULTZ

IPC: C12Q1/68

CPC classification number: C12Q1/6869 ,  C12Q1/6874 ,  C12Q2533/101 ,  C12Q2565/301 ,  C12Q2565/607

Abstract: A system and machine readable medium for nucleic acid sequencing includes disposing template polynucleotide strands in defined spaces disposed on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith; exposing the template polynucleotide strands to a series of flows of nucleotide species flowed according to a predetermined ordering; and determining, for each of the series of flows of nucleotide species, how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands, wherein the predetermined ordering (a) is not a series of consecutive repetitions of a 4-flow permutation of four different nucleotide species, (b) is not specifically tailored to a particular combination of a particular template polynucleotide strand to be sequenced and a particular sequencing primer to be used, and (c) comprises a phase-protecting flow ordering.

Abstract translation: 用于核酸测序的系统和机器可读介质包括在设置在传感器阵列上的限定空间中设置模板多核苷酸链，至少一些模板多核苷酸链具有测序引物和与之可操作地结合的聚合酶; 将模板多核苷酸链暴露于根据预定排序流动的一系列核苷酸类型的流; 并且对于核苷酸种类的每一系列流程，确定针对该特定流出现多少个核苷酸掺入以确定对应于模板多核苷酸链的预测的核苷酸序列，其中预定顺序（a）不是一系列连续的 重复四种不同核苷酸物种的4流置换，（b）不是特定的针对待测序的特定模板多核苷酸链和特定的待测序列的特定组合而定制的，（c） 保护流量顺序。

公开(公告)号：US20160177386A1

公开(公告)日：2016-06-23

申请号：US14975001

申请日：2015-12-18

Applicant: Life Technologies Corporation

Inventor： Vadim MOZHAYSKIY ,  Yutao FU ,  Earl HUBBELL

IPC: C12Q1/68 ,  C12N15/10

CPC classification number: C12Q1/6874 ,  C12N15/1058 ,  C12Q1/6825 ,  C12Q2525/173 ,  C12Q2525/204 ,  C12Q2535/122 ,  C12Q2545/101 ,  C12Q2565/518 ,  C12Q2565/607

Abstract: A method for preparing a homopolymer recalibration panel includes: extracting, from a set of amplicons used in sequencing-by-synthesis, a set of candidate amplicons satisfying a first set of criteria, wherein the first set of criteria includes amplicons known to belong to high-confidence regions of a reference genome with no variants; and selecting, from the set of candidate amplicons, a reduced set of amplicons satisfying a second set of criteria, wherein the second set of criteria includes amplicons that together comprise at least a minimal threshold number of homopolymers of each homopolymer length between a predetermined minimal homopolymer length and a predetermined maximal homopolymer length for one or more of homopolymer types A, T, C, and G.

Abstract translation: 制备均聚物重校准面板的方法包括：从一组合成中使用的扩增子提取一组满足第一组标准的候选扩增子，其中第一组标准包括已知属于高分子的扩增子 没有变体的参考基因组的自信区; 以及从所述候选扩增子集合中选择满足第二组标准的缩减的扩增子集，其中所述第二组标准包括一起包括至少最小阈值数量的预定最小均聚物之间的每个均聚物长度的均聚物的最小阈值数的扩增子 长度和一种或多种均聚物类型A，T，C和G的预定最大均聚物长度。

公开(公告)号：US20160097091A1

公开(公告)日：2016-04-07

申请号：US14856220

申请日：2015-09-16

Applicant: LIFE TECHNOLOGIES CORPORATION ,  LIFE TECHNOLOGIES GmbH

Inventor： Wolfgang HINZ ,  Peter VANDER HORN ,  Earl HUBBELL ,  Christian WOEHLER

IPC: C12Q1/68

CPC classification number: C12Q1/6869 ,  C12Q1/6874 ,  C12Q2535/113 ,  C12Q2565/519

Abstract: In some embodiments, the disclosure relates generally to methods, as well as compositions, systems, kits and apparatuses, for performing nucleotide incorporation, comprising: (a) providing a surface including one or more reaction sites containing a polymerase and a nucleic acid template that has, or is hybridized to, an extendible end; (b) performing a first nucleotide flow by contacting one or more of the reaction sites with a first solution including one or more types of terminator nucleotide; (c) incorporating at least one type of terminator nucleotide at the extendible end of the nucleic acid template contained within at least one of the reaction sites using the polymerase; and (d) detecting a non-optical signal indicating the nucleotide incorporation using a sensor that is attached or operatively linked to the at least one reaction site.

