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1. 发明申请

US20070178501A1 System and method for integrating and validating genotypic, phenotypic and medical information into a database according to a standardized ontology 审中-公开
标题翻译：根据标准化本体将基因型，表型和医学信息整合并验证成数据库的系统和方法
公开(公告)号：US20070178501A1
公开(公告)日：2007-08-02
申请号：US11634550
申请日：2006-12-06
申请人： Matthew Rabinowitz , Jonathan Sheena , Zachary Demko , Christopher Clark , Nigam Shah
发明人： Matthew Rabinowitz , Jonathan Sheena , Zachary Demko , Christopher Clark , Nigam Shah
IPC分类号： C12Q1/68 , G06F19/00 , G06Q50/00
CPC分类号： G06Q50/22 , G06Q50/24
摘要： The system described herein enables clinicians and researchers to use aggregated genetic and phenotypic data from clinical trials and medical records to make the safest, most effective treatment decisions for each patient. This involves (i) the creation of a standardized ontology for genetic, phenotypic, clinical, pharmacokinetic, pharmacodynamic and other data sets, (ii) the creation of a translation engine to integrate heterogeneous data sets into a database using the standardized ontology, and (iii) the development of statistical methods to perform data validation and outcome prediction with the integrated data. The system is designed to interface with patient electronic medical records (EMRs) in hospitals and laboratories to extract a particular patient's relevant data. The system may also be used in the context of generating phenotypic predictions and enhanced medical laboratory reports for treating clinicians. The system may also be used in the context of leveraging the huge amount of data created in medical and pharmaceutical clinical trials. The ontology and validation rules are designed to be flexible so as to accommodate a disparate set of clients. The system is also designed to be flexible so that it can change to accommodate scientific progress and remain optimally configured.
摘要翻译：本文描述的系统使临床医师和研究人员能够使用来自临床试验和医疗记录的综合遗传和表型数据，为每位患者做出最安全，最有效的治疗决定。这涉及（i）为遗传，表型，临床，药代动力学，药效学和其他数据集创建标准化本体，（ii）创建翻译引擎以将异构数据集合集成到使用标准化本体的数据库中，以及（ iii）开发统计方法，使用综合数据进行数据验证和结果预测。该系统旨在与医院和实验室中的患者电子病历（EMR）进行接口，以提取特定患者的相关数据。该系统也可用于产生表型预测和增强的用于治疗临床医师的医学实验室报告。该系统也可以在利用在医疗和药物临床试验中创造的大量数据的背景下使用。本体和验证规则被设计为灵活的，以容纳不同的客户端集合。该系统还被设计为灵活的，以便它可以改变以适应科学进步并保持最佳配置。

2. 发明申请

US20130252824A1 SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA FROM TARGET INDIVIDUALS USING GENETIC DATA FROM GENETICALLY RELATED INDIVIDUALS 有权
标题翻译：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：US20130252824A1
公开(公告)日：2013-09-26
申请号：US13793186
申请日：2013-03-11
申请人： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Johnson
发明人： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Johnson
IPC分类号： G06F19/20
CPC分类号： G06F19/20 , G06F19/18
摘要： 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.
摘要翻译：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。

3. 发明申请

US20110288780A1 Methods for Non-Invasive Prenatal Ploidy Calling 有权
标题翻译：非侵入性产前倍性调用方法
公开(公告)号：US20110288780A1
公开(公告)日：2011-11-24
申请号：US13110685
申请日：2011-05-18
申请人： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
发明人： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
IPC分类号： G06F19/00 , C07H21/04
CPC分类号： C12Q1/6883 , C12Q1/6827 , C12Q1/6869 , C12Q2537/161 , C12Q2537/165 , C12Q2600/112 , C12Q2600/156 , C12Q2600/16 , C12Q2600/172 , G06F19/00 , G06F19/12 , G06F19/18 , G06F19/22 , G06F19/34 , G16H50/30
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.
摘要翻译：本文公开了非侵入性产前倍性呼叫的方法。本文公开了从胎儿母体和胎儿的DNA样本以及来自母亲和任选也来自父亲的基因型数据测量的基因型数据中确定妊娠胎儿染色体倍性状态的方法。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。

