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    Methods for non-invasive prenatal ploidy calling
    11.
    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。

    METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING
    16.
    发明申请
    METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING 审中-公开

    公开(公告)号：US20190256908A1

    公开(公告)日：2019-08-22

    申请号：US16399991

    申请日：2019-04-30

    Applicant: Natera, Inc.

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

    IPC: C12Q1/6869 ,  C12Q1/6862 ,  C12Q1/6806 ,  G16B20/00 ,  C12Q1/6827 ,  C12Q1/6874 ,  C12Q1/6883

    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
    17.
    发明授权
    Methods for allele calling and ploidy calling 有权

    公开(公告)号：US09639657B2

    公开(公告)日：2017-05-02

    申请号：US13846111

    申请日：2013-03-18

    Applicant: Natera, Inc.

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

    IPC: G01N33/50 ,  G06F19/18 ,  C12Q1/68 ,  G06F19/24

    CPC classification number: G06F19/18 ,  C12Q1/6883 ,  C12Q2600/156 ,  G06F19/24

    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
    18.
    发明申请
    METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING 审中-公开
    非侵入式预防性呼吸方法

    公开(公告)号：US20170011166A1

    公开(公告)日：2017-01-12

    申请号：US15273332

    申请日：2016-09-22

    Applicant: Natera, Inc.

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

    IPC: G06F19/18 ,  G06F19/22 ,  C12Q1/68 ,  G06N7/00

    CPC classification number: G16B30/00 ,  C12Q1/6827 ,  C12Q1/6874 ,  C12Q1/6876 ,  C12Q1/6883 ,  C12Q2600/156 ,  C12Q2600/16 ,  G06N7/005 ,  G16B20/00 ,  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。

    SYSTEMS AND METHODS FOR DETERMINING ANEUPLOIDY RISK USING SAMPLE FETAL FRACTION
    19.
    发明申请
    SYSTEMS AND METHODS FOR DETERMINING ANEUPLOIDY RISK USING SAMPLE FETAL FRACTION 审中-公开
    使用样品场分析确定异常风险的系统和方法

    公开(公告)号：US20160371428A1

    公开(公告)日：2016-12-22

    申请号：US15186774

    申请日：2016-06-20

    Applicant: Natera, Inc.

    Inventor： Allison Ryan ,  Katie Kobara ,  Zachary Demko ,  Susan J. Gross

    IPC: G06F19/18 ,  C12Q1/68

    CPC classification number: G16B20/00 ,  C12Q1/6869 ,  C12Q1/6883

    Abstract: Disclosed herein are system, method, and computer program product embodiments for determining aneuploidy risk in a target sample of maternal blood or plasma based on the amount of fetal DNA. An embodiment operates by receiving known genetic data from known prenatal testing samples and genetic data for the target sample. A fetal fraction distribution is determined for the known genetic data based on gestational age and the maternal weight associated with the target sample. A model is then generated based on a fixed ratio reduction of the determined fetal fraction distribution. A fetal fraction based data likelihood for the target sample is then determined for each of the plurality of ploidy states using the generated model. An aneuploidy risk score is then outputted based on applying a Bayesian probability determination that combines each fetal fraction based data likelihood with a previously determined risk score as a conditional value.

    Abstract translation: 本文公开了基于胎儿DNA的量来确定母体血液或血浆的目标样品中非整倍体风险的系统，方法和计算机程序产品实施方案。 一个实施例通过从已知的产前测试样品和目标样品的遗传数据接收已知的遗传数据来操作。 基于孕龄和与目标样本相关的母体重量，确定已知遗传数据的胎儿分数分布。 然后基于确定的胎儿分数分布的固定比例减少产生模型。 然后使用所生成的模型，针对多个倍性状态中的每一个确定目标样本的基于胎儿分数的数据可能性。 然后基于应用将每个基于胎儿分数的数据可能性与先前确定的风险评分相结合的贝叶斯概率确定作为条件值来输出非整倍体风险评分。

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