Patents by Inventor Darya I. Chudova
Darya I. Chudova has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20230332225Abstract: Disclosed are methods for determining at least one sequence of interest of a fetus of a pregnant mother. In various embodiments, the method can determine one or more sequences of interest in a test sample that comprises a mixture of maternal cellular DNA and mother-and-fetus cfDNA. In some embodiments, methods are provided for determining whether the fetus has a genetic disease. In some embodiments, methods are provided for determining whether the fetus is homozygous in a disease causing allele when the mother is heterozygous of the same allele. In some embodiments, methods are provided for determining whether the fetus has a copy number variation (CNV) or a non-CNV genetic sequence anomaly.Type: ApplicationFiled: March 7, 2023Publication date: October 19, 2023Inventors: Anupama Srinivasan, Darya I. Chudova, Richard P. Rava
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Patent number: 11629378Abstract: Disclosed are methods for determining at least one sequence of interest of a fetus of a pregnant mother. In various embodiments, the method can determine one or more sequences of interest in a test sample that comprises a mixture of maternal cellular DNA and mother-and-fetus cfDNA. In some embodiments, methods are provided for determining whether the fetus has a genetic disease. In some embodiments, methods are provided for determining whether the fetus is homozygous in a disease causing allele when the mother is heterozygous of the same allele. In some embodiments, methods are provided for determining whether the fetus has a copy number variation (CNV) or a non-CNV genetic sequence anomaly.Type: GrantFiled: October 13, 2020Date of Patent: April 18, 2023Assignee: Illumina, Inc.Inventors: Anupama Srinivasan, Darya I. Chudova, Richard P. Rava
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Publication number: 20230044849Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter. In some implementations, information from fragments of different sizes are used to evaluate copy number variations. In some implementations, one or more t-statistics obtained from coverage information of the sequence of interest is used to evaluate copy number variations. In some implementations, one or more fetal fraction estimates are combined with one or more t-statistics to determine copy number variations.Type: ApplicationFiled: July 22, 2022Publication date: February 9, 2023Inventors: Sven Duenwald, David A. Comstock, Catalin Barbacioru, Darya I. Chudova, Richard P. Rava, Keith W. Jones, Gengxin Chen, Dimitri Skvortsov
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Patent number: 11430541Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter. In some implementations, information from fragments of different sizes are used to evaluate copy number variations. In some implementations, one or more t-statistics obtained from coverage information of the sequence of interest is used to evaluate copy number variations. In some implementations, one or more fetal fraction estimates are combined with one or more t-statistics to determine copy number variations.Type: GrantFiled: August 31, 2018Date of Patent: August 30, 2022Assignee: Verinata Health, Inc.Inventors: Sven Duenwald, David A. Comstock, Catalin Barbacioru, Darya I. Chudova, Richard P. Rava, Keith W. Jones, Gengxin Chen, Dimitri Skvortsov
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Publication number: 20210371907Abstract: Disclosed are methods for determining copy number variation (CNV) associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation (CNV) of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter, such as a size-weighted coverage or a fraction of fragments in a size range. In some embodiments, the fragment size parameter is adjusted to remove within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples. Also disclosed are systems and computer program products for evaluation of CNV of sequences of interest.Type: ApplicationFiled: June 17, 2021Publication date: December 2, 2021Inventors: Darya I. Chudova, Catalin Barbacioru, Sven Duenwald, David A. Comstock, Richard P. Rava
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Publication number: 20210262040Abstract: The present invention relates to compositions and methods for molecular profiling and diagnostics for genetic disorders and cancer, including but not limited to gene expression product markers associated with cancer or genetic disorders. In particular, the present invention provides algorithms and methods of classifying cancer, for example, thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.Type: ApplicationFiled: March 30, 2021Publication date: August 26, 2021Inventors: Giulia C. KENNEDY, Darya I. CHUDOVA, Eric T. WANG, Jonathan I. WILDE, Duncan H. Whitney, Michael Elashoff
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Publication number: 20210238686Abstract: The present invention relates to compositions, kits, and methods for molecular profiling and cancer diagnostics, including but not limited to genomic DNA markers associated with cancer. In particular, the present invention provides molecular profiles associated with thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.Type: ApplicationFiled: January 25, 2021Publication date: August 5, 2021Inventors: Giulia C. KENNEDY, Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee, Jonathan I. Wilde
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Patent number: 11072814Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation (CNV) of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter, such as a size-weighted coverage or a fraction of fragments in a size range. In some embodiments, the fragment size parameter is adjusted to remove within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples.Type: GrantFiled: December 11, 2015Date of Patent: July 27, 2021Assignee: Verinata Health, Inc.Inventors: Darya I. Chudova, Catalin Barbacioru, Sven Duenwald, David A. Comstock, Richard P. Rava
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Publication number: 20210108265Abstract: Disclosed are methods for determining at least one sequence of interest of a fetus of a pregnant mother. In various embodiments, the method can determine one or more sequences of interest in a test sample that comprises a mixture of maternal cellular DNA and mother-and-fetus cfDNA. In some embodiments, methods are provided for determining whether the fetus has a genetic disease. In some embodiments, methods are provided for determining whether the fetus is homozygous in a disease causing allele when the mother is heterozygous of the same allele. In some embodiments, methods are provided for determining whether the fetus has a copy number variation (CNV) or a non-CNV genetic sequence anomaly.Type: ApplicationFiled: October 13, 2020Publication date: April 15, 2021Inventors: Anupama Srinivasan, Darya I. Chudova, Richard P. Rava