4. 发明申请

US20080243398A1 System and method for cleaning noisy genetic data and determining chromosome copy number 有权
标题翻译：清除嘈杂遗传数据和确定染色体拷贝数的系统和方法
公开(公告)号：US20080243398A1
公开(公告)日：2008-10-02
申请号：US12076348
申请日：2008-03-17
申请人： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Scott Johnson , Dusan Kijacic , Dimitri Petrov , Josh Sweetkind-Singer , Jing Xu
发明人： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Scott Johnson , Dusan Kijacic , Dimitri Petrov , Josh Sweetkind-Singer , Jing Xu
IPC分类号： G01N33/48
CPC分类号： G06F19/16 , C12Q1/6855 , C12Q1/6874 , G06F19/18 , G06F19/24 , G06Q50/22
摘要： 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. Genetic material from the target individual is acquired, amplified and the genetic data is measured using known methods. 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 of the invention, 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 of the invention, the chromosome copy number can be determined from the measured genetic data of a single or small number of cells, with or without genetic information from one or both parents. In another embodiment of the invention, these determinations are made for the purpose of embryo selection in the context of in-vitro fertilization. In another embodiment of the invention, the genetic data can be reconstructed for the purposes of making phenotypic predictions.
摘要翻译：本文公开了一种系统和方法，用于增加测量的遗传数据的保真度，进行等位基因调用，并确定在一组或一组细胞中或从片段DNA中确定非整倍体的状态，其中有限数量的遗传数据是可用的获取，扩增来自目标个体的遗传物质，并使用已知方法测量遗传数据。使用目标基因组与遗传相关个体的基因组之间的预期相似性来重建差或不正确测量的碱基对，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，在多个基因座重建来自胚胎细胞的不完全遗传数据，具有或不具有来自一个的单倍体遗传数据或双亲。在本发明的另一个实施方案中，染色体拷贝数可以从单个或少数细胞的测量的遗传数据确定，具有或不具有来自一个或两个亲本的遗传信息。在本发明的另一个实施方案中，这些确定是为了在体外受精的背景下进行胚胎选择的目的。在本发明的另一个实施方案中，为了进行表型预测的目的，可以重建遗传数据。

5. 发明授权

US10017812B2 Methods for non-invasive prenatal ploidy calling 有权
公开(公告)号：US10017812B2
公开(公告)日：2018-07-10
申请号：US13300235
申请日：2011-11-18
申请人： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
发明人： Matthew Rabinowitz , George Gemelos , Milena Banjevic , Allison Ryan , Zachary Demko , Matthew Hill , Bernhard Zimmermann , Johan Baner
IPC分类号： G01N33/48 , G01N31/00 , G06G7/48 , G06G7/58 , C12Q1/6869 , C12Q1/6827 , G06F19/18 , C12Q1/6883 , C12Q1/6862 , G06F19/24
CPC分类号： C12Q1/6869 , C12Q1/6806 , C12Q1/6827 , C12Q1/686 , C12Q1/6862 , C12Q1/6874 , C12Q1/6883 , C12Q2600/156 , C12Q2600/16 , G06F19/34 , G16B20/00 , G16B40/00 , C12Q2537/161 , C12Q2537/165 , C12Q2537/143
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.

6. 发明申请

US20120185176A1 Methods for Non-Invasive Prenatal Ploidy Calling 审中-公开
标题翻译：非侵入性产前倍性调用方法
公开(公告)号：US20120185176A1
公开(公告)日：2012-07-19
申请号：US13499086
申请日：2010-09-30
申请人： Matthew Rabinowitz , Allison Ryan , George Gemelos , Milena Banjevic , Zachary Demko
发明人： Matthew Rabinowitz , Allison Ryan , George Gemelos , Milena Banjevic , Zachary Demko
IPC分类号： G06F19/00
CPC分类号： G16B30/00 , C12Q1/6827 , C12Q1/6874 , C12Q1/6876 , C12Q1/6883 , C12Q2600/156 , C12Q2600/16 , G06N7/005 , G16B20/00 , C12Q2537/16 , C12Q2537/165
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.
摘要翻译：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。

7. 发明申请

US20140193816A1 SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA FROM TARGET INDIVIDUALS USING GENETIC DATA FROM GENETICALLY RELATED INDIVIDUALS 审中-公开
标题翻译：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：US20140193816A1
公开(公告)日：2014-07-10
申请号：US14156433
申请日：2014-01-15
申请人： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Johnson
发明人： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Johnson
IPC分类号： G06F19/18
CPC分类号： C12Q1/6883 , C12Q1/6827 , C12Q1/6876 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , G16B20/00 , G16B25/00 , G16B30/00 , G16B40/00 , C12Q2537/16 , C12Q2537/165
摘要： 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.
摘要翻译：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获得不完全遗传数据，并使用更大的样本二倍体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亲本的细胞，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。

