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31. 发明申请

US20130034546A1 Analyzing Copy Number Variation in the Detection of Cancer 审中-公开
标题翻译：分析癌症检测中的拷贝数变异
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。

32. 发明申请

US20120149582A1 METHOD FOR DETERMINING COPY NUMBER VARIATIONS 审中-公开
公开(公告)号：US20120149582A1
公开(公告)日：2012-06-14
申请号：US13364809
申请日：2012-02-02
申请人： Richard P. Rava , David A. Comstock , Brian K. Rhees
发明人： Richard P. Rava , David A. Comstock , Brian K. Rhees
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.

33. 发明申请

US20110230358A1 IDENTIFICATION OF POLYMORPHIC SEQUENCES IN MIXTURES OF GENOMIC DNA BY WHOLE GENOME SEQUENCING 审中-公开
标题翻译：通过全基因组序列鉴定基因组DNA混合物中的多态性序列
公开(公告)号：US20110230358A1
公开(公告)日：2011-09-22
申请号：US13009718
申请日：2011-01-19
申请人： Richard P. Rava
发明人： Richard P. Rava
IPC分类号： C40B30/00 , C12Q1/68
CPC分类号： C12Q1/6883 , C12Q1/6827 , C12Q1/6886 , C12Q2600/16 , C12Q2600/172 , C12Q2565/125 , C12Q2535/122
摘要： The present invention relates to methods comprising whole genome sequencing for identifying polymorphisms in samples comprising mixtures of genomes, and for determining and/or monitoring the presence or absence of disorders associated with the identified polymorphisms.
摘要翻译：本发明涉及包含用于鉴定包含基因组混合物的样品中的多态性以及用于确定和/或监测与所鉴定的多态性相关的病症的存在或不存在的全基因组测序的方法。

34. 发明申请

US20120264121A1 RESOLVING GENOME FRACTIONS USING POLYMORPHISM COUNTS 有权
标题翻译：使用多态性计算解决基因组分析
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
IPC分类号： C12Q1/68 , G06F19/20 , C12M1/34
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）。

35. 发明申请

US20120165203A1 SIMULTANEOUS DETERMINATION OF ANEUPLOIDY AND FETAL FRACTION 审中-公开
标题翻译：同时确定骨质疏松症和骨质疏松症
公开(公告)号：US20120165203A1
公开(公告)日：2012-06-28
申请号：US13365240
申请日：2012-02-02
申请人： Stephen Quake , Richard P. Rava , Manjula Chinnappa , David A. Comstock , Gabrielle Heilek
发明人： Stephen Quake , Richard P. Rava , Manjula Chinnappa , David A. Comstock , Gabrielle Heilek
IPC分类号： C12Q1/68 , C40B20/00
CPC分类号： C12Q1/6869 , C12Q1/6806 , C12Q1/6809 , C12Q1/6883 , C12Q2600/106 , C12Q2537/16 , C12Q2537/165 , C12Q2545/101
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 form 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.
摘要翻译：本发明提供用于同时确定胎儿非整倍性的存在或不存在的组合物和方法以及从孕妇获得的样品中的胎儿核酸的相对量。该方法包括使用测序技术，并利用多态性的发生来提供适用于产前诊断实践的流线型非侵入性过程。

36. 发明申请

US20110177517A1 PARTITION DEFINED DETECTION METHODS 有权
标题翻译：分区定义检测方法
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。

37. 发明授权

US06566515B1 Photocleavable protecting groups and methods for their use 有权
标题翻译：可透光保护组及其使用方法
公开(公告)号：US06566515B1
公开(公告)日：2003-05-20
申请号：US09525045
申请日：2000-03-14
申请人： Glenn H. McGall , Ngo Q. Nam , Richard P. Rava
发明人： Glenn H. McGall , Ngo Q. Nam , Richard P. Rava
IPC分类号： C07H2104
CPC分类号： C07H21/00 , B01J2219/00432 , C07B2200/11 , C07H19/10 , C07H19/20 , C07H19/207 , C07K1/061 , C40B40/04 , C40B50/14 , C40B60/14 , G01N33/54353 , Y02P20/55
摘要： Novel compounds are provided which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Ar—C(R1)(R2)—O—C(O)— wherein: Ar is an optionally substituted fused polycyclic aryl or heteroaromatic group or a vinylogous derivative thereof; R1 and R2 are independently H, optionally substituted alkyl, alkenyl or alkynyl, optionally substituted aryl or optionally substituted heteroaromatic, or a vinylogous derivative of the foregoing; and X is a leaving group, a chemical fragment linked to Ar—C(R1)(R2)—O—C(O)— via a heteroatom, or a solid support; provided that when Ar is 1-pyrenyl and R1 and R2 are H, X is not linked to Ar—C(R1)(R2)—O—C(O)— via a nitrogen atom. Preferred embodiments are those in which Ar is a fused polycyclic aromatic hydrocarbon and in which the substituents on Ar, R1 and R2 are electron donating groups. A particularly preferred protecting group is the “PYMOC” protecting group, pyrenylmethyloxycarbonyl, where Ar is pyrenyl and R1 and R2 are H. Also provided is a method of forming, from component molecules, a plurality of compounds on a support, each compound occupying a separate predefined region of the support, using the protected compounds described above.
摘要翻译：提供了新的化合物，其可用作化学合成中的连接基团，优选在寡核苷酸和多肽的固相合成中。这些化合物通常是光不稳定的并且包括可以通过光解去除以揭示反应性基团的保护基团。保护基具有通式Ar-C（R 1）（R 2）-OC（O） - ，其中：Ar是任选取代的稠合多环芳基或杂芳族基团或其杂原子衍生物; R 1和R 2独立地是H，烷基，烯基或炔基，任选取代的芳基或任选取代的杂芳族，或前述的维果衍生物; 和X是离去基团，通过杂原子与固体载体连接至Ar-C（R 1）（R 2）-O-C（O） - 的化学片段; 条件是当Ar为1-芘基且R 1和R 2为H时，X不能通过氮原子与Ar-C（R 1）（R 2）-O-C（O） - 连接。优选的实施方案是其中Ar是稠合多环芳烃并且其中Ar，R 1和R 2上的取代基是给电子基团的实施方案。特别优选的保护基是“PYMOC”保护基团，芘基甲氧基羰基，其中Ar是芘基，R 1和R 2是H.另外提供了一种从成分分子在载体上形成多种化合物的方法，使用上述保护的化合物分离预定区域的载体。

