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1. 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。

2. 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。

3. 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.

4. 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.

5. 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.

6. 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.

7. 发明专利

AU2015252046A1 Methods for Non-Invasive Prenatal Ploidy Calling 未知
公开(公告)号：AU2015252046A1
公开(公告)日：2015-11-19
申请号：AU2015252046
申请日：2015-11-03
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： C12Q1/68
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.

8. 发明专利

HK1252358A1 用於確定倍性的方法及組合物未知
公开(公告)号：HK1252358A1
公开(公告)日：2019-05-24
申请号：HK18111644
申请日：2018-09-11
申请人： NATERA INC
发明人： KIRKIZLAR HUSEYIN ESER , SALARI RAHELEH , SIGURJONSSON STYRMIR , ZIMMERMANN BERNHARD , RYAN ALLISON , VANKAYALAPATI NARESH
IPC分类号： C12Q20060101 , G06F20060101

9. 发明专利

AU2016200643B2 Methods For Allele Calling And Ploidy Calling 未知
公开(公告)号：AU2016200643B2
公开(公告)日：2017-12-21
申请号：AU2016200643
申请日：2016-02-02
申请人： NATERA INC
发明人： RABINOWITZ MATTHEW , GEMELOS GEORGE , BANJEVIC MELINA , RYAN ALLISON , SWEETKIND-SINGER JOSHUA
IPC分类号： C12Q1/68 , G01N33/483
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.

10. 发明专利

AU2015252046B2 Methods for Non-Invasive Prenatal Ploidy Calling 未知
公开(公告)号：AU2015252046B2
公开(公告)日：2017-10-19
申请号：AU2015252046
申请日：2015-11-03
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： C12Q1/68
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.

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