公开(公告)号：US20230348966A1

公开(公告)日：2023-11-02

申请号：US18297049

申请日：2023-04-07

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl Hubbell ,  Christian Koller ,  Nils Homer

IPC: C12Q1/6869 ,  G16B30/00

CPC classification number: C12Q1/6869 ,  G16B30/00 ,  C12Q2535/122

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：US20210217491A1

公开(公告)日：2021-07-15

申请号：US17248083

申请日：2021-01-08

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sowmi Utiramerur ,  Dumitru Brinza ,  Marcin Sikora ,  Christian Koller ,  Earl Hubbell ,  Chantal Roth ,  Rajesh Gottimukkala

IPC: G16B30/00 ,  G16B20/20

Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.

公开(公告)号：US10410739B2

公开(公告)日：2019-09-10

申请号：US14506520

申请日：2014-10-03

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Christian Koller ,  Marcin Sikora ,  Peter Vander Horn

IPC: G16B40/10 ,  C12Q1/6869 ,  G16B30/00 ,  G16B5/00 ,  G16B20/00 ,  G16B25/00

Abstract: A method for nucleic acid sequencing includes receiving observed or measured nucleic acid sequencing data from a sequencing instrument that receives and processes a sample nucleic acid in a termination sequencing-by-synthesis process. The method also includes generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for candidate sequences using a simulation framework. The simulation framework incorporates an estimated carry forward rate (CFR), an estimated incomplete extension rate (IER), an estimated droop rate (DR), an estimated reactivated molecules rate (RMR), and an estimated termination failure rate (TFR), the RMR being greater than or equal to zero and the TFR being lesser than one. The method also includes identifying, from the set of candidate sequences of bases, one candidate sequence leading to optimization of a solver function as corresponding to the sequence for the sample nucleic acid.

公开(公告)号：US10329608B2

公开(公告)日：2019-06-25

申请号：US14048843

申请日：2013-10-08

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl Hubbell ,  Christian Koller ,  Nils Homer

IPC: C12Q1/6869

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：US20180068061A1

公开(公告)日：2018-03-08

申请号：US15672865

申请日：2017-08-09

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sowmi Utiramerur ,  Dumitru Brinza ,  Marcin Sikora ,  Christian Koller ,  Earl Hubbell ,  Chantal Roth ,  Rajesh Gottimukkala

IPC: G06F19/22

CPC classification number: G16B30/00

Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.