38. 发明授权

US06294327B1 Apparatus and method for detecting samples labeled with material having strong light scattering properties, using reflection mode light and diffuse scattering 失效
标题翻译：使用反射模式光和漫射散射光检测用具有强光散射特性的材料标记的样品的装置和方法
公开(公告)号：US06294327B1
公开(公告)日：2001-09-25
申请号：US09013596
申请日：1998-01-26
申请人： Ian D. Walton , Mark O. Trulson , Richard P. Rava
发明人： Ian D. Walton , Mark O. Trulson , Richard P. Rava
IPC分类号： C12Q168
CPC分类号： G01N21/55 , B01J2219/00605 , B01J2219/00612 , B01J2219/00659 , B01J2219/00702
摘要： A system and method for imaging a sample labeled with a material having a strong light scattering and reflecting properties are provided. A typical material having strong light scattering and reflecting properties is a metal colloid. The imaging system employs a light scattering and reflecting illumination technique. The sample can be imaged with reflection mode imaging along or with a combination of reflection mode and scatter mode imaging.
摘要翻译：提供了用具有强光散射和反射特性的材料标记的样品成像的系统和方法。具有强光散射性和反射性的典型材料是金属胶体。成像系统采用光散射和反射照明技术。可以沿着反射模式和散射模式成像的反射模式成像或与反射模式和散射模式成像的组合对样本进行成像。

39. 发明授权

US5562100A Method for laser induced fluorescence of tissue 失效
标题翻译：激光诱导组织荧光的方法
公开(公告)号：US5562100A
公开(公告)日：1996-10-08
申请号：US249086
申请日：1994-05-25
申请人： Carter Kittrell , Robert M. Cothren , Michael S. Feld , Joseph J. Baraga , Kyungwon An , Rebecca Richards-Kortum , Richard P. Rava , Young D. Park , Anand V. Mehta , Paola Taroni , Lucene Tong , Ramachandra R. Dasari
发明人： Carter Kittrell , Robert M. Cothren , Michael S. Feld , Joseph J. Baraga , Kyungwon An , Rebecca Richards-Kortum , Richard P. Rava , Young D. Park , Anand V. Mehta , Paola Taroni , Lucene Tong , Ramachandra R. Dasari
IPC分类号： A61B5/00 , A61B18/24
CPC分类号： A61B5/0084 , A61B18/245 , A61B5/0071 , A61B5/0075 , A61B5/1459 , A61B2562/0238
摘要： A method for laser induced fluorescence of tissue in which laser radiation is used to illuminate and induce fluorescence in the tissue under study to determine the chemical composition or pathologic condition of tissue. The laser radiation and the retrieved fluorescing radiation can be conveyed through a catheter using an array of optical fiber. The fluorescence spectrum of the tissue can be displayed and analyzed to obtain information regarding the chemical composition and medical condition of the tissue inside the human body.
摘要翻译：激光诱导荧光组织的方法，其中使用激光辐射来照射和诱导正在研究的组织中的荧光以确定组织的化学组成或病理状况。激光辐射和所检索的荧光辐射可以使用光纤阵列通过导管输送。可以显示和分析组织的荧光光谱，以获得关于人体内组织的化学成分和医疗状况的信息。

40. 发明授权

US10662474B2 Identification of polymorphic sequences in mixtures of genomic DNA by whole genome sequencing 有权
公开(公告)号：US10662474B2
公开(公告)日：2020-05-26
申请号：US13009718
申请日：2011-01-19
申请人： Richard P. Rava
发明人： Richard P. Rava
IPC分类号： C12Q1/6827 , C12Q1/6883 , C12Q1/6809 , C12Q1/6869 , C12Q1/6886
摘要： The present invention relates to methods comprising whole genome sequencing for identifying polymorphisms in samples comprising mixtures of genomes, and for determining and/or monitoring the presence or absence of disorders associated with the identified polymorphisms.

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