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1. 发明专利

JP2013150622A System and method for cleaning genetic data and using data to make predictions 审中-公开
标题翻译：用于清理遗传数据和使用数据进行预测的系统和方法
公开(公告)号：JP2013150622A
公开(公告)日：2013-08-08
申请号：JP2013063669
申请日：2013-03-26
申请人： Natera Inc , ナテラ, インコーポレイテッド
发明人： RABINOWITZ MATTHEW , BANJEVIC MILENA , DEMKO ZACHARY PAUL , JOHNSON DAVID SCOTT
IPC分类号： C12Q1/68 , C12N15/09 , G06F19/18 , G06F19/22 , G06F19/24
CPC分类号： G06F19/18 , G06F19/22 , G06F19/24
摘要： PROBLEM TO BE SOLVED: To provide a system and method for cleaning genetic data and using the data to make predictions.SOLUTION: A system and method for determining 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.
摘要翻译：要解决的问题：提供清洁遗传数据并使用数据进行预测的系统和方法。解决方案：用于确定一个或一小组细胞或来自片段DNA的遗传数据的系统和方法，其中有限遗传数据的数量可用，并且还用于使用数学模型和给定个体的遗传，表型和/或临床数据来预测可能的表型结果，以及由基因型，表型和/或临床数据组成的相关聚合医学数据患者亚群。使用已知方法获取和扩增目标个体的遗传数据，并且使用目标基因组与基因相关受试者的基因组之间的预期相似性重建差测量的碱基对，缺失的等位基因和缺失区域。

2. 发明申请

WO2015164432A8 DETECTING MUTATIONS AND PLOIDY IN CHROMOSOMAL SEGMENTS 审中-公开
标题翻译：检测染色体片段中的突变和突变
公开(公告)号：WO2015164432A8
公开(公告)日：2015-12-03
申请号：PCT/US2015026957
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阶段化以及个体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，本发明提供用于检测妊娠胎儿中的癌症或染色体异常的方法，系统和计算机可读介质。本发明还提供了用于基于通过倍性测定发现的多态基因座处存在的等位基因不平衡水平来检测循环肿瘤核酸的方法。本发明还提供了用于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用于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。

3. 发明申请

WO2012088456A3 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：WO2012088456A3
公开(公告)日：2013-10-24
申请号：PCT/US2011066938
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： C12Q1/68
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。

4. 发明申请

WO2013052557A3 METHODS FOR PREIMPLANTATION GENETIC DIAGNOSIS BY SEQUENCING 审中-公开
标题翻译：通过测序进行预先植入遗传诊断的方法
公开(公告)号：WO2013052557A3
公开(公告)日：2013-06-20
申请号：PCT/US2012058578
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 , G06F19/20
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来自胚胎的DNA样品确定染色体中胚胎倍性状态的方法。倍性状态通过对来自胚胎活检的一个或多个细胞的DNA测序并分析染色体上多个多态性基因座处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性基因座选择性扩增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在多个多态性基因座上优先富集。

5. 发明专利

CA3041913A1 COMPOSITIONS AND METHODS FOR IDENTIFYING NUCLEIC ACID MOLECULES 未知
公开(公告)号：CA3041913A1
公开(公告)日：2018-06-14
申请号：CA3041913
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.

6. 发明专利

AU2011358564B9 Methods for non-invasive prenatal ploidy calling 未知
公开(公告)号：AU2011358564B9
公开(公告)日：2017-07-13
申请号：AU2011358564
申请日：2011-11-18
申请人： NATERA INC
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
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.

7. 发明专利

AU2011358564A9 Methods for non-invasive prenatal ploidy calling 未知
公开(公告)号：AU2011358564A9
公开(公告)日：2017-07-13
申请号：AU2011358564
申请日：2011-11-18
申请人： NATERA INC
发明人： BANJEVIC MILENA , RYAN ALLISON , DEMKO ZACHARY , HILL MATTHEW , ZIMMERMANN BERNHARD , BANER JOHAN , RABINOWITZ MATTHEW , GEMELOS GEORGE
IPC分类号： G06F19/22 , G01N33/48
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.

