公开(公告)号：US20230131684A1

公开(公告)日：2023-04-27

申请号：US17929782

申请日：2022-09-06

Applicant: LIFE TECHNOLOGIES CORPORATION

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

IPC: C12Q1/6874 ,  G16B30/00

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：US11474070B2

公开(公告)日：2022-10-18

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 ,  G16B30/10 ,  C12Q1/6869 ,  G01N27/27 ,  G16B30/20

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.

公开(公告)号：US11227668B2

公开(公告)日：2022-01-18

申请号：US15889177

申请日：2018-02-05

Applicant: Life Technologies Corporation

Inventor： Marcin Sikora

IPC: G16B20/20 ,  G06F16/24 ,  G16B20/00 ,  G16B40/30 ,  G16B40/20 ,  G16B40/00 ,  G16B20/40

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：US20150278437A1

公开(公告)日：2015-10-01

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: G06F19/20 ,  C12Q1/68

CPC classification number: G16B25/00 ,  C12Q1/686 ,  G16B40/00

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.

Abstract translation: 提供了一种用于设计数字PCR（dPCR）实验的计算机实现方法。 该方法包括从用户接收优化类型的选择。 优化类型可以使动态范围最大化，例如最小化包括实验所需的反应位点，确定稀释因子或确定检测下限的底物数量。 该方法还包括从用户接收实验的精确度量，以及用于实验的反应部位中靶的最小浓度。 该方法还包括基于优化类型确定实验的一组dPCR实验设计因子。 然后将该组dPCR实验设计因子显示给用户。

公开(公告)号：US20140365141A1

公开(公告)日：2014-12-11

申请号：US14463536

申请日：2014-08-19

Applicant: Life Technologies Corporation

Inventor： Marcin Sikora

IPC: G06F19/18 ,  G06F17/30

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.

Abstract translation: 提出了分析基因分型数据的方法和系统。 根据方法和系统的各种实施例，可以执行角度配置搜索。 在各种实施例中，可以执行整个角度配置空间的详尽搜索，以提供对从多个生物样本产生的数据集中的多个点确定的多个角度的拟合。 对于各种实施例，可以定义角度配置空间以确保可以确定全局拟合。 根据各种方法和系统，可以搜索可能的角度配置的数据库，其中每个角度配置可以包括三个角度。 根据各种方法和系统，可能的角度配置的数据库可以包括对于每个角度配置可能发生角度配置的概率。