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    VARIETAL COUNTING OF NUCLEIC ACIDS FOR OBTAINING GENOMIC COPY NUMBER INFORMATION
    113.
    发明申请
    VARIETAL COUNTING OF NUCLEIC ACIDS FOR OBTAINING GENOMIC COPY NUMBER INFORMATION 审中-公开
    用于获取基因组复制号码信息的核酸的数量计数

    公开(公告)号：WO2012054873A2

    公开(公告)日：2012-04-26

    申请号：PCT/US2011/057350

    申请日：2011-10-21

    Applicant: COLD SPRING HARBOR LABORATORY ,  HICKS, James ,  NAVIN, Nicholas ,  TROGE, Jennifer ,  WANG, Zihua ,  WIGLER, Michael

    Inventor： HICKS, James ,  NAVIN, Nicholas ,  TROGE, Jennifer ,  WANG, Zihua ,  WIGLER, Michael

    IPC: C12Q1/68 ,  C12N15/11 ,  C12Q1/48

    CPC classification number: C12Q1/6874 ,  C12Q1/683 ,  C12Q1/6881 ,  C12Q1/6886 ,  C12Q2600/156 ,  G06F19/20 ,  C12Q2525/155 ,  C12Q2525/191 ,  C12Q2535/122 ,  C12Q2537/159 ,  C12Q2537/16

    Abstract: A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to amplification by polymerase chain reaction (PCR), generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules having a different tag that have been assigned to the same location on the genome, thereby obtaining genomic copy number information unaffected by amplification distortion.

    Abstract translation: 一种用于从基因组材料获得未受扩增变形影响的基因组拷贝数信息的方法，包括获得所述基因组材料的片段，用基本上唯一的标签标记片段以产生标记的核酸分子，使得每个标记的核酸分子包含 基因组材料和标签，通过聚合酶链反应（PCR）对标记的核酸分子进行扩增，通过测序PCR反应的产物产生标签相关序列读数，将每个标记的核酸分子分配到与 基因组材料通过将对应于基因组材料的片段读取的每个标签相关序列的子序列映射到基因组上的位置，并计数已经被分配到相同位置的具有不同标签的标记的核酸分子的数目 基因组，从而获得基因组拷贝数信息 由放大变形引起。

    HIGH THROUGHPUT PAIRED-END SEQUENCING OF LARGE-INSERT CLONE LIBRARIES
    115.
    发明申请
    HIGH THROUGHPUT PAIRED-END SEQUENCING OF LARGE-INSERT CLONE LIBRARIES 审中-公开
    大插入式图书馆的高通量配对结果

    公开(公告)号：WO2011143231A2

    公开(公告)日：2011-11-17

    申请号：PCT/US2011035940

    申请日：2011-05-10

    Applicant: BROAD INST ,  GNIRKE ANDREAS ,  NICOL ROBERT ,  WILLIAMS LOUISE ,  COSTELLO MAURA T ,  STEELMAN SCOTT

    Inventor： GNIRKE ANDREAS ,  NICOL ROBERT ,  WILLIAMS LOUISE ,  COSTELLO MAURA T ,  STEELMAN SCOTT

    IPC: C40B30/06

    CPC classification number: C12Q1/6874 ,  C12N15/1027 ,  C12N15/1031 ,  C12N15/1093 ,  C12Q1/6869 ,  C12Q2535/122

    Abstract: The present invention is related to genomic nucleotide sequencing. In particular, the invention describes a paired end sequencing method that improves the yield of long-distance genomic read pairs by constructing long-insert clone libraries (i.e., for example, a fosIll library or a fosCN library) and converting the long-insert clone library using inverse polymerase chain reaction amplification or shearing and recircularization of shortened fragments into a library of co-ligated clone-insert ends. The resultant jumping libraries are compatible with massively parallel sequencing techniques. The compositions and methods disclosed herein contemplate sequencing complex genomes as well as detecting chromosomal structural rearrangements.

