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公开(公告)号：US11111545B2
公开(公告)日：2021-09-07
申请号：US17061877
申请日：2020-10-02
Applicant: Natera, Inc.
Inventor： Joshua Babiarz , Tudor Pompiliu Constantin , Lane A. Eubank , George Gemelos , Matthew Micah Hill , Huseyin Eser Kirkizlar , Matthew Rabinowitz , Onur Sakarya , Styrmir Sigurjonsson , Bernhard Zimmermann , Johan Baner , Allison Ryan , Milena Banjevic , Zachary Demko
IPC: C12Q1/68 , C12Q1/6883 , C12Q1/6811 , C12Q1/6848 , C12Q1/6851 , C12Q1/6855 , C12Q1/6874 , C12Q1/6809
Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.
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22.发明授权公开(公告)号：US11111543B2
公开(公告)日：2021-09-07
申请号：US16803739
申请日：2020-02-27
Applicant: Natera, Inc.
Inventor： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Johnson , Dusan Kijacic , Dimitri Petrov , Joshua Sweetkind-Singer , Jing Xu
IPC: C12Q1/6883 , C12Q1/6876 , G16B40/00 , G16B30/00 , G16B20/00 , C12Q1/6827 , G16B25/00 , C12Q1/6855 , C12Q1/686 , C12Q1/6869
Abstract: 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. 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, 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, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.
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公开(公告)号：US20190256908A1
公开(公告)日：2019-08-22
申请号：US16399991
申请日：2019-04-30
Applicant: Natera, Inc.
Inventor： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
IPC: C12Q1/6869 , C12Q1/6862 , C12Q1/6806 , G16B20/00 , C12Q1/6827 , C12Q1/6874 , C12Q1/6883
Abstract: 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.
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24.发明授权公开(公告)号：US10081839B2
公开(公告)日：2018-09-25
申请号：US15413200
申请日：2017-01-23
Applicant: Natera, Inc.
Inventor： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Johnson , Dusan Kijacic , Dimitri Petrov , Joshua Sweetkind-Singer , Jing Xu
IPC: C12Q1/68 , C12Q1/6876
CPC classification number: C12Q1/6876 , C12Q1/6848 , C12Q1/6851 , C12Q1/6855 , C12Q1/6883 , C12Q2600/156 , C12Q2600/158 , G06N7/005 , G16B20/00 , G16B40/00 , C12Q2525/155 , C12Q2535/122 , C12Q2537/16
Abstract: 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. 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, 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, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.
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公开(公告)号：US20170011166A1
公开(公告)日：2017-01-12
申请号：US15273332
申请日：2016-09-22
Applicant: Natera, Inc.
Inventor： Matthew Rabinowitz , Allison Ryan , George Gemelos , Milena Banjevic , Zachary Demko
CPC classification number: G16B30/00 , C12Q1/6827 , C12Q1/6874 , C12Q1/6876 , C12Q1/6883 , C12Q2600/156 , C12Q2600/16 , G06N7/005 , G16B20/00 , C12Q2537/16 , C12Q2537/165
Abstract: 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.
Abstract translation: 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。
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Patent Agency Ranking
26.发明申请SYSTEMS AND METHODS FOR DETERMINING ANEUPLOIDY RISK USING SAMPLE FETAL FRACTION 审中-公开使用样品场分析确定异常风险的系统和方法公开(公告)号：US20160371428A1
公开(公告)日：2016-12-22
申请号：US15186774
申请日：2016-06-20
Applicant: Natera, Inc.
Inventor： Allison Ryan , Katie Kobara , Zachary Demko , Susan J. Gross
CPC classification number: G16B20/00 , C12Q1/6869 , C12Q1/6883
Abstract: Disclosed herein are system, method, and computer program product embodiments for determining aneuploidy risk in a target sample of maternal blood or plasma based on the amount of fetal DNA. An embodiment operates by receiving known genetic data from known prenatal testing samples and genetic data for the target sample. A fetal fraction distribution is determined for the known genetic data based on gestational age and the maternal weight associated with the target sample. A model is then generated based on a fixed ratio reduction of the determined fetal fraction distribution. A fetal fraction based data likelihood for the target sample is then determined for each of the plurality of ploidy states using the generated model. An aneuploidy risk score is then outputted based on applying a Bayesian probability determination that combines each fetal fraction based data likelihood with a previously determined risk score as a conditional value.
