Patents by Inventor Richard P. Rava
Richard P. Rava 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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Patent number: 11952623Abstract: The invention provides compositions and methods for simultaneously determining the presence or absence of fetal aneuploidy and the relative amount of fetal nucleic acids in a sample obtained from a pregnant female. The method encompasses the use of sequencing technologies and exploits the occurrence of polymorphisms to provide a streamlined noninvasive process applicable to the practice of prenatal diagnostics.Type: GrantFiled: September 2, 2021Date of Patent: April 9, 2024Assignee: VERINATA HEALTH, INC.Inventors: Stephen Quake, Richard P. Rava, Manjula Chinnappa, David A Comstock, Gabrielle Heilek
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Patent number: 11884975Abstract: The invention provides methods for determining aneuploidy and/or fetal fraction in maternal samples comprising fetal and maternal cfDNA by massively parallel sequencing. The method comprises a novel protocol for preparing sequencing libraries that unexpectedly improves the quality of library DNA while expediting the process of analysis of samples for prenatal diagnoses.Type: GrantFiled: March 5, 2021Date of Patent: January 30, 2024Assignee: VERINATA HEALTH, INC.Inventors: Richard P. Rava, Manjula Chinnappa, David A. Comstock, Gabrielle Heilek, Brian Kent Rhees
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Patent number: 11875899Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.Type: GrantFiled: September 18, 2019Date of Patent: January 16, 2024Assignee: Verinata Health, Inc.Inventors: Richard P. Rava, Brian K. Rhees
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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: 11697846Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.Type: GrantFiled: July 26, 2019Date of Patent: July 11, 2023Assignee: Verinata Health, Inc.Inventors: Richard P. Rava, Brian K. Rhees
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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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Publication number: 20220275426Abstract: Provided herein, are matrices and methods for the stabilization of proteins and nucleic acids. The stabilized proteins and nucleic acids described herein can be in a sample taken from a subject and can be subsequently stabilized and stored on the matrix. An analyte of interest can be concentrated and eluted for analysis from this sample. The stabilized proteins and nucleic acids described herein can be components of a sample preparation reagent, and the reagent is stored on the matrix and hydration of the matrix with a sample can result in a reaction occurring.Type: ApplicationFiled: November 5, 2021Publication date: September 1, 2022Inventors: Alicia JACKSON, Dagmar BEYERLEIN, Sonya CLARK, Richard P. RAVA
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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: 20220228197Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the present method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.Type: ApplicationFiled: April 8, 2022Publication date: July 21, 2022Applicant: Verinata Health, Inc.Inventors: Richard P. Rava, David A. Comstock, Brian Kent Rhees
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Patent number: 11332774Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the present method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.Type: GrantFiled: July 25, 2017Date of Patent: May 17, 2022Assignee: Verinata Health, Inc.Inventors: Richard P Rava, David A Comstock, Brian Kent Rhees
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Publication number: 20220106639Abstract: The invention includes a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions.Type: ApplicationFiled: December 17, 2021Publication date: April 7, 2022Inventors: Richard P. Rava, Brian Kent Rhees
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Patent number: 11286520Abstract: A method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions.Type: GrantFiled: July 31, 2017Date of Patent: March 29, 2022Assignee: Verinata Health, Inc.Inventors: Richard P Rava, Brian Kent Rhees
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Publication number: 20220017958Abstract: The invention provides compositions and methods for simultaneously determining the presence or absence of fetal aneuploidy and the relative amount of fetal nucleic acids in a sample obtained from a pregnant female. The method encompasses the use of sequencing technologies and exploits the occurrence of polymorphisms to provide a streamlined noninvasive process applicable to the practice of prenatal diagnostics.Type: ApplicationFiled: September 2, 2021Publication date: January 20, 2022Applicant: Verinata Health, Inc.Inventors: Stephen Quake, Richard P. Rava, Manjula Chinnappa, David A. Comstock, Gabrielle Heilek
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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: 20210340613Abstract: The invention provides methods for determining aneuploidy and/or fetal fraction in maternal samples comprising fetal and maternal cfDNA by massively parallel sequencing. The method comprises a novel protocol for preparing sequencing libraries that unexpectedly improves the quality of library DNA while expediting the process of analysis of samples for prenatal diagnoses.Type: ApplicationFiled: March 5, 2021Publication date: November 4, 2021Inventors: Richard P. Rava, Manjula Chinnappa, David A. Comstock, Gabrielle Heilek, Brian Kent Rhees
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Patent number: 11130995Abstract: The invention provides compositions and methods for simultaneously determining the presence or absence of fetal aneuploidy and the relative amount of fetal nucleic acids in a sample obtained from a pregnant female. The method encompasses the use of sequencing technologies and exploits the occurrence of polymorphisms to provide a streamlined noninvasive process applicable to the practice of prenatal diagnostics.Type: GrantFiled: July 31, 2017Date of Patent: September 28, 2021Assignee: Verinata Health, Inc.Inventors: Stephen Quake, Richard P Rava, Manjula Chinnappa, David A Comstock, Gabrielle Heilek
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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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Publication number: 20210082538Abstract: The present invention provides a method capable of detecting single or multiple fetal chromosomal aneuploidies in a maternal sample comprising fetal and maternal nucleic acids, and verifying that the correct determination has been made. The method is applicable to determining copy number variations (CNV) of any sequence of interest in samples comprising mixtures of genomic nucleic acids derived from two different genomes, and which are known or are suspected to differ in the amount of one or more sequence of interest. The method is applicable at least to the practice of noninvasive prenatal diagnostics, and to the diagnosis and monitoring of conditions associated with a difference in sequence representation in healthy versus diseased individuals.Type: ApplicationFiled: July 27, 2020Publication date: March 18, 2021Inventor: Richard P. RAVA