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1.发明申请METHOD, COMPUTER-ACCESSIBLE MEDIUM, AND SYSTEMS FOR GENERATING A GENOME WIDE HAPLOTYPE SEQUENCE 有权方法，计算机可访问介质和用于产生基因型宽带序列的系统公开(公告)号：US20150120209A1
公开(公告)日：2015-04-30
申请号：US14269670
申请日：2014-05-05
摘要： Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the genome wide restriction map(s) and locations of detectable oligonucleotide probes of the genome wide probe map(s) and defining a consensus map indicating restriction sites based on the genome wide restriction map(s) and/or locations of detectable oligonucleotide probes based on each of the genome wide probe map(s).
摘要翻译： 提供了用于产生基因组宽探针图和/或基因组宽单倍型序列的方法，计算机可访问介质和系统。 特别地，通过获得与至少一个用至少一个限制酶切割的至少一个双链核酸分子杂交的多个可检测的寡核苷酸探针，并检测可检测的寡核苷酸探针的位置，可以产生基因组宽探针图。 例如，可以通过分析至少一个基因组宽限制图与至少一个基因组宽的探针图来分析基因组宽单倍型序列，以确定基因组宽限制图的限制性位点与可检测的寡核苷酸探针的位置之间的距离 的基因组宽探针图并且基于基因组宽的探针图基于全基因组宽限制图和/或可检测的寡核苷酸探针的位置来定义表示限制性位点的共有图谱。
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2.发明授权Methods, computer-accessible medium, and systems for generating a genome wide haplotype sequence 有权方法，计算机可访问介质和用于产生基因组宽单倍型序列的系统公开(公告)号：US08718951B2
公开(公告)日：2014-05-06
申请号：US13422703
申请日：2012-03-16
摘要： Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the genome wide restriction map(s) and locations of detectable oligonucleotide probes of the genome wide probe map(s) and defining a consensus map indicating restriction sites based on the genome wide restriction map(s) and/or locations of detectable oligonucleotide probes based on each of the genome wide probe map(s).
摘要翻译： 提供了用于产生基因组宽探针图和/或基因组宽单倍型序列的方法，计算机可访问介质和系统。 特别地，通过获得与至少一个用至少一个限制酶切割的至少一个双链核酸分子杂交的多个可检测的寡核苷酸探针，并检测可检测的寡核苷酸探针的位置，可以产生基因组宽探针图。 例如，可以通过分析至少一个基因组宽限制图与至少一个基因组宽的探针图来分析基因组宽单倍型序列，以确定基因组宽限制图的限制性位点与可检测的寡核苷酸探针的位置之间的距离 的基因组宽探针图并且基于基因组宽的探针图基于全基因组宽限制图和/或可检测的寡核苷酸探针的位置来定义表示限制性位点的共有图谱。
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公开(公告)号：US20120183953A1
公开(公告)日：2012-07-19
申请号：US13096408
申请日：2011-04-28
申请人： Nianqing XIAO , John K. HENKHAUS , Bin ZHU , Deacon SWEENEY , Thomas ANANTHARAMAN , Ryan PTASHKIN
发明人： Nianqing XIAO , John K. HENKHAUS , Bin ZHU , Deacon SWEENEY , Thomas ANANTHARAMAN , Ryan PTASHKIN
CPC分类号： C12Q1/6869 , C12Q2521/301 , C12Q2523/31 , C12Q2565/601
摘要： The invention generally relates to methods for assembling sequence contigs. In certain embodiments, methods of the invention involve converting sequence contigs into maps, generating a plurality of single molecule restriction maps, aligning single molecule restriction maps to ends of the maps of the sequence contigs, thereby producing extended sequence contigs, and aligning extended sequence contigs.
