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公开(公告)号：US20110178719A1
公开(公告)日：2011-07-21
申请号：US13057350
申请日：2009-08-04
Applicant: Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Joshua Sweetkind-Singer
Inventor： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Joshua Sweetkind-Singer
CPC classification number: G16B20/00 , C12Q1/6883 , C12Q2600/156 , G16B40/00
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.
Abstract translation: 本文公开了一种用于在一个或一小组细胞中或其中有限数量的遗传数据可用的等位基因调用和用于确定倍性状态的系统和方法。 重建不良或不正确的碱基对，缺失的等位基因和缺失区域，并使用目标基因组与遗传相关个体基因组知识之间的预期相似性来确定单倍型。 在一个实施方案中，使用来自双亲和可能的一个或多个精子和/或同胞胚胎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。 在另一个实施方案中，可以使用相同的输入数据来确定染色体拷贝数。 在另一个实施方案中，进行这些测定用于IVF期间的胚胎选择，用于非侵入性产前诊断或用于进行表型预测。
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公开(公告)号：US20110288780A1
公开(公告)日：2011-11-24
申请号：US13110685
申请日：2011-05-18
Applicant: Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
Inventor： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
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: Methods for non-invasive prenatal ploidy calling are disclosed herein. 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 are disclosed herein. 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: 本文公开了非侵入性产前倍性呼叫的方法。 本文公开了从胎儿母体和胎儿的DNA样本以及来自母亲和任选也来自父亲的基因型数据测量的基因型数据中确定妊娠胎儿染色体倍性状态的方法。 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。
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公开(公告)号：US08825412B2
公开(公告)日：2014-09-02
申请号：US13110685
申请日：2011-05-18
Applicant: Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
Inventor： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
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: Methods for non-invasive prenatal ploidy calling are disclosed herein. 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 are disclosed herein. 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: 本文公开了非侵入性产前倍性呼叫的方法。 本文公开了从胎儿母体和胎儿的DNA样本以及来自母亲和任选也来自父亲的基因型数据测量的基因型数据中确定妊娠胎儿染色体倍性状态的方法。 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。
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公开(公告)号：US20130225422A1
公开(公告)日：2013-08-29
申请号：US13846111
申请日：2013-03-18
Applicant: Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Joshua Sweetkind-Singer
Inventor： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Joshua Sweetkind-Singer
IPC: G06F19/18
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.
Abstract translation: 本文公开了一种用于在一个或一小组细胞中或其中有限数量的遗传数据可用的等位基因调用和用于确定倍性状态的系统和方法。 重建不良或不正确的碱基对，缺失的等位基因和缺失区域，并使用目标基因组与遗传相关个体基因组知识之间的预期相似性来确定单倍型。 在一个实施方案中，使用来自双亲和可能的一个或多个精子和/或同胞胚胎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。 在另一个实施方案中，可以使用相同的输入数据来确定染色体拷贝数。 在另一个实施方案中，进行这些测定用于IVF期间的胚胎选择，用于非侵入性产前诊断或用于进行表型预测。
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公开(公告)号：US20120270212A1
公开(公告)日：2012-10-25
申请号：US13300235
申请日：2011-11-18
Applicant: MATTHEW RABINOWITZ , GEORGE GEMELOS , MILENA BANJEVIC , ALLISON RYAN , ZACHARY DEMKO , MATTHEW HILL , BERNHARD ZIMMERMANN , JOHAN BANER
Inventor： MATTHEW RABINOWITZ , GEORGE GEMELOS , MILENA BANJEVIC , ALLISON RYAN , ZACHARY DEMKO , MATTHEW HILL , BERNHARD ZIMMERMANN , JOHAN BANER
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。
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Patent Agency Ranking
6.发明授权公开(公告)号：US10113196B2
公开(公告)日：2018-10-30
申请号：US13335043
申请日：2011-12-22
Applicant: Allison Ryan , Styrmir Sigurjonsson , Milena Banjevic , George Gemelos , Matthew Hill , Johan Baner , Matthew Rabinowitz , Zachary Demko
Inventor： Allison Ryan , Styrmir Sigurjonsson , Milena Banjevic , George Gemelos , Matthew Hill , Johan Baner , Matthew Rabinowitz , Zachary Demko
IPC: C12Q1/6869 , C12Q1/6876 , G06F19/14
Abstract: Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.
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公开(公告)号：US20130261004A1
公开(公告)日：2013-10-03
申请号：US13846160
申请日：2013-03-18
Applicant: Allison Ryan , Styrmir Sigurjonsson , Milena Banjevic , George Gemelos , Matthew Hill , Johan Baner , Matthew Rabinowitz , Zachary Demko
Inventor： Allison Ryan , Styrmir Sigurjonsson , Milena Banjevic , George Gemelos , Matthew Hill , Johan Baner , Matthew Rabinowitz , Zachary Demko
IPC: C12Q1/68
CPC classification number: C12Q1/6869 , C12Q1/6876 , C12Q2600/156 , G16B10/00
Abstract: Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.
Abstract translation: 本文公开了非侵入性产前亲子鉴定的方法。 该方法使用从怀孕母亲获得的血浆进行的遗传测量，以及所称父亲的遗传测量以及母亲的遗传测量，以确定所称父亲是否是胎儿的生物之父。 这通过基于信息学的方法来实现，该方法可以将母体血浆中发现的胎儿DNA的遗传指纹与所称父亲的遗传指纹进行比较。
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公开(公告)号：US20130178373A1
公开(公告)日：2013-07-11
申请号：US13791397
申请日：2013-03-08
Applicant: Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
Inventor： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
IPC: C12Q1/68
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.
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公开(公告)号：US20120122701A1
公开(公告)日：2012-05-17
申请号：US13335043
申请日：2011-12-22
Applicant: Allison Ryan , Styrmir Sigurjonsson , Milena Banjevic , George Gemelos , Matthew Hill , Johan Baner , Matthew Rabinowitz , Zachary Demko
Inventor： Allison Ryan , Styrmir Sigurjonsson , Milena Banjevic , George Gemelos , Matthew Hill , Johan Baner , Matthew Rabinowitz , Zachary Demko
CPC classification number: C12Q1/6869 , C12Q1/6876 , C12Q2600/156 , G06F19/14
Abstract: Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.
Abstract translation: 本文公开了非侵入性产前亲子鉴定的方法。 该方法使用从怀孕母亲获得的血浆进行的遗传测量，以及所称父亲的遗传测量以及母亲的遗传测量，以确定所称父亲是否是胎儿的生物之父。 这通过基于信息学的方法来实现，该方法可以将母体血浆中发现的胎儿DNA的遗传指纹与所称父亲的遗传指纹进行比较。
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公开(公告)号：US10017812B2
公开(公告)日：2018-07-10
申请号：US13300235
申请日：2011-11-18
Applicant: Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
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 , C12Q1/6869 , C12Q1/6827 , G06F19/18 , C12Q1/6883 , C12Q1/6862 , G06F19/24
CPC classification number: C12Q1/6869 , C12Q1/6806 , C12Q1/6827 , C12Q1/686 , C12Q1/6862 , C12Q1/6874 , C12Q1/6883 , C12Q2600/156 , C12Q2600/16 , G06F19/34 , G16B20/00 , G16B40/00 , C12Q2537/161 , C12Q2537/165 , C12Q2537/143
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.
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