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1. 发明申请

US20230044849A1 USING CELL-FREE DNA FRAGMENT SIZE TO DETERMINE COPY NUMBER VARIATIONS 有权
公开(公告)号：US20230044849A1
公开(公告)日：2023-02-09
申请号：US17871853
申请日：2022-07-22
申请人： Verinata Health, Inc.
发明人： Sven Duenwald , David A. Comstock , Catalin Barbacioru , Darya I. Chudova , Richard P. Rava , Keith W. Jones , Gengxin Chen , Dimitri Skvortsov
IPC分类号： G16B20/10 , G16B30/00 , G16B20/00 , G16B25/00 , C12Q1/6869 , G16H50/20 , G16H10/40 , G16B40/10 , G16B20/20 , G16Z99/00 , C12Q1/6883 , G16H50/30
摘要： 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.

2. 发明申请

US20220017958A1 SIMULTANEOUS DETERMINATION OF ANEUPLOIDY AND FETAL FRACTION 有权
公开(公告)号：US20220017958A1
公开(公告)日：2022-01-20
申请号：US17465163
申请日：2021-09-02
申请人： Verinata Health, Inc.
发明人： Stephen Quake , Richard P. Rava , Manjula Chinnappa , David A. Comstock , Gabrielle Heilek
IPC分类号： C12Q1/6869 , C12Q1/6806 , C12Q1/6809 , G16B30/10 , G16H10/40 , G16B20/10
摘要： 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.

3. 发明授权

US10741269B2 Method for improving the sensitivity of detection in determining copy number variations 有权
公开(公告)号：US10741269B2
公开(公告)日：2020-08-11
申请号：US15031246
申请日：2014-10-21
申请人： Verinata Health, Inc.
发明人： Darya I. Chudova , Diana Abdueva , Richard P. Rava
IPC分类号： G16B25/00 , G16H50/20
摘要： 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.

4. 发明申请

US20200251180A1 RESOLVING GENOME FRACTIONS USING POLYMORPHISM COUNTS 审中-公开
公开(公告)号：US20200251180A1
公开(公告)日：2020-08-06
申请号：US16853347
申请日：2020-04-20
申请人： Verinata Health, Inc.
发明人： Richard P. Rava , Brian K. Rhees , John P. Burke
IPC分类号： G16B30/00 , G16B20/00 , G16B45/00 , C12Q1/6827 , C12Q1/6883 , C12Q1/6809 , C12Q1/6876
摘要： Methods of reliably estimating genomic fraction (e.g., fetal fraction) from polymorphisms such as small base variations or insertions-deletions are disclosed. Sequenced data from a multigenomic source is used to determine allele counts for one or more of the polymorphisms. For one or more of the polymorphisms, zygosity is assigned, and genomic fraction is determined from the zygosity and allele counts. Certain embodiments employ SNPs as the relevant polymorphism. The disclosed methods can be applied as part of an intentional, pre-designed re-sequencing study targeted against known polymorphisms or can be used in a retrospective analysis of variations found by coincidence in overlapping sequences generated from maternal plasma (or any other setting where a mixture of DNA from several people are present).

5. 发明申请

US20170220735A1 USING CELL-FREE DNA FRAGMENT SIZE TO DETERMINE COPY NUMBER VARIATIONS 审中-公开
公开(公告)号：US20170220735A1
公开(公告)日：2017-08-03
申请号：US15382508
申请日：2016-12-16
申请人： Verinata Health, Inc.
发明人： Sven Duenwald , David A. Comstock , Catalin Barbacioru , Darya I. Chudova , Richard P. Rava , Keith W. Jones , Gengxin Chen , Dimitri Skvortsov
IPC分类号： G06F19/22 , G06F19/20 , G06F19/00 , C12Q1/68
CPC分类号： G06F19/22 , C12Q1/6869 , C12Q1/6883 , C12Q2600/154 , C12Q2600/156 , G06F19/00 , G06F19/18 , G06F19/20 , G06F19/24 , G06F19/34 , G16H50/20 , C12Q2537/16 , C12Q2537/165
摘要： 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.