摘要翻译： 本发明一般涉及组装序列重叠群的方法。 在某些实施方案中，本发明的方法涉及将序列重叠群转化为图，产生多个单分子限制性图谱，将单分子限制图谱对准序列重叠群的图的末端，从而产生扩增序列重叠群，并对齐扩增序列重叠群 。
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4.发明申请公开(公告)号：US20050255508A1
公开(公告)日：2005-11-17
申请号：US11093565
申请日：2005-03-30
CPC分类号： G06F19/22
摘要： The present invention relates to a method, system and software arrangement for determining the co-associations of allele types across consecutive loci and hence for reconstructing two haplotypes of a diploid individual from genotype data generated by mapping experiments with single molecules, families or populations. The haplotype reconstruction system, method and software arrangement of the present invention can utilize a procedure that is nearly linear in the number of polymorphic markers examined, and is therefore quicker, more accurate, and more efficient than other population-based approaches. The system, method, and software arrangement of the present invention may be useful to assist with the diagnosis and treatment of any disease, which has a genetic component.
摘要翻译： 本发明涉及用于确定跨连续基因座的等位基因类型的共同关联的方法，系统和软件装置，因此用于通过用单个分子，家族或群体的测绘实验产生的基因型数据重建二倍体个体的两个单体型。 本发明的单倍型重建系统，方法和软件安排可以利用所检查的多态性标记数量几乎是线性的程序，因此比其他基于群体的方法更快，更准确，更有效。 本发明的系统，方法和软件安排可能有助于诊断和治疗任何具有遗传成分的疾病。
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5.发明申请METHODS, COMPUTER-ACCESSIBLE MEDIUM, AND SYSTEMS FOR GENERATING A GENOME WIDE HAPLOTYPE SEQUENCE 有权方法，计算机可访问的介质和用于生成基因型大分子序列的系统公开(公告)号：US20080228457A1
公开(公告)日：2008-09-18
申请号：US12046988
申请日：2008-03-12
IPC分类号： G06G7/48
摘要： Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the at least one genome wide restriction map and locations of detectable oligonucleotide probes of the at least one genome wide probe map and defining a consensus map indicating restriction sites based on each of the at least one genome wide restriction map and locations of detectable oligonucleotide probes based on each of the at least one genome wide probe map.
摘要翻译： 提供了用于产生基因组宽探针图和/或基因组宽单倍型序列的方法，计算机可访问介质和系统。 特别地，通过获得与至少一个用至少一个限制酶切割的至少一个双链核酸分子杂交的多个可检测的寡核苷酸探针，并检测可检测的寡核苷酸探针的位置，可以产生基因组宽探针图。 例如，可以通过分析至少一个基因组宽限制性图谱与至少一个基因组宽的探针图来分析至少一个全基因组限制性图谱的限制性位点与可检测的寡核苷酸探针的位置之间的距离来产生全基因组单倍型序列 的所述至少一个基因组宽探针图并且基于所述至少一个全基因组限制图中的每一个和基于所述至少一个全基因组宽度探针图中的每一个的可检测寡核苷酸探针的位置来定义指示限制性位点的共有图。
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6.发明申请METHODS, COMPUTER-ACCESSIBLE MEDIUM, AND SYSTEMS FOR GENERATING A GENOME WIDE HAPLOTYPE SEQUENCE 有权方法，计算机可访问的介质和用于生成基因型大分子序列的系统公开(公告)号：US20130045879A1
公开(公告)日：2013-02-21
申请号：US13422703
申请日：2012-03-16
摘要： Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the genome wide restriction map(s) and locations of detectable oligonucleotide probes of the genome wide probe map(s) and defining a consensus map indicating restriction sites based on the genome wide restriction map(s) and/or locations of detectable oligonucleotide probes based on each of the genome wide probe map(s).