Abstract translation: 本文公开了基于胎儿DNA的量来确定母体血液或血浆的目标样品中非整倍体风险的系统，方法和计算机程序产品实施方案。 一个实施例通过从已知的产前测试样品和目标样品的遗传数据接收已知的遗传数据来操作。 基于孕龄和与目标样本相关的母体重量，确定已知遗传数据的胎儿分数分布。 然后基于确定的胎儿分数分布的固定比例减少产生模型。 然后使用所生成的模型，针对多个倍性状态中的每一个确定目标样本的基于胎儿分数的数据可能性。 然后基于应用将每个基于胎儿分数的数据可能性与先前确定的风险评分相结合的贝叶斯概率确定作为条件值来输出非整倍体风险评分。
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27.发明申请SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA FROM TARGET INDIVIDUALS USING GENETIC DATA FROM GENETICALLY RELATED INDIVIDUALS 审中-公开使用遗传资料从遗传相关个体清除目标个体的噪声遗传数据的系统和方法公开(公告)号：US20160369345A1
公开(公告)日：2016-12-22
申请号：US15191197
申请日：2016-06-23
Applicant: Natera, Inc.
Inventor： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Johnson
CPC classification number: C12Q1/6883 , C12Q1/6827 , C12Q1/6876 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , G06F19/18 , G06F19/20 , G06F19/22 , G06F19/24 , C12Q2537/16 , C12Q2537/165
Abstract: 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. 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. In accordance with one embodiment of the invention, incomplete genetic data from an embryonic cell is reconstructed using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals. In accordance with another embodiment of the invention, incomplete genetic data from a fetus is acquired from fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals. In one embodiment, the genetic data can be reconstructed for the purposes of making phenotypic predictions. In another embodiment, the genetic data can be used to detect for aneuploides and uniparental disomy.
Abstract translation: 用于确定有限数量的遗传数据可用的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。 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。 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重建来自胚胎细胞的不完整遗传数据，具有或不具有来自一个或两个亲本的单倍体细胞的遗传数据 ，和/或从其他相关个体获取的遗传数据。 根据本发明的另一个实施方案，从胎儿细胞或从母体血液中分离的无细胞胎儿DNA获得来自胎儿的不完整遗传数据，并且使用来自较大样本的更完整的遗传数据重建不完全遗传数据 来自一个或两个父母的二倍体细胞，具有或不具有来自一个或两个亲本的单倍体细胞的遗传数据和/或从其他相关个体获取的遗传数据。 在一个实施方案中，为了进行表型预测的目的，可以重建遗传数据。 在另一个实施方案中，遗传数据可以用于检测非整倍体和单亲二倍体。
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公开(公告)号：US20160357904A1
公开(公告)日：2016-12-08
申请号：US15243915
申请日：2016-08-22
Applicant: Natera, Inc.
Inventor： Matthew Rabinowitz , Allison Ryan , George Gemelos , Milena Banjevic , Zachary Demko
CPC classification number: G06F19/22 , C12Q1/6827 , C12Q1/6874 , C12Q1/6876 , C12Q1/6883 , C12Q2600/156 , C12Q2600/16 , G06F19/18 , G06N7/005 , C12Q2537/16 , C12Q2537/165
Abstract: 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.
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29.发明授权System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals 有权使用遗传相关个体的遗传数据清除来自目标个体的嘈杂遗传数据的系统和方法公开(公告)号：US09424392B2
公开(公告)日：2016-08-23
申请号：US13793133
申请日：2013-03-11
Applicant: Natera, Inc.
Inventor： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Johnson
CPC classification number: C12Q1/6883 , C12Q1/6827 , C12Q1/6876 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , G06F19/18 , G06F19/20 , G06F19/22 , G06F19/24 , C12Q2537/16 , C12Q2537/165
Abstract: 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, are disclosed. 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. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.
Abstract translation: 公开了一种用于确定一个或一小组细胞遗传数据的系统和方法，或从有限数量的遗传数据获得的片段DNA。 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。 根据本发明的一个实施方案，从母体血液中分离的胚胎细胞，胎儿细胞或无细胞胎儿DNA获得不完整的遗传数据，并且使用更大的样本的更完整的遗传数据来重建不完整的遗传数据 来自一个或两个父母的二倍体细胞，具有或不具有来自一个或两个亲本的单倍体细胞的遗传数据和/或从其他相关个体获取的遗传数据。
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公开(公告)号：US20150072872A1
公开(公告)日：2015-03-12
申请号：US14546321
申请日：2014-11-18
Applicant: Natera, Inc.
Inventor： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
CPC classification number: C12Q1/6883 , C12Q1/6827 , C12Q1/6869 , C12Q2537/161 , C12Q2537/165 , C12Q2600/112 , C12Q2600/156 , C12Q2600/16 , C12Q2600/172 , G06F19/34 , G16B5/00 , G16B20/00 , G16B30/00 , G16H50/30
Abstract: The present disclosure provides 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. 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.
Abstract translation: 本公开提供了用于从胎儿母体和胎儿的DNA样品测量的基因型数据以及来自母亲的基因型数据以及任选地还可以从父亲的基因型数据确定胎儿胎儿中染色体的倍性状态的方法 。 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。
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