公开(公告)号：US20230133734A1

公开(公告)日：2023-05-04

申请号：US17865019

申请日：2023-01-23

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL ,  Jonathan SCHULTZ

IPC: C12Q1/6869 ,  C12Q1/6874

Abstract: A system for nucleic acid sequencing includes a machine-readable memory and a processor configured to execute machine-readable instructions. The instructions, when executed by the processor, cause the system to expose template polynucleotide strands in a plurality of defined spaces of a sensor array to a series of flows of nucleotide species, the series comprising a sequence of random flows; and obtain, for each of the series of flows of nucleotide species, a signal indicative of how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands.

公开(公告)号：US20200216898A1

公开(公告)日：2020-07-09

申请号：US16822220

申请日：2020-03-18

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL

IPC: C12Q1/6874 ,  C12N15/10 ,  B01J19/00 ,  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：US20130231870A1

公开(公告)日：2013-09-05

申请号：US13754566

申请日：2013-01-30

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Charles SUGNET ,  Simon CAWLEY ,  Mohit GUPTA ,  Iztok MARJANOVIC ,  Todd REARICK ,  Mark BEAUCHEMIN ,  Earl HUBBELL

IPC: H03M7/30

CPC classification number: H03M7/30 ,  G06F19/24

Abstract: A compression method includes measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises at least one region associated with expected measured values and at least one region associated with unpredictable measured values; applying a first compression process to the waveform, the first compression process including an averaging of one or more frames in one or more portions of the waveform; and applying a second compression process to the waveform, the second compression process including a truncating of data corresponding to a portion of the waveform that is not related to a nucleotide incorporation component of the waveform.

Abstract translation: 压缩方法包括测量与传感器阵列上发生的化学事件相关联的波形，其中所述波形包括与预期测量值相关联的至少一个区域和与不可预测的测量值相关联的至少一个区域; 对所述波形应用第一压缩处理，所述第一压缩处理包括所述波形的一个或多个部分中的一个或多个帧的平均值; 以及对所述波形应用第二压缩处理，所述第二压缩处理包括对应于与所述波形的核苷酸掺入成分无关的所述波形的一部分的数据的截断。

公开(公告)号：US20250019759A1

公开(公告)日：2025-01-16

申请号：US18782286

申请日：2024-07-24

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL ,  Christian KOLLER ,  Nils HOMER

IPC: C12Q1/6869 ,  G16B30/00

Abstract: A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.

公开(公告)号：US20240309431A1

公开(公告)日：2024-09-19

申请号：US18530606

申请日：2023-12-06

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL

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

CPC classification number: 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：US20200370202A1

公开(公告)日：2020-11-26

申请号：US16893585

申请日：2020-06-05

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL

IPC: C40B20/04 ,  C40B50/16 ,  C40B70/00

Abstract: A method for sequencing a polynucleotide sample having a barcode sequence, includes: introducing a series of nucleotides to the polynucleotide sample according to a predetermined flow ordering; obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-tolerant code capable of distinguishing the barcode sequence from other barcode sequences in the presence of one or more errors.

公开(公告)号：US20200082907A1

公开(公告)日：2020-03-12

申请号：US16561194

申请日：2019-09-05

Applicant: LIFE TECHNOLOGIES CORPORATION

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

IPC: G16B25/00 ,  G16B30/00 ,  G01N27/414

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.

公开(公告)号：US20180330051A1

公开(公告)日：2018-11-15

申请号：US15974976

申请日：2018-05-09

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL ,  Sowmi UTIRAMERUR

IPC: G06F19/22 ,  C12Q1/6874 ,  G06F19/24

CPC classification number: G06F19/22 ,  C12Q1/6874 ,  G06F19/24

Abstract: A method for evaluating variant likelihood includes: providing a plurality of template polynucleotide strands, sequencing primers, and polymerase in a plurality of defined spaces disposed on a sensor array; exposing the plurality of template polynucleotide strands, sequencing primers, and polymerase to a series of flows of nucleotide species according to a predetermined order; obtaining measured values corresponding to an ensemble of sequencing reads for at least some of the template polynucleotide strands in at least one of the defined spaces; and evaluating a likelihood that a variant sequence is present given the measured values corresponding to the ensemble of sequencing reads, the evaluating comprising: determining a measurement confidence value for each read in the ensemble of sequencing reads and modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands.

公开(公告)号：US20170194985A1

公开(公告)日：2017-07-06

申请号：US15368765

申请日：2016-12-05

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Charles Sugnet ,  Simon CAWLEY ,  Mohit GUPTA ,  Iztok MARJANOVIC ,  Todd REARICK ,  Mark BEAUCHEMIN ,  Earl HUBBELL

IPC: H03M7/30 ,  G06F19/24

CPC classification number: H03M7/30 ,  G16B40/00

Abstract: A compression method includes measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises at least one region associated with expected measured values and at least one region associated with unpredictable measured values; applying a first compression process to the waveform, the first compression process including an averaging of one or more frames in one or more portions of the waveform; applying a keyframe delta compression to the frame-averaged data; forming a compressed data structure including a keyframe and calculated differences subsequent to the keyframe; and storing one or more compressed data structures in memory.

公开(公告)号：US20220213544A1

公开(公告)日：2022-07-07

申请号：US17546151

申请日：2021-12-09

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL

IPC: C12Q1/6874 ,  C12N15/10 ,  B01J19/00 ,  C40B20/04 ,  C40B70/00

Abstract: A system for nucleic acid sequencing is provided. The system comprises a sequencing device configured to expose a tagged polynucleotide comprising a combinatorial barcode sequence and a sample polynucleotide to sequential nucleotide flows, each flow comprising one species of nucleotide and the sequential flows being in a predetermined order based on the species of nucleotide such that exposing of the tagged polynucleotide to the sequential nucleotide flows causes incorporations of nucleotides from the sequential nucleotide flows into the tagged polynucleotide over the barcode sequence The sequencing device is configured to detect a series of signals over the barcode sequence resulting from the incorporations, wherein the predetermined order of nucleotide flows comprises a repetition of a flow order motif that is based on a sequence motif. The system comprises a computing device configured to resolve the detected series of signals to determine the combinatorial barcode sequence.