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1. 发明申请

WO2011146632A1 METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING 审中-公开
标题翻译：非侵入式预防性呼吸方法
公开(公告)号：WO2011146632A1
公开(公告)日：2011-11-24
申请号：PCT/US2011/037018
申请日：2011-05-18
申请人： GENE SECURITY NETWORK INC. , RABINOWITZ, Matthew , GEMELOS, George , BANJEVIC, Milena , RYAN, Allison , DEMKO, Zachary , HILL, Matthew , ZIMMERMANN, Bernhard , BANER, Johan
发明人： RABINOWITZ, Matthew , GEMELOS, George , BANJEVIC, Milena , RYAN, Allison , DEMKO, Zachary , HILL, Matthew , ZIMMERMANN, Bernhard , BANER, Johan
IPC分类号： C12Q1/68
CPC分类号： 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
摘要： 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.
摘要翻译：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。

2. 发明申请

WO2011041485A1 METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING 审中-公开
标题翻译：非侵入式预防性呼吸方法
公开(公告)号：WO2011041485A1
公开(公告)日：2011-04-07
申请号：PCT/US2010/050824
申请日：2010-09-30
申请人： GENE SECURITY NETWORK, INC. , RABINOWITZ, Matthew , RYAN, Allison , GEMELOS, George , BANJEVIC, Milena , DEMKO, Zachary
发明人： RABINOWITZ, Matthew , RYAN, Allison , GEMELOS, George , BANJEVIC, Milena , DEMKO, Zachary
IPC分类号： C12Q1/68 , C07H21/04 , G01N33/50
CPC分类号： G06F19/22 , C12Q1/6827 , C12Q1/6874 , C12Q1/6876 , C12Q1/6883 , C12Q2600/156 , C12Q2600/16 , G06F19/18 , G06N7/005 , C12Q2537/16 , C12Q2537/165
摘要： 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.
摘要翻译：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。

3. 发明申请

WO2010017214A1 METHODS FOR ALLELE CALLING AND PLOIDY CALLING 审中-公开
标题翻译：用于呼叫和呼叫呼叫的方法
公开(公告)号：WO2010017214A1
公开(公告)日：2010-02-11
申请号：PCT/US2009/052730
申请日：2009-08-04
申请人： GENE SECURITY NETWORK, INC. , RABINOWITZ, Matthew , GEMELOS, George , BANJEVIC, Milena , RYAN, Allison , SWEETKIND-SINGER, Joshua
发明人： RABINOWITZ, Matthew , GEMELOS, George , BANJEVIC, Milena , RYAN, Allison , SWEETKIND-SINGER, Joshua
IPC分类号： G01N33/483 , C12Q1/68
CPC分类号： G06F19/18 , C12Q1/6883 , C12Q2600/156 , G06F19/24
摘要： 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.
摘要翻译：本文公开了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。

4. 发明申请

WO2012088456A2 METHODS FOR NON-INVASIVE PRENATAL PATERNITY TESTING 审中-公开
标题翻译：非侵入性预防性试验方法
公开(公告)号：WO2012088456A2
公开(公告)日：2012-06-28
申请号：PCT/US2011/066938
申请日：2011-12-22
申请人： NATERA, INC. , RYAN, Allison , SIGURJONSSON, Styrmir , BANJEVIC, Milena , GEMELOS, George , HILL, Matthew , BANER, Johan , RABINOWITZ, Matthew , DEMKO, Zachary
发明人： RYAN, Allison , SIGURJONSSON, Styrmir , BANJEVIC, Milena , GEMELOS, George , HILL, Matthew , BANER, Johan , RABINOWITZ, Matthew , DEMKO, Zachary
IPC分类号： G06F19/00 , C07H21/04
CPC分类号： C12Q1/6869 , C12Q1/6876 , C12Q2600/156 , G06F19/14
摘要： 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.
摘要翻译：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。

5. 发明申请

WO2012108920A1 METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING 审中-公开
标题翻译：非侵入式预防性呼吸方法
公开(公告)号：WO2012108920A1
公开(公告)日：2012-08-16
申请号：PCT/US2011/061506
申请日：2011-11-18
申请人： NATERA, INC , RABINOWITZ, Matthew , GEMELOS, George , BANJEVIC, Milena , RYAN, Allison , DEMKO, Zachary , HILL, Matthew , ZIMMERMANN, Bernhard , BANER, Johan
发明人： RABINOWITZ, Matthew , GEMELOS, George , BANJEVIC, Milena , RYAN, Allison , DEMKO, Zachary , HILL, Matthew , ZIMMERMANN, Bernhard , BANER, Johan
IPC分类号： G06F19/22 , G01N33/48
CPC分类号： C12Q1/6869 , C12Q1/6806 , C12Q1/6827 , C12Q1/6862 , C12Q1/6874 , C12Q1/6883 , C12Q2600/156 , G06F19/18 , G06F19/24 , C12Q2537/161 , C12Q2537/165
摘要： 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.
摘要翻译：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。