6. 发明授权

US09115401B2 Partition defined detection methods 有权
标题翻译：分区定义检测方法
公开(公告)号：US09115401B2
公开(公告)日：2015-08-25
申请号：US14187052
申请日：2014-02-21
申请人： Verinata Health, Inc.
发明人： Richard P. Rava , Brian K. Rhees , John P. Burke
IPC分类号： G01N33/48 , G01N31/00 , C12Q1/68 , G06F19/18 , G06F19/12 , G06F17/11 , G06F17/10 , G06F19/22 , G06F19/24
CPC分类号： G06F19/22 , C12Q1/6827 , C12Q1/6883 , C12Q1/6886 , C12Q2600/156 , G06F17/10 , G06F17/11 , G06F19/12 , G06F19/18 , G06F19/24 , C12Q2537/16 , C12Q2537/165
摘要： Methods are disclosed for resolving measurement problems such problems in measuring chromosomal copy number. Some disclosed methods involve first selecting a primary assay element characteristic to partition. Such characteristic may be a source of experimental variability such as the GC content of measured DNA sequences. Additionally, the disclosed methods may employ an abundance or copy number function to transform the assay element frequencies into an abundance, dose, copy number score, or the like. In some cases, the disclosed methods estimate an amount of certain fetal DNA in a sample. The methods can further compare the estimated amount to a measured amount of fetal DNA in the sample. The comparison can be used to determine the fetal sex or aneuploidy.
摘要翻译：公开了用于解决测量染色体拷贝数测量问题的方法。一些公开的方法涉及首先选择分析特征的主要测定元件。这种特征可能是实验变异性的来源，例如测量的DNA序列的GC含量。另外，所公开的方法可以使用丰度或拷贝数函数将测定元件频率转换为丰度，剂量，拷贝数分数等。在一些情况下，所公开的方法估计样品中某些胎儿DNA的量。该方法可以进一步将估计量与样品中测量的胎儿DNA量进行比较。比较可用于确定胎儿的性别或非整倍体。

7. 发明申请

US20140038830A1 DETECTING AND CLASSIFYING COPY NUMBER VARIATION 有权
标题翻译：检测和分类复制数变化
公开(公告)号：US20140038830A1
公开(公告)日：2014-02-06
申请号：US13843258
申请日：2013-03-15
申请人： Verinata Health, Inc.
发明人： Anupama Srinivasan , Richard P. Rava
IPC分类号： G06F19/22 , G06F19/00 , C12Q1/68
CPC分类号： G06F19/3431 , C12Q1/6883 , G06F19/00 , G06F19/22 , G06F19/24 , G16H50/30
摘要： 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.
摘要翻译：本发明提供了一种用于确定测试样品中感兴趣的序列的拷贝数变异（CNV）的方法，其包括已知或怀疑在一个或多个感兴趣序列的量上不同的核酸的混合物。该方法包括统计方法，其考虑了由过程相关，染色体间和序列间变异性引起的应变变异性。该方法适用于确定任何胎儿非整倍性的CNV，以及已知或怀疑与各种医学状况相关的CNV。可以根据该方法确定的CNV包括染色体1-22，X和Y，其他染色体多糖体中的任何一个或多个的三体和单体，以及任何一个或多个染色体的区段的缺失和/或重复，其中只能通过测试一次测试样品的核酸来检测。

8. 发明授权

US11884975B2 Sequencing methods and compositions for prenatal diagnoses 有权
公开(公告)号：US11884975B2
公开(公告)日：2024-01-30
申请号：US17193279
申请日：2021-03-05
申请人： Verinata Health, Inc.
发明人： Richard P. Rava , Manjula Chinnappa , David A. Comstock , Gabrielle Heilek , Brian Kent Rhees
IPC分类号： C12Q1/6869 , C12Q1/6806 , C12Q1/6809 , G16B30/10 , G16B20/10 , G16H10/40 , C12Q1/6883
CPC分类号： C12Q1/6869 , C12Q1/6806 , C12Q1/6809 , G16B20/10 , G16B30/10 , G16H10/40 , C12Q1/6883 , C12Q2600/106 , C12Q2600/112 , C12Q1/6809 , C12Q2537/16 , C12Q2537/165 , C12Q2545/101
摘要： 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.

9. 发明授权

US10718020B2 Methods of fetal abnormality detection 有权
公开(公告)号：US10718020B2
公开(公告)日：2020-07-21
申请号：US15279066
申请日：2016-09-28
申请人： Verinata Health, Inc.
发明人： Yue-Jen Chuu , Richard P. Rava
IPC分类号： C12Q1/6883 , C12Q1/6869 , C12Q1/6809 , C12Q1/68
摘要： Methods and kits for selectively enriching non-random polynucleotide sequences are provided. Methods and kits for generating libraries of sequences are provided. Methods of using selectively enriched non-random polynucleotide sequences for detection of fetal aneuploidy are provided.

10. 发明申请

US20200048704A1 DETECTING AND CLASSIFYING COPY NUMBER VARIATION 审中-公开
公开(公告)号：US20200048704A1
公开(公告)日：2020-02-13
申请号：US16523883
申请日：2019-07-26
申请人： Verinata Health, Inc.
发明人： Richard P. Rava , Brian K. Rhees
IPC分类号： C12Q1/6874 , G16B30/00 , C12Q1/6869 , C12Q1/6809 , C12Q1/6806
摘要： 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.

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