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    Methods for non-invasive prenatal ploidy calling
    71.
    发明授权
    Methods for non-invasive prenatal ploidy calling 有权

    公开(公告)号：US10174369B2

    公开(公告)日：2019-01-08

    申请号：US15917383

    申请日：2018-03-09

    Applicant: Natera, Inc.

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

    IPC: G01N33/48 ,  C12Q1/6869 ,  C12Q1/6827 ,  G06F19/18 ,  C12Q1/6883 ,  C12Q1/6862 ,  C12Q1/6806 ,  C12Q1/6874 ,  G06F19/24

    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.

    METHODS FOR ALLELE CALLING AND PLOIDY CALLING
    74.
    发明申请
    METHODS FOR ALLELE CALLING AND PLOIDY CALLING 审中-公开

    公开(公告)号：US20160371432A1

    公开(公告)日：2016-12-22

    申请号：US15257836

    申请日：2016-09-06

    Applicant: Natera, Inc.

    Inventor： Matthew Rabinowitz ,  George Gemelos ,  Milena Banjevic ,  Allison Ryan ,  Joshua Sweetkind-Singer

    IPC: G06F19/24 ,  G06F19/22 ,  G06F19/18 ,  C12Q1/68

    CPC classification number: G16B40/00 ,  C12Q1/6827 ,  C12Q1/6883 ,  C12Q2600/156 ,  G16B20/00 ,  G16B30/00 ,  C12Q2537/16

    Abstract: Disclosed herein is a system and method for making allele calls, and for determining the ploidy state, in one or a small set of cells, or where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed and the haplotypes are determined using expected similarities between the target genome and the knowledge of the genomes of genetically related individuals. In one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the genetic data from both parents, and possibly one or more sperm and/or sibling embryos. In another embodiment, the chromosome copy number can be determined using the same input data. In another embodiment, these determinations are made for embryo selection during IVF, for non-invasive prenatal diagnosis, or for making phenotypic predictions.

    Methods for non-invasive prenatal ploidy calling
    78.
    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：US08949036B2

    公开(公告)日：2015-02-03

    申请号：US14100928

    申请日：2013-12-09

    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 ,  G06F19/12 ,  G06F19/22

    CPC classification number: C12Q1/6883 ,  C12Q1/6827 ,  C12Q1/6869 ,  C12Q2537/161 ,  C12Q2537/165 ,  C12Q2600/112 ,  C12Q2600/156 ,  C12Q2600/16 ,  C12Q2600/172 ,  G06F19/00 ,  G06F19/12 ,  G06F19/18 ,  G06F19/22 ,  G06F19/34 ,  G16H50/30

    Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a sample of DNA from the mother of the fetus and from the fetus, and from genotypic data from the mother and optionally also from the father. The ploidy state is determined by using a joint distribution model to create a set 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. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias.

    Abstract translation: 本公开提供了用于从胎儿母体和胎儿的DNA样品测量的基因型数据以及来自母亲的基因型数据以及任选地还可以从父亲的基因型数据确定胎儿胎儿中染色体的倍性状态的方法 。 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一组预期等位基因分布，并将预期等位基因分布与在混合样品中测量的测量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。 在一个实施方案中，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位点。

    Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data
    80.
    发明申请
    Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data 审中-公开
    使用父母马赛克数据进行非侵入性产前检测的方法

    公开(公告)号：US20140100126A1

    公开(公告)日：2014-04-10

    申请号：US13970436

    申请日：2013-08-19

    Applicant: Natera, Inc.

    Inventor： Matthew Rabinowitz

    IPC: C12Q1/68

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

    Abstract: Provided herein are methods for determining the ploidy state of one or more chromosome in a developing fetus. The subject methods provide for increase accuracy by utilizing information about the mosaicism level of one or more chromosomes of interest in the mother of fetus. The mosaicism level of one or more chromosomes of interest is determine for the maternal tissue that is used as the source of nucleic acid for genetic analysis that are used to determine the ploidy state of the fetal chromosome or chromosomes of interest. For example, if 5% white blood cells of mother are missing a copy of the X chromosome, this information can be used when determining fetal ploidy level, rather than operating under the assumption that the maternal X chromosome are present in two copies. Utilization of the mosaicism data can be used to increase the reliability and accuracy of the determination of the ploidy state of a chromosome of interest.

    Abstract translation: 本文提供了确定发育中的胎儿中一种或多种染色体的倍性状态的方法。 主题方法通过利用关于胎儿母亲感兴趣的一种或多种染色体的嵌合水平的信息来提高准确度。 确定感兴趣的一个或多个染色体的母体组织，其用作用于确定胎儿染色体或感兴趣染色体的倍性状态的用于遗传分析的核酸来源的母体组织。 例如，如果母亲的5％白细胞缺少X染色体的拷贝，则可以在确定胎儿倍性水平时使用该信息，而不是在假设母体X染色体存在于两个拷贝中的情况下进行操作。 镶嵌数据的利用可用于增加感兴趣的染色体的倍性状态的确定的可靠性和准确性。

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