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公开(公告)号：EP2623613B8
公开(公告)日：2016-09-07
申请号：EP13164430.4
申请日：2011-09-20
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6855 , C12N15/1065 , C12Q1/6869 , C12Q1/6886 , C12Q1/70 , G06F19/18 , C12Q2525/179 , C12Q2525/191 , C12Q2545/101
摘要： Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.
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2.发明公开METHODS AND COMPOSITIONS FOR POLYNUCLEOTIDE LIBRARY PRODUCTION, IMMORTALIZATION AND REGION OF INTEREST EXTRACTION 有权方法产生和长期存在的多核苷酸图书馆与提取相关领域THEREOF
公开(公告)号：EP2585593A2
公开(公告)日：2013-05-01
申请号：EP11773540.7
申请日：2011-06-20
发明人： OSBORNE, Robert , SLATTER, Andrew
IPC分类号： C12N15/10
CPC分类号： C40B50/06 , C12N15/1093 , C12Q1/6806 , C12Q2521/101 , C12Q2525/191 , C12Q2563/179 , C12Q2525/151 , C12Q2525/185 , C12Q2525/204 , C12Q2531/131 , C12Q2535/138
摘要： Aspects of the present invention are drawn to methods and compositions for the genetic analysis of regions of interest (ROI) from one or more starting polynucleotide sample(s). In certain aspects, adapter tagged polynucleotide fragments from a plurality of initial polynucleotide samples are pooled, circularized and amplified to produce an immortalized library. Multiple ROI's from this immortalized library are amplified (e.g., in independent iPCR reactions) to generate amplicons, and, in some embodiments, pooled to form a pooled ROI amplicon sample. In certain embodiments, the amplicons for each ROI amplicon in the pooled ROI amplicon sample are present at known molar or mass ratios. The pooled ROI amplicon sample can be analyzed/processed as desired, e.g., sequenced using next generation sequencing technology.
摘要翻译： 本发明的各方面提出一种用于从一个或多个起始多核苷酸样品（多个）感兴趣区域（ROI）的区域的基因分析方法和组合物。 在某些方面，适配器标记的多核苷酸片段从初始多核苷酸样品的多元性汇集，环化和放大以产生在永生化文库。 从该永生化库中的多个ROI的扩增（例如，在独立的iPCR中的反应），以产生扩增子，并且在一些实施例中，合并，以形成合并的ROI扩增子样品。 在某些实施方案中，在合并样本ROI扩增每个ROI的扩增子扩增子存在于已知摩尔或质量比。 将合并的ROI扩增子样品进行分析/根据需要进行处理，E. G.使用下一代测序技术测序。
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3.发明公开Methods and compositions for isolating nucleic acid sequence variants 审中-公开Verfahren und Zusammensetzungen zur Isolierung vonNukleinsäuresequenzvarianten
公开(公告)号：EP2395113A1
公开(公告)日：2011-12-14
申请号：EP11164766.5
申请日：2008-06-27
发明人： Brenner, Sydney
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6827 , C12Q1/6869 , C12Q2565/537 , C12Q2533/101 , C12Q2525/186 , C12Q2531/119 , C12Q2565/514 , C12Q2535/101
摘要： The invention is drawn to isolating sequence variants of a genetic locus of interest using a modified iterative primer extension method. The nucleic acids analysed are generally single stranded and have a reference sequence which is used as a basis for performing iterative single nucleotide extension reactions from a hybridized polymerization primer. The iterative polymerization reactions are configured such that polymerization of the strand will continue if the sequence of the nucleic acid being analysed matches the reference sequence, whereas polymerization will be terminated if the nucleic acid being analysed does not match the reference sequence. Nucleic acid strands that have mutations can be isolated using a variety of methods and sequenced to determine the precise identity of the mutation/polymorphism. By performing the method on both strands of the nucleic acid being analysed, virtually all possible mutations can be identified.
摘要翻译： 本发明是使用改进的迭代引物延伸方法来分离遗传基因座的序列变体。 分析的核酸通常是单链的，并且具有参考序列，其用作从杂交聚合引物进行迭代单核苷酸延伸反应的基础。 配置迭代聚合反应，使得如果待分析的核酸序列与参考序列匹配，则链的聚合将持续，而如果所分析的核酸与参考序列不一致则聚合将终止。 可以使用多种方法分离具有突变的核酸链，并进行测序以确定突变/多态性的精确同一性。 通过对正在分析的核酸的两条链进行该方法，实际上可以鉴定所有可能的突变。
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公开(公告)号：EP1713936B1
公开(公告)日：2009-12-09
申请号：EP05713268.0
申请日：2005-02-10
发明人： BRENNER, Sydney
CPC分类号： C12Q1/6827 , C12Q1/6834 , C12Q2563/131 , C12Q2525/186 , C12Q2525/161
摘要： The invention provides methods for sorting polynucleotides from a population based on predetermined sequence characteristics. In one aspect, the method of the invention is carried out by extending a primer annealed polynucleotides having predetermined sequence characteristics to incorporate a predetermined terminator having a capture moiety, capturing polynucleotides having extended primers by a capture agent that specifically binds to the capture moiety, and melting the captured polynucleotides from the extended primers to form a subpopulation of polynucleotides having the predetermined sequence characteristics. In another aspect, the method of the invention is carried out on a population of tagged polynucleotides so that after a subpopulation is selected, the members of the subpopulation may be simultaneously analyzed using the unique tags on the polynucleotides to convey analytical information to a hybridization array for a readout.
