公开(公告)号：US10984888B2

公开(公告)日：2021-04-20

申请号：US14428312

申请日：2013-09-13

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Nivedita Sumi Majumdar ,  Thomas Wessel ,  David C. Woo ,  Marcin Sikora ,  Gordon A. Janaway ,  Shweta Raizada ,  Joanna Lankester ,  Jeffrey A. Marks ,  Daniel Wessel

IPC: G16B25/00 ,  G16B40/00 ,  C12Q1/686

Abstract: A computer-implemented method for designing a digital PCR (dPCR) experiment is provided. The method includes receiving, from a user, a selection of optimization type. The optimization type may be maximizing the dynamic range, minimizing the number of substrates including reaction sites needed for the experiment, determining a dilution factor, or determining the lower limit of detection, for example. The method further includes receiving, from the user, a precision measure for an experiment, and a minimum concentration of a target in a reaction site for the experiment. The method also includes determining a set of dPCR experiment design factors for the experiment based on the optimization type. The set of dPCR experiment design factors is then displayed to the user.

公开(公告)号：US20180157788A1

公开(公告)日：2018-06-07

申请号：US15889177

申请日：2018-02-05

Applicant: Life Technologies Corporation

Inventor： Marcin Sikora

IPC: G06F19/18 ,  G06F17/30 ,  G06F19/24

CPC classification number: G16B20/00 ,  G06F16/24 ,  G16B40/00

Abstract: Methods and systems for the analysis of genotyping data are presented. According to various embodiments of methods and systems, an angle configuration search may be performed. In various embodiments, an exhaustive search over the entirety of an angle configuration space may be performed to provide a fit to a plurality of angles determined for a plurality of points in a data set generated from a plurality of biological samples. For various embodiments, the angle configuration space may be defined to ensure that a global fit may be determined. According to various methods and systems, a data base of possible angle configurations may be searched, in which each angle configuration may include three angles. According to various methods and systems, a data base of possible angle configurations may include for each angle configuration a probability that the angle configuration may occur.

公开(公告)号：US20250061970A1

公开(公告)日：2025-02-20

申请号：US18816167

申请日：2024-08-27

Applicant: Life Technologies Corporation

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

IPC: G16B30/10 ,  G16B20/20 ,  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：US11453912B2

公开(公告)日：2022-09-27

申请号：US16364336

申请日：2019-03-26

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Melville Davey ,  Michael Meyer ,  Marcin Sikora ,  Simon Cawley ,  Kirk Pastorian

IPC: C12Q1/6874 ,  G16B30/00 ,  G16B99/00

Abstract: A method of estimating a parameter related to sequencing of a sample nucleic acid template includes: receiving signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto an array of wells including (i) a first well containing the sample nucleic acid template and (ii) a plurality of other sample-containing wells; determining sequence information for the sample nucleic acid template using signal data from the first well; and constructing a phase-state model for a set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter that is determined using signal data from the plurality of other sample-containing wells.

公开(公告)号：US10760125B2

公开(公告)日：2020-09-01

申请号：US15923633

申请日：2018-03-16

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Marcin Sikora

IPC: C12Q1/6874 ,  G16B30/00

Abstract: A method for designing test or control sequences may include identifying, using a variant caller, loci with systematic errors present in a plurality of sequencing runs included in a training set of sequencing runs obtained using sequencing-by-synthesis; and selecting a representative set of loci, including selecting from the identified loci an approximately equal number of loci involving errors in A, T, C, and G homopolymers and selecting from the identified loci an approximately equal number of loci involving homopolymers having a length of two, three, and four.

公开(公告)号：US10273540B2

公开(公告)日：2019-04-30

申请号：US13967665

申请日：2013-08-15

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Melville Davey ,  Michael Meyer ,  Marcin Sikora ,  Simon Cawley ,  Kirk Pastorian

IPC: G06F19/10 ,  C12Q1/6874

Abstract: A method of estimating a parameter related to sequencing of a sample nucleic acid template includes: receiving signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto an array of wells including (i) a first well containing the sample nucleic acid template and (ii) a plurality of other sample-containing wells; determining sequence information for the sample nucleic acid template using signal data from the first well; and constructing a phase-state model for a set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter that is determined using signal data from the plurality of other sample-containing wells.

公开(公告)号：US20210313010A1

公开(公告)日：2021-10-07

申请号：US17207488

申请日：2021-03-19

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Nivedita Sumi Majumdar ,  Thomas Wessel ,  David C. Woo ,  Marcin Sikora ,  Gordon A. Janaway ,  Shweta Raizada ,  Joanna Lankester ,  Jeffrey A. Marks ,  Daniel Wessel

IPC: G16B25/20 ,  G16B25/00 ,  G16B40/00 ,  C12Q1/686

Abstract: A computer-implemented method for designing a digital PCR (dPCR) experiment is provided. The method includes receiving, from a user, a selection of optimization type. The optimization type may be maximizing the dynamic range, minimizing the number of substrates including reaction sites needed for the experiment, determining a dilution factor, or determining the lower limit of detection, for example. The method further includes receiving, from the user, a precision measure for an experiment, and a minimum concentration of a target in a reaction site for the experiment. The method also includes determining a set of dPCR experiment design factors for the experiment based on the optimization type. The set of dPCR experiment design factors is then displayed to the user.

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.