摘要翻译： 提供了用于产生基因组宽探针图和/或基因组宽单倍型序列的方法，计算机可访问介质和系统。 特别地，通过获得与至少一个用至少一个限制酶切割的至少一个双链核酸分子杂交的多个可检测的寡核苷酸探针，并检测可检测的寡核苷酸探针的位置，可以产生基因组宽探针图。 例如，可以通过分析至少一个基因组宽限制图与至少一个基因组宽的探针图来分析基因组宽单倍型序列，以确定基因组宽限制图的限制性位点与可检测的寡核苷酸探针的位置之间的距离 的基因组宽探针图并且基于基因组宽的探针图基于全基因组宽限制图和/或可检测的寡核苷酸探针的位置来定义表示限制性位点的共有图谱。
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7.发明申请PROCESS, SOFTWARE ARRANGEMENT AND COMPUTER-ACCESSIBLE MEDIUM FOR OBTAINING INFORMATION ASSOCIATED WITH A HAPLOTYPE 有权过程，软件安排和计算机可访问的媒体，用于获取与HAPLOTYPE相关的信息公开(公告)号：US20110087437A1
公开(公告)日：2011-04-14
申请号：US12890464
申请日：2010-09-24
IPC分类号： G06F19/00
CPC分类号： G06F19/22
摘要： The present invention relates to a method, system and software arrangement for determining the co-associations of allele types across consecutive loci and hence for reconstructing two haplotypes of a diploid individual from genotype data generated by mapping experiments with single molecules, families or populations. The haplotype reconstruction system, method and software arrangement of the present invention can utilize a procedure that is nearly linear in the number of polymorphic markers examined, and is therefore quicker, more accurate, and more efficient than other population-based approaches. The system, method, and software arrangement of the present invention may be useful to assist with the diagnosis and treatment of any disease, which has a genetic component.
摘要翻译： 本发明涉及用于确定跨连续基因座的等位基因类型的共同关联的方法，系统和软件装置，因此用于通过用单个分子，家族或群体的测绘实验产生的基因型数据重建二倍体个体的两个单体型。 本发明的单倍型重建系统，方法和软件安排可以利用所检查的多态性标记数量几乎是线性的程序，因此比其他基于群体的方法更快，更准确，更有效。 本发明的系统，方法和软件安排可能有助于诊断和治疗任何具有遗传成分的疾病。
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8.发明授权System and process for validating, aligning and reordering one or more genetic sequence maps using at least one ordered restriction map 有权使用至少一个有序限制图来验证，对准和重新排序一个或多个遗传序列图的系统和过程公开(公告)号：US07831392B2
公开(公告)日：2010-11-09
申请号：US10432766
申请日：2001-09-28
申请人： Marco Antoniotti , Bhubaneswar Mishra , Thomas Anantharaman , Salvatore Paxia , David C. Schwartz
发明人： Marco Antoniotti , Bhubaneswar Mishra , Thomas Anantharaman , Salvatore Paxia , David C. Schwartz
CPC分类号： G06F19/22
摘要： A method and system are provided for comparing ordered segments of a first DNA restriction map with ordered segments of a second DNA restriction map to determine a level of accuracy the first DNA map and/or the second DNA map. In particular, the first and second DNA maps can be received (the first DNA map corresponding to a sequence DNA map, and the second DNA map corresponding to a genomic consensus DNA map as provided in an optical DNA map). Then, the accuracy of the first DNA map and/or the second DNA map is validated based on information associated with the first and second DNA maps. In addition, a method and system are provided for aligning a plurality of DNA sequences with a ordered DNA restriction map. The DNA sequences and the DNA map are received (the DNA sequences being fragments of a genome and the DNA map corresponding to a genomic consensus DNA map which relates to an optical ordered DNA map). Then, a level of accuracy of the DNA sequences and the DNA map is obtained based on information associated with the DNA sequences and the DNA map by means of the method and system described above. The locations of the DNA map at which the DNA sequences are capable of being associated with particular segments of the DNA map are located. Furthermore, it is possible to obtain locations of the DNA map (without the validation) by locating an optimal one of the locations for each of the DNA sequences for each of the locations.
