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21. 发明专利

CA2824387A1 METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING 未知
公开(公告)号：CA2824387A1
公开(公告)日：2012-08-16
申请号：CA2824387
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： C12Q1/68 , C12P19/34 , C40B10/00 , G01N33/48 , G06F19/10
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.

22. 发明专利

CA3037126A1 METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING 未知
公开(公告)号：CA3037126A1
公开(公告)日：2011-11-24
申请号：CA3037126
申请日：2011-05-18
申请人： NATERA INC
发明人： BANER JOHAN , BANJEVIC MILENA , DEMKO ZACHARY , GEMELOS GEORGE , HILL MATTHEW , RABINOWITZ MATTHEW , RYAN ALLISON , ZIMMERMAN BERNHARD
IPC分类号： C12Q1/6806 , C12N15/10
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.

23. 发明专利

CA2774252A1 METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING 未知
公开(公告)号：CA2774252A1
公开(公告)日：2011-04-07
申请号：CA2774252
申请日：2010-09-30
申请人： NATERA INC
发明人： RABINOWITZ MATTHEW , RYAN ALLISON , GEMELOS GEORGE , BANJEVIC MILENA , DEMKO ZACHARY
IPC分类号： C12Q1/68 , G06F19/18
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.

24. 发明专利

AU2022202083A1 Detecting mutations and ploidy in chromosomal segments 未知
公开(公告)号：AU2022202083A1
公开(公告)日：2022-04-14
申请号：AU2022202083
申请日：2022-03-28
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
摘要： The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants . In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.

25. 发明专利

CA2774252C METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING 未知
公开(公告)号：CA2774252C
公开(公告)日：2020-04-14
申请号：CA2774252
申请日：2010-09-30
申请人： NATERA INC
发明人： RABINOWITZ MATTHEW , RYAN ALLISON , GEMELOS GEORGE , BANJEVIC MILENA , DEMKO ZACHARY
IPC分类号： C12Q1/68 , C12Q1/6809
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.

26. 发明专利

ES2640776T3 Métodos para denominar de forma no invasiva ploidía prenatal 未知
公开(公告)号：ES2640776T3
公开(公告)日：2017-11-06
申请号：ES10821214
申请日：2010-09-30
申请人： NATERA INC
发明人： RABINOWITZ MATTHEW , RYAN ALLISON , GEMELOS GEORGE , BANJEVIC MILENA , DEMKO ZACHARY
IPC分类号： G06F19/18 , C12Q1/68
摘要： Un método para determinar el número de copias de un cromosoma de interés en un feto utilizando mediciones genotípicas obtenidas en ADN que flota libremente del feto encontrado en la sangre materna, en el que el ADN que flota libremente del feto se m ezcla con material genético de la madre del feto, comprendiendo el método: obtener mediciones genotípicas para un conjunto de SNP que comprende una pluralidad de SNP del cromosoma de interés y una pluralidad de SNP de al menos un cromosoma que se espera que sea disómico en el feto en una muestra mixta que comprende el ADN que flota libremente del feto mezclado con ADN materno que flota libremente, en el que la medición del material genético se realiza en material genético que se amplifica antes de medirlo y en el que la medición genotípica se realiza en 1.000 a 20.000 SNP utilizando secuenciación de alto rendimiento; crear en un ordenador un conjunto de hipótesis de estados de ploidía en las que cada hipótesis de los estados de ploidía es un posible estado de ploidía del cromosoma de interés en el feto en las que el conjunto de hipótesis de los estados de ploidía comprende nueve hipótesis posibles que corresponden a diferentes estados de ploidía: H00 (0, 0); H01 (0, 1); H02 (0, 2); H10 (1, 0); H11 (1, 1); H12 (1, 2); H20 (2, 0); H21 (2, 1); y H22 (2, 2), en las que (m, f) se refieren a la hipótesis en la que m es el número de un cromosoma dado heredado de la madre y f es el número de cromosomas dado heredado del padre; determinar en un ordenador, la probabilidad de cada una de las hipótesis dadas las mediciones genotípicas en la muestra mixta; y usar las probabilidades determinadas de cada hipótesis para determinar el número de copias más probable del cromosoma de interés en el feto, en las que las probabilidades determinadas son la estimación de probabilidades de máxima probabilidad y en el que la muestra mixta es una muestra de sangre materna y el ADN fetal no está purificado.

27. 发明专利

ES2634665T3 Método y sistema para detectar anormalidades cromosómicas 未知
公开(公告)号：ES2634665T3
公开(公告)日：2017-09-28
申请号：ES11175867
申请日：2006-11-22
申请人： NATERA INC
发明人： RABINOWITZ MATTHEW , BANJEVIC MILENA , DEMKO ZACHARY PAUL , JOHNSON DAVID SCOTT
IPC分类号： G06F19/18 , G06F19/22 , G06F19/24
摘要： Un método ex vivo en el que la medición de múltiples loci de SNP en un segmento determinado de un cromosoma determinado de un feto humano se utiliza para determinar el número de veces que el segmento en cuestión está presente en el genoma del feto; dicho método comprende: (i) crear un conjunto de una o varias hipótesis acerca del número de veces que el segmento en cuestión está presente en el genoma del feto, (ii) medir la cantidad de material genético para algunos o todos los posibles alelos en una pluralidad de loci de SNP en el segmento en cuestión, utilizando instrumentos y técnicas tomados del grupo formado por las sondas de inversión molecular (MIP), los microarrays de genotipificación, el ensayo de genotipificación SNP Taqman, la PCR cuantitativa, el sistema de genotipificación Illumina, otros ensayos de genotipificación, la hibridación fluorescente in situ (FISH) y combinaciones de estas, (iii) determinar las probabilidades relativas de cada una de las hipótesis considerando las mediciones del material genético fetal, donde la determinación de las probabilidades relativas de cada hipótesis se lleva a cabo utilizando técnicas cuantitativas que no hacen determinaciones de alelos y donde la desviación media y estándar para la medición de cada locus es conocida, desconocida o uniforme, y (iv) utilizar las probabilidades relativas asociadas a cada hipótesis para determinar el estado más probable del material genético real del feto, donde la determinación del número de veces que el segmento de cromosoma en cuestión está presente en el genoma del feto sirve para detectar una anomalía cromosómica, la cual se selecciona de una lista que comprende monosomía, disomía uniparental, trisomía, otras aneuploidías, translocación no balanceada y combinaciones de estas.

28. 发明专利

AU2011358564B2 Methods for non-invasive prenatal ploidy calling 未知
公开(公告)号：AU2011358564B2
公开(公告)日：2017-06-22
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.

29. 发明专利

AU2015249846A1 Detecting mutations and ploidy in chromosomal segments 未知
公开(公告)号：AU2015249846A1
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.

30. 发明专利

HK1208940A1 METHODS FOR NON-INVASIVE PRE-NATAL PLOIDY CALLING 未知
公开(公告)号：HK1208940A1
公开(公告)日：2016-03-18
申请号：HK15109616
申请日：2015-09-30
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： G06F20060101 , C12Q20060101
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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