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    SYSTEMS AND METHODS FOR GENOTYPING BY ANGLE CONFIGURATION SEARCH
    2.
    发明申请
    SYSTEMS AND METHODS FOR GENOTYPING BY ANGLE CONFIGURATION SEARCH 审中-公开

    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.

    Control nucleic acid sequences for use in sequencing-by-synthesis and methods for designing the same
    5.
    发明授权
    Control nucleic acid sequences for use in sequencing-by-synthesis and methods for designing the same 有权

    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.

    Methods and systems for modeling phasing effects in sequencing using termination chemistry
    8.
    发明授权
    Methods and systems for modeling phasing effects in sequencing using termination chemistry 有权

    公开(公告)号：US11636922B2

    公开(公告)日：2023-04-25

    申请号：US16550374

    申请日：2019-08-26

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Christian Koller ,  Marcin Sikora ,  Peter Vander Horn

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

    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.

    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING
    10.
    发明申请
    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING 审中-公开

    公开(公告)号：US20190170680A1

    公开(公告)日：2019-06-06

    申请号：US16196502

    申请日：2018-11-20

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Marcin Sikora ,  Melville Davey ,  Christian Koller ,  Simon Cawley ,  Alan Williams ,  David Kulp

    IPC: G01N27/414 ,  G16B30/00

    Abstract: A method for nucleic acid sequencing includes receiving a plurality of observed or measured signals indicative of a parameter observed or measured for a plurality of defined spaces; determining, for at least some of the defined spaces, whether the defined space comprises one or more sample nucleic acids; processing, for at least some of the defined spaces, the observed or measured signal to improve a quality of the observed or measured signal; generating, for at least some of the defined spaces, a set of candidate sequences of bases for the defined space using one or more metrics adapted to associate a score or penalty to the candidate sequences of bases; and selecting the candidate sequence leading to a highest score or a lowest penalty as corresponding to the correct sequence for the one or more sample nucleic acids in the defined space.

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