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公开(公告)号：US08700341B2
公开(公告)日：2014-04-15
申请号：US13009708
申请日：2011-01-19
申请人： Richard P. Rava , Brian K. Rhees , John P. Burke
发明人： Richard P. Rava , Brian K. Rhees , John P. Burke
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。
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公开(公告)号：US20130029852A1
公开(公告)日：2013-01-31
申请号：US13555037
申请日：2012-07-20
申请人： Richard P. Rava , Brian K. Rhees
发明人： Richard P. Rava , Brian K. Rhees
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6809 , C12Q1/6869 , C12Q1/6883 , C12Q1/6886 , C12Q2600/106 , G06F19/22 , C12Q2537/16 , C12Q2537/165 , C12Q2545/101
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。
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公开(公告)号：US10388403B2
公开(公告)日：2019-08-20
申请号：US13555010
申请日：2012-07-20
申请人： Richard P. Rava , Brian K. Rhees
发明人： Richard P. Rava , Brian K. Rhees
IPC分类号： G06F19/22 , C12Q1/68 , G11C17/00 , G16B30/00 , C12Q1/6806 , C12Q1/6869 , C12Q1/6809 , G16H50/30 , G16H50/20 , C12Q1/6883 , C12Q1/6886
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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公开(公告)号：US20120237928A1
公开(公告)日：2012-09-20
申请号：US13400028
申请日：2012-02-17
CPC分类号： C12Q1/6806 , C12Q1/6809 , C12Q1/6869 , C12Q1/6883 , C12Q1/6886 , C12Q2600/106 , G16B30/00 , C12Q2537/16 , C12Q2537/165 , C12Q2545/101
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。
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公开(公告)号：US09447453B2
公开(公告)日：2016-09-20
申请号：US13445778
申请日：2012-04-12
申请人： Richard P. Rava , Brian K. Rhees , John P. Burke
发明人： Richard P. Rava , Brian K. Rhees , John P. Burke
CPC分类号： G06F19/22 , C12Q1/6809 , C12Q1/6827 , C12Q1/6876 , C12Q1/6883 , C12Q2600/156 , G06F19/18 , G06F19/24 , G06F19/26 , C12Q2535/122 , C12Q2537/16 , C12Q2537/165
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).
摘要翻译： 公开了从诸如小碱基变异或插入缺失的多态性可靠地估计基因组分数（例如胎儿级分）的方法。 来自多基因组源的序列数据用于确定一个或多个多态性的等位基因计数。 对于一个或多个多态性，分配接合性，并且从接合度和等位基因计数确定基因组分数。 某些实施方案使用SNP作为相关多态性。 所公开的方法可以作为针对已知多态性的有意的，预先设计的重排序研究的一部分来应用，或者可以用于回顾性分析由母体血浆（或任何其他设置 来自几个人的DNA的混合物存在）。
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公开(公告)号：US20130034546A1
公开(公告)日：2013-02-07
申请号：US13555010
申请日：2012-07-20
申请人： Richard P. Rava , Brian K. Rhees
发明人： Richard P. Rava , Brian K. Rhees
IPC分类号： G06F19/18 , G06Q50/24 , A61P35/00 , C40B20/00 , A61K39/395
CPC分类号： G16B30/00 , C12Q1/6806 , C12Q1/6809 , C12Q1/6869 , C12Q1/6883 , C12Q1/6886 , C12Q2600/106 , G16H50/20 , G16H50/30 , C12Q2537/16 , C12Q2537/165 , C12Q2545/101
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。
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公开(公告)号：US20120149582A1
公开(公告)日：2012-06-14
申请号：US13364809
申请日：2012-02-02
IPC分类号： C40B20/00
CPC分类号： C12Q1/6806 , C12Q1/6809 , C12Q1/6869 , C12Q1/6883 , C12Q1/6886 , C12Q2600/106 , G16B30/00 , C12Q2545/101 , C12Q2535/122 , C12Q2531/113 , C12Q2537/16 , C12Q2537/165
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 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.
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公开(公告)号：US20120264121A1
公开(公告)日：2012-10-18
申请号：US13445778
申请日：2012-04-12
申请人： Richard P. Rava , Brian K. Rhees , John P. Burke
发明人： Richard P. Rava , Brian K. Rhees , John P. Burke
CPC分类号： G06F19/22 , C12Q1/6809 , C12Q1/6827 , C12Q1/6876 , C12Q1/6883 , C12Q2600/156 , G06F19/18 , G06F19/24 , G06F19/26 , C12Q2535/122 , C12Q2537/16 , C12Q2537/165
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).
摘要翻译： 公开了从诸如小碱基变异或插入缺失的多态性可靠地估计基因组分数（例如胎儿级分）的方法。 来自多基因组源的序列数据用于确定一个或多个多态性的等位基因计数。 对于一个或多个多态性，分配接合性，并且从接合度和等位基因计数确定基因组分数。 某些实施方案使用SNP作为相关多态性。 所公开的方法可以作为针对已知多态性的有意的，预先设计的重排序研究的一部分来应用，或者可以用于回顾性分析由母体血浆（或任何其他设置 来自几个人的DNA的混合物存在）。
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公开(公告)号：US20110177517A1
公开(公告)日：2011-07-21
申请号：US13009708
申请日：2011-01-19
申请人： Richard P. Rava , Brian K. Rhees , John P. Burke
发明人： Richard P. Rava , Brian K. Rhees , John P. Burke
IPC分类号： C12Q1/68
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。
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公开(公告)号：US09260745B2
公开(公告)日：2016-02-16
申请号：US13555037
申请日：2012-07-20
申请人： Richard P. Rava , Brian K. Rhees
发明人： Richard P. Rava , Brian K. Rhees
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6809 , C12Q1/6869 , C12Q1/6883 , C12Q1/6886 , C12Q2600/106 , G06F19/22 , C12Q2537/16 , C12Q2537/165 , C12Q2545/101
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。
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