Abstract translation: 在一些实施方案中，本公开一般涉及用于进行核苷酸掺入的方法以及组合物，系统，试剂盒和装置，其包括：（a）提供包含一个或多个含有聚合酶和核酸模板的反应位点的表面，所述反应位点 已经或被杂交到可延伸的一端; （b）通过使一个或多个所述反应位点与包含一种或多种类型的终止子核苷酸的第一溶液接触来进行第一核苷酸流; （c）使用所述聚合酶在至少一个所述反应位点内的所述核酸模板的可延伸末端掺入至少一种类型的终止子核苷酸; 和（d）使用附着或可操作地连接至少一个反应位点的传感器检测表示核苷酸掺入的非光学信号。

公开(公告)号：US20130090860A1

公开(公告)日：2013-04-11

申请号：US13645058

申请日：2012-10-04

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Marcin SIKORA ,  Earl HUBBELL ,  Simon CAWLEY ,  Christian KOLLER

IPC: G06F19/20

CPC classification number: G16B25/00 ,  G01N27/27 ,  G01N27/4145 ,  G16B30/00

Abstract: A method for nucleic acid sequencing includes: receiving a signal comprising measurements of a parameter measured in response to a plurality of nucleotide flows flowed in a space comprising a sample nucleic acid; normalizing the signal to obtain a normalized signal; adaptively normalizing the normalized signal to obtain an adaptively normalized signal; and predicting a sequence of base calls corresponding to the sample nucleic acid using the adaptively normalized signal.

Abstract translation: 用于核酸测序的方法包括：接收包含响应于在包含样品核酸的空间中流动的多个核苷酸流测量的参数的测量值的信号; 对信号进行归一化以获得归一化信号; 自适应地归一化归一化信号以获得自适应归一化信号; 以及使用自适应归一化信号来预测对应于样本核酸的碱基呼叫序列。

公开(公告)号：US20230360726A1

公开(公告)日：2023-11-09

申请号：US18130134

申请日：2023-04-03

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL ,  Sowmi UTIRAMERUR

IPC: C12Q1/6874 ,  C12Q1/6869 ,  G16B20/20 ,  G16B30/00 ,  G16B40/00

CPC classification number: G16B20/20 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B30/00 ,  G16B40/00

Abstract: A method comprises receiving an ensemble of sequencing reads based on measurements from a plurality of microwells of a sensor array; assigning measured values to the ensemble of sequencing reads; calculating model-predicted values utilizing a predictive model of nucleotide incorporations resulting from flows of nucleotide species according to a predetermined order; modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands, the modifying based on variations between model-predicted values for different hypothesized sequences obtained using the predictive model of nucleotide incorporations resulting from the flows of nucleotide species according to the predetermined order; calculating a measurement confidence value for each read in the ensemble of sequencing reads, the confidence value representing variations between the measured values and the modified model-predicted values; and identifying a plurality of reads in the ensemble as corresponding to a variant sequence.

公开(公告)号：US20230193379A1

公开(公告)日：2023-06-22

申请号：US17811192

申请日：2022-07-07

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Vadim Mozhayskiy ,  Yutao FU ,  Earl HUBBELL

IPC: C12Q1/6874 ,  C12Q1/6825 ,  C12N15/10

CPC classification number: C12Q1/6874 ,  C12Q1/6825 ,  C12N15/1058

Abstract: A method for preparing a homopolymer recalibration panel includes: extracting, from a set of amplicons used in sequencing-by-synthesis, a set of candidate amplicons satisfying a first set of criteria, wherein the first set of criteria includes amplicons known to belong to high-confidence regions of a reference genome with no variants; and selecting, from the set of candidate amplicons, a reduced set of amplicons satisfying a second set of criteria, wherein the second set of criteria includes amplicons that together comprise at least a minimal threshold number of homopolymers of each homopolymer length between a predetermined minimal homopolymer length and a predetermined maximal homopolymer length for one or more of homopolymer types A, T, C, and G.