6. 发明申请

WO2008115497A2 SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA AND DETERMINING CHROMSOME COPY NUMBER 审中-公开
标题翻译：用于清除噪声遗传数据的系统和方法，并确定复杂的编号
公开(公告)号：WO2008115497A2
公开(公告)日：2008-09-25
申请号：PCT/US2008/003547
申请日：2008-03-17
申请人： GENE SECURITY NETWORK , RABINOWITZ, Matthew , SWEETKIND-SINGER, Josh , BANJEVIC, Milena , JOHNSON, David, Scott , KIJACIC, Dusan , PETROV, Dimitri , XU, Jing , DEMKO, Zachary, P.
发明人： RABINOWITZ, Matthew , SWEETKIND-SINGER, Josh , BANJEVIC, Milena , JOHNSON, David, Scott , KIJACIC, Dusan , PETROV, Dimitri , XU, Jing , DEMKO, Zachary, P.
IPC分类号： G06F19/00
CPC分类号： G06F19/22 , G06F19/18 , G06F19/20 , G06F19/24
摘要： 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. Genetic material from the target individual is acquired, amplified and the genetic data is measured using known methods. 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 of the invention, 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 of the invention, the chromosome copy number can be determined from the measured genetic data of a single or small number of cells, with or without genetic information from one or both parents. In another embodiment of the invention, these determinations are made for the purpose of embryo selection in the context of in-vitro fertilization. In another embodiment of the invention, the genetic data can be reconstructed for the purposes of making phenotypic predictions.
摘要翻译：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获取，扩增来自目标个体的遗传物质，并使用已知方法测量遗传数据。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。根据本发明的一个实施方案，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的单倍体遗传数据或双亲。在本发明的另一个实施方案中，染色体拷贝数可以从单个或少数细胞的测量的遗传数据确定，具有或不具有来自一个或两个亲本的遗传信息。在本发明的另一个实施方案中，这些确定是为了在体外受精的背景下进行胚胎选择的目的。在本发明的另一个实施方案中，为了进行表型预测的目的，可以重建遗传数据。

7. 发明申请

WO2007062164A3 SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA AND USING DATA TO MAKE PREDICTIONS 审中-公开
公开(公告)号：WO2007062164A3
公开(公告)日：2007-05-31
申请号：PCT/US2006/045281
申请日：2006-11-22
申请人： GENE SECURITY NETWORK LLC , RABINOWITZ, Matthew , BANJEVIC, Milena , DEMKO, Zachary, Paul , JOHNSON, David, Scott
发明人： RABINOWITZ, Matthew , BANJEVIC, Milena , DEMKO, Zachary, Paul , JOHNSON, David, Scott
IPC分类号： G06F19/00
摘要： 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, and also for predicting likely phenotypic outcomes using mathematical models and given genetic, phenotypic and/or clinical data of an individual, and also relevant aggregated medical data consisting of genotypic, phenotypic, and/or clinical data from germane patient subpopulations. 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.

8. 发明申请

WO2009105531A1 METHODS FOR CELL GENOTYPING 审中-公开
标题翻译：细胞基因分析方法
公开(公告)号：WO2009105531A1
公开(公告)日：2009-08-27
申请号：PCT/US2009/034506
申请日：2009-02-19
申请人： GENE SECURITY NETWORK, INC. , RABINOWITZ, Matthew , JOHNSON, David, S. , BANER, Johan , DEMKO, Zachary, P. , CINNIOGLU, Cengiz
发明人： RABINOWITZ, Matthew , JOHNSON, David, S. , BANER, Johan , DEMKO, Zachary, P. , CINNIOGLU, Cengiz
IPC分类号： G01N33/48 , C12Q1/68
CPC分类号： C12Q1/6876 , C12Q2600/156 , C12Q2600/16 , C12Q2600/172
摘要： Methods for cell genotyping are disclosed herein. A method for determining the genomic data of one or a small number of cells, or from fragmentary DNA, where a limited quantity of genetic data is available may include adding one or more targeted primers to a whole genome amplification of a cell, increasing the accuracy with which key alleles are measured in the context of a whole genome amplification. The genetic material from a single cell may be divided into fractions, each of which may be separately genotyped, allowing the reconstruction of the cells haplotype. The genetic material from a single cell may be divided into fractions, each of which may be separately genotyped, and the distribution of the various alleles in the different fractions may be used to determine the ploidy state of one or a plurality of chromosomes in the cell.
摘要翻译：本文公开了细胞基因分型的方法。用于确定有限数量的遗传数据可用的一个或少数细胞或来自片段DNA的基因组数据的方法可包括向细胞的全基因组扩增添加一种或多种靶向引物，增加细胞的准确度在全基因组扩增的情况下测量关键等位基因。来自单个细胞的遗传物质可以被分成各自的部分，每一个可以分开进行基因分型，允许重建细胞单元型。来自单个细胞的遗传物质可以分成各自的部分，每个可以分别进行基因分型，并且可以使用不同级分中各种等位基因的分布来确定细胞中一条或多条染色体的倍性状态。

