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    SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA FROM TARGET INDIVIDUALS USING GENETIC DATA FROM GENETICALLY RELATED INDIVIDUALS
    43.
    发明申请
    SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA FROM TARGET INDIVIDUALS USING GENETIC DATA FROM GENETICALLY RELATED INDIVIDUALS 有权
    使用遗传资料从遗传相关个体清除目标个体的噪声遗传数据的系统和方法

    公开(公告)号：US20170029893A1

    公开(公告)日：2017-02-02

    申请号：US15293257

    申请日：2016-10-13

    Applicant: Natera, Inc.

    Inventor： Matthew Rabinowitz ,  Milena Banjevic ,  Zachary Demko ,  David Johnson

    IPC: C12Q1/68 ,  G06F19/22

    CPC classification number: C12Q1/6883 ,  C12Q1/6827 ,  C12Q1/6876 ,  C12Q2600/118 ,  C12Q2600/156 ,  C12Q2600/158 ,  G06F19/18 ,  G06F19/20 ,  G06F19/22 ,  G06F19/24 ,  C12Q2537/16 ,  C12Q2537/165

    Abstract: A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

    Abstract translation: 公开了一种用于确定一个或一小组细胞遗传数据的系统和方法，或从有限数量的遗传数据获得的片段DNA。 使用已知方法获取和扩增目标个体的遗传数据，并且使用目标基因组与基因相关受试者的基因组之间的预期相似性重建差测量的碱基对，缺失的等位基因和缺失区域。 根据本发明的一个实施方案，从母体血液中分离的胚胎细胞，胎儿细胞或无细胞胎儿DNA获得不完整的遗传数据，并且使用更大的样本的更完整的遗传数据来重建不完整的遗传数据 来自一个或两个父母的二倍体细胞，具有或不具有来自一个或两个亲本的单倍体细胞的遗传数据和/或从其他相关个体获取的遗传数据。

    Methods for non-invasive prenatal ploidy calling
    47.
    发明授权
    Methods for non-invasive prenatal ploidy calling 有权
    非侵入性产前倍性调用方法

    公开(公告)号：US09228234B2

    公开(公告)日：2016-01-05

    申请号：US14080656

    申请日：2013-11-14

    Applicant: Natera, Inc.

    Inventor： Matthew Rabinowitz ,  Allison Ryan ,  George Gemelos ,  Milena Banjevic ,  Zachary Demko

    IPC: G01N33/48 ,  G01N31/00 ,  G06G7/48 ,  G06G7/58 ,  C12Q1/68 ,  G06F19/18

    CPC classification number: G06F19/22 ,  C12Q1/6827 ,  C12Q1/6874 ,  C12Q1/6876 ,  C12Q1/6883 ,  C12Q2600/156 ,  C12Q2600/16 ,  G06F19/18 ,  G06N7/005 ,  C12Q2537/16 ,  C12Q2537/165

    Abstract: Disclosed herein are methods for determining the copy number of a chromosome in a fetus in the context of non-invasive prenatal diagnosis. In an embodiment, the measured genetic data from a sample of genetic material that contains both fetal DNA and maternal DNA is analyzed, along with the genetic data from the biological parents of the fetus, and the copy number of the chromosome of interest is determined. In an embodiment, the maternal serum is measured using a single-nucleotide polymorphism (SNP) microarray, along with parental genomic data, and the determination of the chromosome copy number is used to make clinical decisions pertaining to the fetus.

    Abstract translation: 本文公开了用于在非侵入性产前诊断的上下文中确定胎儿中染色体的拷贝数的方法。 在一个实施方案中，分析来自含有胎儿DNA和母体DNA的遗传物质的样品的测量的遗传数据以及来自胎儿的生物亲本的遗传数据，并确定感兴趣的染色体的拷贝数。 在一个实施方案中，使用单核苷酸多态性（SNP）微阵列以及亲本基因组数据测量母体血清，并且使用染色体拷贝数的确定来进行与胎儿有关的临床决定。

    Methods for non-invasive prenatal ploidy calling
    48.
    发明授权
    Methods for non-invasive prenatal ploidy calling 有权
    非侵入性产前倍性调用方法

    公开(公告)号：US09163282B2

    公开(公告)日：2015-10-20

    申请号：US13791397

    申请日：2013-03-08

    Applicant: Natera, Inc.