8. 发明授权

US08515679B2 System and method for cleaning noisy genetic data and determining chromosome copy number 有权
标题翻译：清除嘈杂遗传数据和确定染色体拷贝数的系统和方法
公开(公告)号：US08515679B2
公开(公告)日：2013-08-20
申请号：US12076348
申请日：2008-03-17
申请人： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Scott Johnson , Dusan Kijacic , Dimitri Petrov , Josh Sweetkind-Singer , Jing Xu
发明人： Matthew Rabinowitz , Milena Banjevic , Zachary Demko , David Scott Johnson , Dusan Kijacic , Dimitri Petrov , Josh Sweetkind-Singer , Jing Xu
IPC分类号： G01N33/48 , G01N31/00 , G06G7/48 , G06G7/58
CPC分类号： G06F19/16 , C12Q1/6855 , C12Q1/6874 , G06F19/18 , G06F19/24 , G06Q50/22
摘要： 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. Genetic material from the target individual is acquired, amplified and the genetic data is measured using known methods. 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 of the invention, 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 of the invention, the chromosome copy number can be determined from the measured genetic data of a single or small number of cells, with or without genetic information from one or both parents. In another embodiment of the invention, these determinations are made for the purpose of embryo selection in the context of in-vitro fertilization. In another embodiment of the invention, the genetic data can be reconstructed for the purposes of making phenotypic predictions.
摘要翻译：本文公开了一种系统和方法，用于增加测量的遗传数据的保真度，进行等位基因调用，并确定在一组或一组细胞中或从片段DNA中确定非整倍体的状态，其中有限数量的遗传数据是可用的获取，扩增来自目标个体的遗传物质，并使用已知方法测量遗传数据。使用目标基因组与遗传相关个体的基因组之间的预期相似性来重建差或不正确测量的碱基对，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，在多个基因座重建来自胚胎细胞的不完全遗传数据，具有或不具有来自一个的单倍体遗传数据或双亲。在本发明的另一个实施方案中，染色体拷贝数可以从单个或少数细胞的测量的遗传数据确定，具有或不具有来自一个或两个亲本的遗传信息。在本发明的另一个实施方案中，这些确定是为了在体外受精的背景下进行胚胎选择的目的。在本发明的另一个实施方案中，为了进行表型预测的目的，可以重建遗传数据。

9. 发明申请

US20110033862A1 METHODS FOR CELL GENOTYPING 审中-公开
标题翻译：细胞基因分析方法
公开(公告)号：US20110033862A1
公开(公告)日：2011-02-10
申请号：US12918445
申请日：2009-02-19
申请人： Matthew Rabinowitz , David S. Johnson , Johan Baner , Zachary Demko , Cengiz Cinnioglu
发明人： Matthew Rabinowitz , David S. Johnson , Johan Baner , Zachary Demko , Cengiz Cinnioglu
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6876 , C12Q2600/156 , C12Q2600/16 , C12Q2600/172
摘要： Methods for cell genotyping are disclosed herein. A method for determining the genomic data of one or a small number of cells, or from fragmentary DNA, where a limited quantity of genetic data is available may include adding one or more targeted primers to a whole genome amplification of a cell, increasing the accuracy with which key alleles are measured in the context of a whole genome amplification. The genetic material from a single cell may be divided into fractions, each of which may be separately genotyped, allowing the reconstruction of the cells haplotype. The genetic material from a single cell may be divided into fractions, each of which may be separately genotyped, and the distribution of the various alleles in the different fractions may be used to determine the ploidy state of one or a plurality of chromosomes in the cell.
摘要翻译：本文公开了细胞基因分型的方法。用于确定有限数量的遗传数据可用的一个或少数细胞或来自片段DNA的基因组数据的方法可包括向细胞的全基因组扩增添加一种或多种靶向引物，增加细胞的准确度在全基因组扩增的情况下测量关键等位基因。来自单个细胞的遗传物质可以被分成各自的部分，每一个可以分开进行基因分型，允许重建细胞单元型。来自单个细胞的遗传物质可以分成各自的部分，每个可以分别进行基因分型，并且可以使用不同级分中各种等位基因的分布来确定细胞中一条或多条染色体的倍性状态。

10. 发明授权

US10113196B2 Prenatal paternity testing using maternal blood, free floating fetal DNA and SNP genotyping 有权
公开(公告)号：US10113196B2
公开(公告)日：2018-10-30
申请号：US13335043
申请日：2011-12-22
申请人： Allison Ryan , Styrmir Sigurjonsson , Milena Banjevic , George Gemelos , Matthew Hill , Johan Baner , Matthew Rabinowitz , Zachary Demko
发明人： Allison Ryan , Styrmir Sigurjonsson , Milena Banjevic , George Gemelos , Matthew Hill , Johan Baner , Matthew Rabinowitz , Zachary Demko
IPC分类号： C12Q1/6869 , C12Q1/6876 , 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.

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