9. 发明申请

WO2009146335A1 METHODS FOR EMBRYO CHARACTERIZATION AND COMPARISON 审中-公开
标题翻译：用于胚胎表征和比较的方法
公开(公告)号：WO2009146335A1
公开(公告)日：2009-12-03
申请号：PCT/US2009/045335
申请日：2009-05-27
申请人： GENE SECURITY NETWORK, INC. , RABINOWITZ, Matthew , JOHNSON, David, S. , SHAH, Nigam , GEMELOS, George
发明人： RABINOWITZ, Matthew , JOHNSON, David, S. , SHAH, Nigam , GEMELOS, George
IPC分类号： A61B17/435
CPC分类号： C12Q1/6883 , C12Q2600/156
摘要： Disclosed herein are methods for determining which embryos from a group of embryos are most likely to implant and develop as desired. In an embodiment of the present disclosure, one or more cells are biopsied from each of the embryos, and the genetic condition of those cells are determined. Within a group of embryos that each test positive for aneuploidy, the likelihood that each embryo contains euploid cells may be determined from the type of aneuploidy observed in the biopsied cells. This knowledge may be used to make a decision as to which embryos to transfer to a uterus. In an embodiment of the present disclosure, these determinations are made for the purpose of embryo selection in the context of in vitro fertilization.
摘要翻译：本文公开了用于根据需要确定来自一组胚胎最可能植入和发育的胚胎的方法。在本公开的一个实施方案中，从每个胚胎活检一个或多个细胞，并确定那些细胞的遗传条件。在一组胚胎中，每个胚胎均检测到非整倍体阳性，每个胚胎含有整倍体细胞的可能性可以从活检细胞中观察到的非整倍体类型确定。这些知识可能被用来决定哪些胚胎转移到子宫。在本公开的一个实施方案中，这些确定是为了在体外受精的背景下进行胚胎选择的目的。

10. 发明申请

WO2013052557A2 METHODS FOR PREIMPLANTATION GENETIC DIAGNOSIS BY SEQUENCING 审中-公开
标题翻译：通过序列预测遗传学诊断的方法
公开(公告)号：WO2013052557A2
公开(公告)日：2013-04-11
申请号：PCT/US2012/058578
申请日：2012-10-03
申请人： NATERA, INC. , RABINOWITZ, Matthew , HILL, Matthew , ZIMMERMANN, Bernhard , BANER, Johan , RYAN, Allison , GEMELOS, George
发明人： RABINOWITZ, Matthew , HILL, Matthew , ZIMMERMANN, Bernhard , BANER, Johan , RYAN, Allison , GEMELOS, George
IPC分类号： C12Q1/68 , G06F19/24 , G06F19/20
CPC分类号： C12Q1/6858 , C12Q1/6883 , C12Q2600/156 , G06F19/18 , C12Q2535/122 , C12Q2545/114
摘要： The present disclosure provides methods for determining the ploidy status of an embryo at a chromosome from a sample of DNA from an embryo. The ploidy state is determined by sequencing the DNA from one or more cells biopsied from the embryo, and analyzing the relative amounts of each allele at a plurality of polymorphic loci on the chromosome. In an embodiment, the ploidy state is determined by comparing the observed allele ratios to the expected allele ratios for different ploidy states. In an embodiment, the DNA is selectively amplified at a plurality of polymorphic loci by targeted sequencing. 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.
摘要翻译：本公开提供了用于从胚胎的DNA样品测定染色体上胚胎的倍性状态的方法。倍性状态通过对来自胚胎活检的一个或多个细胞的DNA进行测序，并分析染色体上多个多态性位点处的每个等位基因的相对量来确定。在一个实施方案中，通过将观察到的等位基因比率与不同倍性状态的预期等位基因比率进行比较来确定倍性状态。在一个实施方案中，通过靶向测序在多个多态位点选择性扩增DNA。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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