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：US10557174B2

公开(公告)日：2020-02-11

申请号：US15080801

申请日：2016-03-25

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Gordon A. Janaway ,  Mark Andersen ,  Kornelija Zgonc ,  Michael C. Pallas ,  Marcin Sikora ,  Casey R. McFarland ,  Ferrier N. Le ,  Haopeng Wang ,  Jian Gong ,  Gothami Padmabandu

IPC: C12Q1/6886 ,  C12Q1/686 ,  G01N21/64

Abstract: Methods and systems for quantification of a target nucleic acid in a sample are provided. The method includes forming a plurality of discrete sample portions. Each of the plurality of discrete sample portions comprising a portion of the sample, and a reaction mixture. The method further includes amplifying the plurality of discrete sample portions to form a plurality of discrete processed sample portions. At least one discrete processed sample portion containing nucleic acid amplification reaction products. Fluorescence signals are detected from the at least one of the plurality of discrete processed sample portions to determine a presence of the at least one target nucleic acid. The method also includes determining the respective volumes of the plurality of the plurality of discrete processed sample portions, and estimating the number of copies-per-unit-volume of the at least one target nucleic acid in the sample. Estimating the number of copies-per-unit-volume is based on the number of discrete processed sample portions determined to contain the at least one target nucleic acid therein.

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：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.

公开(公告)号：US20160188795A1

公开(公告)日：2016-06-30

申请号：US14952001

申请日：2015-11-25

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Marcin Sikora ,  Alan BLANCHARD

IPC: G06F19/22 ,  C12Q1/68

CPC classification number: G16B25/00 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B30/00 ,  G16B99/00 ,  C12Q2565/102 ,  C12Q2521/501

Abstract: Disclosed are systems and methods for polynucleotide sequencing where detection and correction of base calling errors can be achieved without reliance on a reference sequence. In certain embodiments, redundant information can be introduced during measurement so as to allow such detection of errors. Such redundant information and measurements can be facilitated by encoding of nucleotide sequence being measured. Various examples of such encoding, redundancy introduction, and decoding are provided.

公开(公告)号：US20160188794A1

公开(公告)日：2016-06-30

申请号：US14951964

申请日：2015-11-25

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Marcin Sikora ,  Alan Blanchard

IPC: G06F19/20

CPC classification number: G16B25/00 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B30/00 ,  G16B99/00 ,  C12Q2565/102 ,  C12Q2521/501

Abstract: Disclosed are systems and methods for polynucleotide sequencing where detection and correction of base calling errors can be achieved without reliance on a reference sequence. In certain embodiments, redundant information can be introduced during measurement so as to allow such detection of errors. Such redundant information and measurements can be facilitated by encoding of nucleotide sequence being measured. Various examples of such encoding, redundancy introduction, and decoding are provided.

Abstract translation: 公开了用于多核苷酸测序的系统和方法，其中可以在不依赖参考序列的情况下实现基本呼叫错误的检测和校正。 在某些实施例中，可以在测量期间引入冗余信息，以允许这种错误检测。 可以通过编码被测量的核苷酸序列来促进这种冗余信息和测量。 提供了这种编码，冗余引入和解码的各种示例。