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公开(公告)号：EP1987162A2
公开(公告)日：2008-11-05
申请号：EP07762572.1
申请日：2007-01-22
发明人： BRENNER, Sydney
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6837 , C12Q1/6827 , C12Q2563/179 , C12Q2537/113 , C12Q2525/186
摘要： The present invention provides methods and compositions for tagging nucleic acid sequence fragments, e.g., a set of nucleic acid sequence fragments from a single genome, with one or more unique members of a collection of oligonucleotide tags, or sequence tokens, which, in turn, can be identified using a variety of readout platforms. As a general rule, a given sequence token is used once and only once in any tag sequence. In addition, the present invention also provides methods for using the sequence tokens to efficiently determine variations in nucleotide sequences in the associated nucleic acid sequence fragments.
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6.发明公开SORTING ASYMMETRICALLY TAGGED NUCLEIC ACIDS BY SELECTIVE PRIMER EXTENSION 审中-公开所提供同位素标记选择性引物延伸不对称标签排序
公开(公告)号：EP2432899A1
公开(公告)日：2012-03-28
申请号：EP10732743.9
申请日：2010-05-21
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6809 , C12Q2531/107 , C12Q2525/191 , C12Q2525/155
摘要： The present invention provides methods and compositions for amplifying and sorting adapter tagged nucleic acid fragments using selective primer extension. Immortalized pooled polynucleotide samples and method of producing the same are also provided.
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公开(公告)号：EP3224374A1
公开(公告)日：2017-10-04
申请号：EP15797459.3
申请日：2015-11-12
IPC分类号： C12Q1/68
摘要： Providing herein, among other things, is a method for preparing a nucleic acid for sequencing. In some embodiments, the method comprises a) amplifying a nucleic acid template using a dNTP mix that contains 5-methyl dCTP, thereby producing product nucleic acid molecules that contains methylcytosines; b) digesting the product nucleic acid molecules with a methylation-dependent restriction endonuclease, thereby cleaving the product nucleic acid molecules at sites that are adjacent to at least some of the methylcytosine and producing fragments of the product nucleic acid molecules; and c) ligating double-stranded adaptors onto the ends of the fragments to produce adaptor-ligated products.
摘要翻译： 描述了用于制备用于测序的核酸的方法。 该方法包括a）使用含有5-甲基dCTP的dNTP混合物扩增核酸模板，从而产生含有甲基胞嘧啶的产物核酸分子; b）用MspJI家族限制性内切核酸酶消化产物核酸分子，由此在与至少一些甲基胞嘧啶邻近的位点切割产物核酸分子，并产生产物核酸分子的片段; 和c）将双链接头连接到片段的末端以产生接头连接产物。 所用的酶包括MspJI，FspEI，LpnPI和SgeI。 扩增方法可以是PCR或等温扩增。 还描述了用于实施包括含有5-甲基dCTP，一种或多种MspJI家族限制性内切核酸酶和双链衔接子的dNTP混合物的方法的试剂盒。
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公开(公告)号：EP2820155B1
公开(公告)日：2017-07-26
申请号：EP13721058.9
申请日：2013-02-26
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6806 , C12Q1/6853 , C12Q2521/301 , C12Q2525/161 , C12Q2525/179
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9.发明授权METHODS FOR POLYNUCLEOTIDE LIBRARY PRODUCTION, IMMORTALIZATION AND REGION OF INTEREST EXTRACTION 有权方法产生和长期存在的多核苷酸图书馆与提取相关领域THEREOF
公开(公告)号：EP2585593B1
公开(公告)日：2017-03-01
申请号：EP11773540.7
申请日：2011-06-20
发明人： OSBORNE, Robert , SLATTER, Andrew
IPC分类号： C12Q1/68
CPC分类号： C40B50/06 , C12N15/1093 , C12Q1/6806 , C12Q2521/101 , C12Q2525/191 , C12Q2563/179 , C12Q2525/151 , C12Q2525/185 , C12Q2525/204 , C12Q2531/131 , C12Q2535/138
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公开(公告)号：EP3077539A1
公开(公告)日：2016-10-12
申请号：EP14841366.9
申请日：2014-11-26
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , G06F19/22 , C12Q2535/122 , C12Q2545/101
摘要： A method of evaluating a sequence variation in a sample is provided. In some embodiments, the method may involve: amplifying a nucleic acid product from an initial sample; fragmenting an amount of the nucleic acid product to produce fragments; attaching an adaptor to each end of the fragments to produce adaptor-tagged fragments; sampling no more than 10% of the tagged fragments and amplifying them; sequencing at least some of the copies of the fragments to produce a plurality of sequence reads; grouping sequence reads for copies of fragments that have the same fragmentation breakpoints; deriving a consensus sequence for each of the read groups; and aligning the consensus sequences with a reference sequence.
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