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Patent number: 10934587Abstract: The present invention relates to compositions, kits, and methods for molecular profiling and cancer diagnostics, including but not limited to genomic DNA markers associated with cancer. In particular, the present invention provides molecular profiles associated with thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.Type: GrantFiled: January 13, 2014Date of Patent: March 2, 2021Assignee: Veracyte, Inc.Inventors: Giulia Kennedy, Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee, Jonathan I. Wilde
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Patent number: 10837055Abstract: Disclosed are methods for determining at least one sequence of interest of a fetus of a pregnant mother. In various embodiments, the method can determine one or more sequences of interest in a test sample that comprises a mixture of maternal cellular DNA and mother-and-fetus cfDNA. In some embodiments, methods are provided for determining whether the fetus has a genetic disease. In some embodiments, methods are provided for determining whether the fetus is homozygous in a disease causing allele when the mother is heterozygous of the same allele. In some embodiments, methods are provided for determining whether the fetus has a copy number variation (CNV) or a non-CNV genetic sequence anomaly.Type: GrantFiled: August 9, 2018Date of Patent: November 17, 2020Assignee: Illumina, Inc.Inventors: Anupama Srinivasan, Darya I. Chudova, Richard P. Rava
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Patent number: 10741269Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation (CNV) of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by removing within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples. Also disclosed are systems and computer program products for evaluation of CNV of sequences of interest.Type: GrantFiled: October 21, 2014Date of Patent: August 11, 2020Assignee: Verinata Health, Inc.Inventors: Darya I. Chudova, Diana Abdueva, Richard P. Rava
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Patent number: 10731223Abstract: The present invention relates to compositions and methods for molecular profiling and diagnostics for genetic disorders and cancer, including but not limited to gene expression product markers associated with cancer or genetic disorders. In particular, the present invention provides algorithms and methods of classifying cancer, for example, thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.Type: GrantFiled: September 12, 2017Date of Patent: August 4, 2020Assignee: Veracyte, Inc.Inventors: Giulia C. Kennedy, Darya I. Chudova, Eric T. Wang, Jonathan I. Wilde
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Publication number: 20200202974Abstract: The present invention relates to compositions and methods for molecular profiling and diagnostics for genetic disorders and cancer, including but not limited to gene expression product markers associated with cancer or genetic disorders. In particular, the present invention provides algorithms and methods of classifying cancer, for example, thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.Type: ApplicationFiled: February 4, 2020Publication date: June 25, 2020Inventors: Giulia C. KENNEDY, Darya I. CHUDOVA, Eric T. WANG, Jonathan I. WILDE
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Publication number: 20200176078Abstract: The present invention relates to compositions and methods for molecular profiling and diagnostics for genetic disorders and cancer, including but not limited to gene expression product markers associated with cancer or genetic disorders. In particular, the present invention provides algorithms and methods of classifying cancer, for example, thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.Type: ApplicationFiled: February 4, 2020Publication date: June 4, 2020Inventors: Giulia C. KENNEDY, Darya I. CHUDOVA, Eric T. WANG, Jonathan I. WILDE
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Patent number: 10672504Abstract: The present invention relates to compositions and methods for molecular profiling and diagnostics for genetic disorders and cancer, including but not limited to gene expression product markers associated with cancer or genetic disorders. In particular, the present invention provides algorithms and methods of classifying cancer, for example, thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.Type: GrantFiled: March 14, 2019Date of Patent: June 2, 2020Assignee: Veracyte, Inc.Inventors: Giulia C. Kennedy, Darya I. Chudova, Eric T. Wang, Jonathan I. Wilde, Bonnie H. Anderson, Hui Wang, Moraima Pagan, Nusrat Rabbee
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Publication number: 20190318805Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions, including syndromes related to CNV of subchromosomal regions. In some embodiments, methods are provided for determining CNV of fetuses using maternal samples comprising maternal and fetal cell free DNA. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by removing within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples. In some embodiments, syndrome related biases in sample data are also removed to increase signal to noise ratio. Also disclosed are systems for evaluation of CNV of sequences of interest.Type: ApplicationFiled: April 25, 2019Publication date: October 17, 2019Inventors: Darya I. Chudova, Diana Abdueva
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Publication number: 20190252039Abstract: The present invention relates to compositions and methods for molecular profiling and diagnostics for genetic disorders and cancer, including but not limited to gene expression product markers associated with cancer or genetic disorders. In particular, the present invention provides algorithms and methods of classifying cancer, for example, thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.Type: ApplicationFiled: March 14, 2019Publication date: August 15, 2019Inventors: Giulia C. KENNEDY, Darya I. CHUDOVA, Eric T. WANG, Jonathan I. WILDE
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Patent number: 10318704Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions, including syndromes related to CNV of subchromosomal regions. In some embodiments, methods are provided for determining CNV of fetuses using maternal samples comprising maternal and fetal cell free DNA. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by removing within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples. In some embodiments, syndrome related biases in sample data are also removed to increase signal to noise ratio. Also disclosed are systems for evaluation of CNV of sequences of interest.Type: GrantFiled: May 29, 2015Date of Patent: June 11, 2019Assignee: Verinata Health, Inc.Inventors: Darya I. Chudova, Diana Abdueva
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Publication number: 20190172551Abstract: The present invention relates to compositions and methods for molecular profiling and diagnostics for genetic disorders and cancer, including but not limited to gene expression product markers associated with cancer or genetic disorders. In particular, the present invention provides algorithms and methods of classifying cancer, for example, thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.Type: ApplicationFiled: January 15, 2019Publication date: June 6, 2019Inventors: Giulia C. KENNEDY, Darya I. CHUDOVA, Eric T. WANG, Jonathan I. WILDE