公开(公告)号：US20210108254A1

公开(公告)日：2021-04-15

申请号：US17025763

申请日：2020-09-18

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL

IPC: C12Q1/6825 ,  C12Q1/6869 ,  C12Q1/6874

Abstract: A method for nucleic acid sequencing may include disposing a plurality of template nucleic acid molecules in a plurality of defined spaces disposed on a sensor array, at least some of the plurality of template nucleic acid molecules having a sequencing primer and a polymerase operably bound therewith; advancing one or more nucleotide species over the plurality of template nucleic acid molecules with the sequencing primer and the polymerase operably bound therewith; measuring a signal generated by nucleotide incorporations resulting from advancing the one or more nucleotide species; and exposing the plurality of template nucleic acid molecules to a cleaving reagent subsequent to the advancing and measuring. The cleaving reagent can remove labeling reagents attached to the one or more nucleotide species. The advancing and measuring steps can be performed for different orders of the one or more nucleotide species prior to a subsequent exposing of the plurality of template nucleic acid molecules to the cleaving reagent.

公开(公告)号：US20190218599A1

公开(公告)日：2019-07-18

申请号：US16362407

申请日：2019-03-22

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL

IPC: C12Q1/6825 ,  C12Q1/6874

CPC classification number: C12Q1/6825 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2533/101 ,  C12Q2565/301 ,  C12Q2565/607

Abstract: A method for nucleic acid sequencing may include disposing a plurality of template nucleic acid molecules in a plurality of defined spaces disposed on a sensor array, at least some of the plurality of template nucleic acid molecules having a sequencing primer and a polymerase operably bound therewith; advancing one or more nucleotide species over the plurality of template nucleic acid molecules with the sequencing primer and the polymerase operably bound therewith; measuring a signal generated by nucleotide incorporations resulting from advancing the one or more nucleotide species; and exposing the plurality of template nucleic acid molecules to a cleaving reagent subsequent to the advancing and measuring. The cleaving reagent can remove labeling reagents attached to the one or more nucleotide species. The advancing and measuring steps can be performed for different orders of the one or more nucleotide species prior to a subsequent exposing of the plurality of template nucleic acid molecules to the cleaving reagent.

公开(公告)号：US20180119217A1

公开(公告)日：2018-05-03

申请号：US15561445

申请日：2016-03-18

Applicant: LIFE TECHNOLOGIES CORPORATION ,  LIFE TECHNOLOGIES GMBH

Inventor： Wolfgang HINZ ,  Steven MENCHEN ,  Ronald GRAHAM ,  Peter VANDER HORN ,  Earl HUBBELL ,  Christian WOEHLER ,  Roman ROZHKOV ,  Barnett ROSENBLUM

IPC: C12Q1/6874

CPC classification number: C12Q1/6874 ,  C12Q2565/607

Abstract: In some embodiments, the disclosure relates generally to methods, as well as related, systems, compositions, kits and apparatuses, for nucleic acid analysis that involve the use of modified nucleotides, including terminator nucleotides and/or tagged nucleotides, in a template-dependent nucleotide incorporation reaction. In some embodiments, the nucleic acid analysis can be conducted at a single reaction site, or at a plurality of reaction sites in an array of reaction sites. Optionally, the array contains a plurality of reaction sites having about 1-100 million, or about 100-250 million, or about 200-500 million, or about 500-900 million, or more reaction sites. Optionally, each reaction site is in contact with, operatively coupled, or capacitively coupled to one or more sensors that are ion-sensitive FETs (isFETs) or chemically-sensitive FETs (chemFETs) sensors. Optionally, the reaction sites are in fluid communication with each other.