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1. 发明申请

WO2018106798A1 COMPOSITIONS AND METHODS FOR IDENTIFYING NUCLEIC ACID MOLECULES 审中-公开
公开(公告)号：WO2018106798A1
公开(公告)日：2018-06-14
申请号：PCT/US2017/064899
申请日：2017-12-06
申请人： NATERA, INC.
发明人： ZIMMERMANN, Bernhard , SWENERTON, Ryan , RABINOWITZ, Matthew , SIGURJONSSON, Styrmir , GEMELOS, George , GANGULY, Apratim , SETHI, Himanshu
IPC分类号： C12Q1/6869
摘要： The present disclosure provides methods and compositions for sequencing nucleic acid molecules and identifying individual sample nucleic acid molecules using Molecular Index Tags (MITs). Furthermore, reaction mixtures, kits, and adapter libraries are provided.

2. 发明申请

WO2015026967A1 METHODS OF USING LOW FETAL FRACTION DETECTION 审中-公开
标题翻译：使用低分辨率检测的方法
公开(公告)号：WO2015026967A1
公开(公告)日：2015-02-26
申请号：PCT/US2014/051926
申请日：2014-08-20
申请人： NATERA, INC.
发明人： RYAN, Allison , RABINOWITZ, Matthew , MCADOO, Sallie , SIGURJONSSON, Styrmir
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , A61B5/150038 , C12Q1/6876 , C12Q2600/156
摘要： One embodiment is a method of evaluating a fetus for genetic abnormalities (or the risk of genetic abnormalities), comprising, obtaining a blood sample from a pregnant human subject, measuring the fetal fraction of cell free fetal DNA in the blood sample, determining if the fetal fraction of cell free fetal DNA in the blood sample is within the lowest 1 percentile of a reference population, and generating a report indicating that an invasive genetic analysis procedure should be performed. In some embodiments the reference population is matched for gestational age or maternal weight of both gestational age and maternal weight. In some embodiments the test population is matched for gestational age or maternal weight of both gestational age and maternal weight. Genetic abnormalities that can be detected include aneuploidy.
摘要翻译：一个实施方案是评估胎儿遗传异常（或遗传异常风险）的方法，包括：从怀孕的人类受试者获得血液样品，测量血液样品中无细胞胎儿DNA的胎儿部分，确定是否血液样本中无细胞胎儿DNA的胎儿部分在参考群体的最低1百分位数之内，并产生一个报告，指示应进行侵入性遗传分析程序。在一些实施方案中，参考群体与胎龄和母体体重的胎龄或母体重量相匹配。在一些实施方案中，测试群体匹配胎龄和母体体重的孕龄或母体体重。可检测到的遗传异常包括非整倍体。

3. 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。

4. 发明申请

WO2015164432A1 DETECTING MUTATIONS AND PLOIDY IN CHROMOSOMAL SEGMENTS 审中-公开
标题翻译：检测染色体部位的突变体和细菌
公开(公告)号：WO2015164432A1
公开(公告)日：2015-10-29
申请号：PCT/US2015/026957
申请日：2015-04-21
申请人： NATERA, INC.
发明人： BABIARZ, Joshua , CONSTANTIN, Tudor Pompiliu , EUBANK, Lane A. , GEMELOS, George , HILL, Matthew Micah , KIRKIZLAR, Huseyin Eser , RABINOWITZ, Matthew , SAKARYA, Onur , SIGURJONSSON, Styrmir , ZIMMERMAN, Bernhard
IPC分类号： C12Q1/68 , G06F19/16
CPC分类号： C12Q1/6869 , C12Q2539/10 , G06F19/16
摘要： The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes based on phasing of the alleles and determination of individual and joint probabilities and a best-fit model. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus. The invention also provides methods for detecting circulating tumor nucleic acids based on the level of allelic imbalance present at the polymorphic loci found by ploidy determination. The invention also provides a method for detecting single nucleotide variants based on an estimation of amplification efficiency and error rate and a method for detecting single nucleotide variants based on a median variant allele frequency for a plurality of control samples from individuals.
摘要翻译：本发明提供了用于基于等位基因的定相和单个和联合概率的确定以及最佳拟合模型来检测染色体片段或整个染色体的倍性的方法，系统和计算机可读介质。在一些方面，本发明提供了用于检测胎儿胎儿的癌症或染色体异常的方法，系统和计算机可读介质。本发明还提供了基于通过倍性测定发现的多态性位点处存在的等位基因不平衡水平检测循环肿瘤核酸的方法。本发明还提供了基于扩增效率和错误率的估计来检测单核苷酸变体的方法，以及基于来自个体的多个对照样品的中值变异等位基因频率来检测单核苷酸变体的方法。

5. 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。

6. 发明申请

WO2013130848A1 INFORMATICS ENHANCED ANALYSIS OF FETAL SAMPLES SUBJECT TO MATERNAL CONTAMINATION 审中-公开
标题翻译：信息增强分析场效应物质污染
公开(公告)号：WO2013130848A1
公开(公告)日：2013-09-06
申请号：PCT/US2013/028378
申请日：2013-02-28
申请人： NATERA, INC. , RABINOWITZ, Matthew , BANER, Johan , GEMELOS, George , HILL, Matthew, M. , SIGURJONSSON, Styrmir
发明人： RABINOWITZ, Matthew , BANER, Johan , GEMELOS, George , HILL, Matthew, M. , SIGURJONSSON, Styrmir
IPC分类号： C12Q1/68
CPC分类号： G06F19/18 , C12Q1/6827
摘要： 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.
摘要翻译：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。

7. 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。

8. 发明申请

WO2023034090A1 METHODS FOR NON-INVASIVE PRENATAL TESTING 审中-公开
公开(公告)号：WO2023034090A1
公开(公告)日：2023-03-09
申请号：PCT/US2022/041323
申请日：2022-08-24
申请人： NATERA, INC.
发明人： DEMKO, Zachary , RABINOWITZ, Matthew , GEMELOS, George
IPC分类号： C12Q1/6883
摘要： The present disclosure provides methods for preparing a preparation of amplified DNA derived from a blood sample of a pregnant woman useful for identifying pregnancies having high risks of preterm birth, preeclampsia, small for gestational age, spontaneous termination, and/or non-livebirth, comprising: (a) extracting cell-free DNA from the blood sample; (b) performing targeted multiplex amplification on the extracted DNA to amplify 200-20,000 SNP loci in a single reaction volume; and (c) performing high-throughput sequencing on the amplified DNA to obtain sequence reads and using the sequence reads to determine the ploidy state of the one or more chromosomes of interest; wherein a fetal fraction of less than 2.8% and/or no-call of the ploidy state of the one or more chromosomes of interest is indicative of pregnancies having high risks of preterm birth, preeclampsia, small for gestational age, spontaneous termination, and/or non-livebirth.

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