8. 发明专利

ES2620431T3 Métodos para la determinación de alelos y de ploidía 未知
公开(公告)号：ES2620431T3
公开(公告)日：2017-06-28
申请号：ES09805452
申请日：2009-08-04
申请人： NATERA INC
发明人： RABINOWITZ MATTHEW , GEMELOS GEORGE , BANJEVIC MILENA , RYAN ALLISON , SWEETKIND-SINGER JOSHUA
IPC分类号： G06F19/18 , C12Q1/68
摘要： Un método para la determinación de un estado de ploidía de por lo menos un cromosoma en un individuo objetivo, comprendiendo este método: obtener datos genéticos del individuo objetivo y de uno o más individuos relacionados utilizando un medio para medir datos genéticos, donde el medio se selecciona de un grupo que comprende sondas de inversión molecular, microarrays de genotipado, un ensayo de genotipado, hibridación de fluorescencia in situ (FISH), secuenciación, otras plataformas de genotipado de alto rendimiento, y combinaciones de lo anterior, y donde los datos genéticos son las respuestas medidas en varios loci de polimorfismo de un solo nucleótido (SNP) en por lo menos un cromosoma, comprendiendo el o los individuos relacionados mencionados uno o ambos progenitores del individuo objetivo; crear un conjunto de por lo menos una hipótesis de estado de ploidía para por lo menos un cromosoma del individuo objetivo, donde cada una de las hipótesis del estado de ploidía es un posible estado de ploidía de por lo menos un cromosoma, donde 0, 1, o 2 copias del cromosoma proceden de cada progenitor; utilizar dos o más técnicas especializadas que son algoritmos aplicados sobre los datos genéticos obtenidos para determinar, para cada técnica especializada utilizada, una probabilidad estadística de cada hipótesis de estado de ploidía en el conjunto, considerando los datos genéticos obtenidos, donde las técnicas especializadas se seleccionan de entre: la técnica de la presencia de homólogos, técnica que utiliza datos genéticos obtenidos de ambos progenitores, donde uno de los progenitores es heterocigoto en un SNP, y el otro es homocigoto en ese SNP, donde la técnica de presencia de homólogos comprende: 1 ajustar por fases los datos genéticos obtenidos de los progenitores y calcular los umbrales de ruido por cromosoma; 2 segmentar por lo menos un cromosoma; 3 calcular las tasas de pérdidas de SNP por segmento para los genotipos parentales de interés; 4 calcular las tasas de pérdidas de SNP para cada progenitor en por lo menos un cromosoma y las probabilidades de hipótesis en cada segmento; 5 combinar las probabilidades en los segmentos de cromosoma de producir una probabilidad de datos, dada la hipótesis de cadena parental para cromosomas completos; y 6 comprobar las determinaciones no válidas y calcular una probabilidad para cada hipótesis de estado de ploidía; la técnica de permutación, técnica que compara la relación entre distribuciones de los datos genéticos obtenidos del individuo objetivo para distintos genotipos parentales utilizando un algoritmo estadístico para determinar la probabilidad de cada hipótesis de estado de ploidía, considerando los datos genéticos obtenidos; y la técnica de la presencia parental, que detecta, independientemente para cada progenitor, para un cromosoma determinado, si hay o no contribución del genoma de ese progenitor, basado en distancias entre conjuntos de genotipos parentales en el punto más amplio en las curvas de función de distribución acumulativa, que representa gráficamente las distribuciones observadas de los datos genéticos obtenidos para distintos genotipos parentales, y asigna probabilidades a cada hipótesis de estado de ploidía calculando un resumen estadístico para cada progenitor y comparando con modelos de datos para casos en los que un cromosoma parental está presente, y casos en los que no está presente un cromosoma parental; combinar para cada hipótesis de estado de ploidía, las probabilidades estadísticas determinadas por las dos o más técnicas especializadas, para determinar probabilidades estadísticas combinadas; y determinar el estado de ploidía para por lo menos un cromosoma en el individuo objetivo, basado en las probabilidades estadísticas combinadas de cada una de las hipótesis de estado de ploidía, donde el estado de ploidía con la mayor probabilidad estadística combinada se determina que es el estado de ploidía de por lo menos un cromosoma.

9. 发明专利

AU2015249846A2 Detecting mutations and ploidy in chromosomal segments 未知
公开(公告)号：AU2015249846A2
公开(公告)日：2016-11-10
申请号：AU2015249846
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
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.

10. 发明专利

AU2011348100B2 Methods for non-invasive prenatal paternity testing 未知
公开(公告)号：AU2011348100B2
公开(公告)日：2016-08-25
申请号：AU2011348100
申请日：2011-12-22
申请人： NATERA INC
发明人： RYAN ALLISON , SIGURJONSSON STYRMIR , BANJEVIC MILENA , GEMELOS GEORGE , HILL MATTHEW , BANER JOHAN , RABINOWITZ MATTHEW , DEMKO ZACHARY
IPC分类号： C12Q1/68 , G16B10/00
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.

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