摘要翻译： 提供了一种方法和系统，用于将第一DNA限制性图谱的有序区段与第二DNA限制图谱的有序区段进行比较，以确定第一DNA图谱和/或第二DNA图谱的准确度。 特别地，可以接收第一个和第二个DNA图谱（对应于序列DNA图谱的第一个DNA图谱，和对应于光学DNA图谱中提供的基因组共有DNA图谱的第二个DNA图谱）。 然后，基于与第一和第二DNA图相关联的信息来验证第一DNA图和/或第二DNA图的准确性。 此外，提供了用于使多个DNA序列与有序DNA限制图对齐的方法和系统。 接受DNA序列和DNA图谱（DNA序列是基因组的片段，DNA图谱对应于涉及光学有序DNA图谱的基因组共有DNA图谱）。 然后，通过上述方法和系统，基于与DNA序列和DNA图谱相关的信息，获得DNA序列和DNA图谱的准确度。 DNA序列的DNA图谱位置可以与DNA图谱的特定片段相关联。 此外，通过为每个位置定位每个DNA序列的最佳位置之一，可以获得DNA图谱的位置（无需验证）。
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9.发明授权Process, software arrangement and computer-accessible medium for obtaining information associated with a haplotype 有权过程，软件安排和计算机可访问介质，用于获得与单倍体相关的信息公开(公告)号：US07805282B2
公开(公告)日：2010-09-28
申请号：US11093565
申请日：2005-03-30
CPC分类号： G06F19/22
摘要： The present invention relates to a method, system and software arrangement for determining the co-associations of allele types across consecutive loci and hence for reconstructing two haplotypes of a diploid individual from genotype data generated by mapping experiments with single molecules, families or populations. The haplotype reconstruction system, method and software arrangement of the present invention can utilize a procedure that is nearly linear in the number of polymorphic markers examined, and is therefore quicker, more accurate, and more efficient than other population-based approaches. The system, method, and software arrangement of the present invention may be useful to assist with the diagnosis and treatment of any disease, which has a genetic component.
摘要翻译： 本发明涉及用于确定跨连续基因座的等位基因类型的共同关联的方法，系统和软件装置，因此用于通过用单个分子，家族或群体的测绘实验产生的基因型数据重建二倍体个体的两个单体型。 本发明的单倍型重建系统，方法和软件安排可以利用所检查的多态性标记数量几乎是线性的程序，因此比其他基于群体的方法更快，更准确，更有效。 本发明的系统，方法和软件安排可能有助于诊断和治疗任何具有遗传成分的疾病。
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10.发明授权Methods, computer-accessible medium, and systems for generating a genome wide haplotype sequence 有权方法，计算机可访问介质和用于产生基因组宽单倍型序列的系统公开(公告)号：US08140269B2
公开(公告)日：2012-03-20
申请号：US12046988
申请日：2008-03-12
摘要： Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the at least one genome wide restriction map and locations of detectable oligonucleotide probes of the at least one genome wide probe map and defining a consensus map indicating restriction sites based on each of the at least one genome wide restriction map and locations of detectable oligonucleotide probes based on each of the at least one genome wide probe map.
摘要翻译： 提供了用于产生基因组宽探针图和/或基因组宽单倍型序列的方法，计算机可访问介质和系统。 特别地，通过获得与至少一个用至少一个限制酶切割的至少一个双链核酸分子杂交的多个可检测的寡核苷酸探针，并检测可检测的寡核苷酸探针的位置，可以产生基因组宽探针图。 例如，可以通过分析至少一个基因组宽限制性图谱与至少一个基因组宽的探针图来分析至少一个全基因组限制性图谱的限制性位点与可检测的寡核苷酸探针的位置之间的距离来产生全基因组单倍型序列 的所述至少一个基因组宽探针图并且基于所述至少一个全基因组限制图中的每一个和基于所述至少一个全基因组宽度探针图中的每一个的可检测寡核苷酸探针的位置来定义指示限制性位点的共有图。
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