    Inventor： Matthew Rabinowitz ,  George Gemelos ,  Milena Banjevic ,  Allison Ryan ,  Zachary Demko ,  Matthew Hill ,  Bernhard Zimmermann ,  Johan Baner

    IPC: G01N33/48 ,  G01N31/00 ,  G06G7/48 ,  G06G7/58 ,  C12Q1/68 ,  G06F19/18 ,  G06F19/24

    CPC classification number: C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/6862 ,  C12Q1/6874 ,  C12Q1/6883 ,  C12Q2600/156 ,  G06F19/18 ,  G06F19/24 ,  C12Q2537/161 ,  C12Q2537/165

    Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

    Abstract translation: 本公开提供了从包括来自胎儿母体和胎儿的DNA的DNA的混合样品测量的基因型数据以及任选地来自母体的基因型数据以及任选地从胎儿的基因型数据确定胎儿胎儿的染色体的倍性状态的方法 父亲。 通过使用联合分布模型来确定给定父母基因型数据的不同可能胎儿倍性状态的多个预期等位基因分布，并将预期等位基因分布与混合样品中测量的等位基因分布的模式进行比较来确定倍性状态， 并选择其预期等位基因分布模式与观察到的等位基因分布模式最接近的倍性状态。 DNA的混合样品可以以使等位基因偏倚最小化的方式优先富集在多个多态性位点，例如使用大规模复用的靶向PCR。

    SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA AND DETERMINING CHROMOSOME COPY NUMBER
    49.
    发明申请
    SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA AND DETERMINING CHROMOSOME COPY NUMBER 审中-公开
    用于清除噪声遗传数据和确定染色体拷贝数的系统和方法

    公开(公告)号：US20140032128A1

    公开(公告)日：2014-01-30

    申请号：US13949212

    申请日：2013-07-23

    Applicant: Natera, Inc.

    Inventor： Matthew Rabinowitz ,  Milena Banjevic ,  Zachary Demko ,  David Johnson ,  Dusan Kijacic ,  Dimitri Petrov ,  Joshua Sweetkind-Singer ,  Jing Xu

    IPC: G06F19/16

    CPC classification number: G06F19/16 ,  C12Q1/6855 ,  C12Q1/6874 ,  G06F19/18 ,  G06F19/24 ,  G06Q50/22

    Abstract: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.

    Abstract translation: 本文公开了一种系统和方法，用于增加测量的遗传数据的保真度，进行等位基因调用，并确定在一组或一组细胞中或从片段DNA中确定非整倍体的状态，其中有限数量的遗传数据 是可用的 使用目标基因组与遗传相关个体的基因组之间的预期相似性来重建差或不正确测量的碱基对，缺失的等位基因和缺失区域。 根据一个实施方案，使用来自一个或两个亲本的二倍体细胞的较大样本的更完整的遗传数据，在多个基因座重建来自胚胎细胞的不完全遗传数据，具有或不具有来自一个或两个亲本的单倍体遗传数据 。 在另一个实施方案中，可以从测量的遗传数据确定染色体拷贝数，具有或不具有来自一个或两个亲本的遗传信息。

    Informatics Enhanced Analysis of Fetal Samples Subject to Maternal Contamination
    50.
    发明申请
    Informatics Enhanced Analysis of Fetal Samples Subject to Maternal Contamination 审中-公开
    母亲污染胎儿样本的信息学增强分析

    公开(公告)号：US20130196862A1

    公开(公告)日：2013-08-01

    申请号：US13780022

    申请日：2013-02-28

    Applicant: Natera, Inc.

    Inventor： Matthew Rabinowitz ,  Johan Baner ,  George Gemelos ,  Mathew M. Hill ,  Stymir Sigurjonsson

    IPC: C12Q1/68

    CPC classification number: C12Q1/6883 ,  C12Q1/6881 ,  C12Q2600/156 ,  G16B20/00

    Abstract: The invention provides methods for chromosome copy number calling on genetic samples, such as fetal samples subject to contamination from maternal DNA. The present disclosure provides methods for determining the ploidy status of a chromosome in a fetus (such as a gestating fetus or a POC sample) from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. In some embodiments, the ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

    Abstract translation: 本发明提供了染色体拷贝数调用基因样品的方法，例如受母体DNA污染的胎儿样品。 本公开提供了从包含来自胎儿母体和胎儿的DNA的DNA的混合样品测量的基因型数据中确定胎儿（例如胎儿胎儿或POC样品）中染色体的倍性状态的方法 ，以及来自母亲和父亲的基因型数据。 在一些实施方案中，通过使用联合分布模型来确定给定父母基因型数据的不同可能的胎儿倍性状态的多个预期等位基因分布，并将预期的等位基因分布与所测量的等位基因分布的模式进行比较来确定倍性状态 混合样品，并选择其预期等位基因分布模式与观察到的等位基因分布模式最为匹配的倍性状态。 DNA的混合样品可以以使等位基因偏倚最小化的方式优先富集在多个多态性位点，例如使用大规模复用的靶向PCR。

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