    Abstract translation: 本发明涉及基因组核苷酸测序。 特别地，本发明描述了一种配对末端测序方法，通过构建长插入克隆文库（例如，fosIll文库或fosCN文库）并转化长插入克隆，提高长距离基因组读取对的产量 文库使用反向聚合酶链反应扩增或剪切并将缩短的片段再循环到共连接的克隆插入末端的文库中。 所得到的跳转库与大规模并行测序技术相兼容。 本文公开的组合物和方法考虑了对复合基因组的测序以及检测染色体结构重排。

    GENOTYPING METHOD
    116.
    发明申请
    GENOTYPING METHOD 审中-公开
    基因方法

    公开(公告)号：WO2011059285A3

    公开(公告)日：2011-10-06

    申请号：PCT/KR2010008055

    申请日：2010-11-15

    Applicant: GENOMICTREE INC ,  AN SUNG WHAN ,  OH MYUNG SOK

    Inventor： AN SUNG WHAN ,  OH MYUNG SOK

    IPC: C12Q1/68 ,  C12N15/11

    CPC classification number: C12Q1/6874 ,  C12Q1/68 ,  C12Q1/6869 ,  C12Q1/6886 ,  C12Q1/701 ,  C12Q1/708 ,  C12Q2525/185 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2563/179 ,  C12Q2565/301 ,  C12Q2600/156 ,  C12Q2600/16 ,  C12Q2525/155

    Abstract: The present invention relates to a genotyping method, and more particularly, to an ID sequence provided for each genotype and to a multi-genotyping method using the ID sequence. When pyrosequencing is performed using the ID sequence of the present invention, a unique and simple pyrogram can be obtained for each genotype, and thus a genotyping process for virus genes, disease genes, bacterial genes and individual identifying genes can be performed in a simple and efficient manner. The primer for the genotyping method of the present invention can be variously applied to all genotyping methods using sequencings adopting a distribution system.

    Abstract translation: 本发明涉及基因分型方法，更具体地说，涉及针对每种基因型提供的ID序列和使用该ID序列的多基因分型方法。 当使用本发明的ID序列进行焦磷酸测序时，可以获得针对每个基因型的唯一且简单的热解，因此病毒基因，疾病基因，细菌基因和个体鉴定基因的基因分型过程可以简单和 有效的方式。 本发明的基因分型方法的引物可以使用采用分配系统的序列，各种应用于所有基因分型方法。

    UNIVERSAL MICROBIAL DIAGNOSIS, DETECTION, QUANTIFICATION, AND SPECIMEN-TARGETED THERAPY
    117.
    发明申请
    UNIVERSAL MICROBIAL DIAGNOSIS, DETECTION, QUANTIFICATION, AND SPECIMEN-TARGETED THERAPY 审中-公开
    通用微生物诊断，检测，定量和标本治疗

    公开(公告)号：WO2011011094A1

    公开(公告)日：2011-01-27

    申请号：PCT/US2010/002099

    申请日：2010-07-26

    Applicant: DOWD, Scot, E. ,  WOLCOTT, Randall, D. ,  KENNEDY, John, P.

    Inventor： DOWD, Scot, E. ,  WOLCOTT, Randall, D. ,  KENNEDY, John, P.

    IPC: C12Q1/68 ,  C12P19/34

    CPC classification number: C12Q1/6809 ,  C12Q1/689 ,  Y02A50/56 ,  Y02A50/57 ,  Y02A50/59 ,  C12Q2525/15 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2563/179

    Abstract: Microbial ecology of a specimen is evaluated using an approach (Level I) that utilizes nucleic acid amplification with specific gene primers that will identify panels of microorganisms and antibiotic-resistance factors generating a diagnostic report (optionally with quantification of each microorganism or antibiotic-resistance factor) and an approach (Level II) that utilizes universal or semi-universal primers to amplify conserved genes at a general or specific taxonomic level that are tagged specimen specifically using a genetic or chemical marker that is specific to the specimen from which it was derived, then sequencing the amplified products with highly-parallel, high-throughput technology to provide comprehensive sequences of the microbial population in the specimen followed by analysis of this sequence information and specific targeted information from Level I and/or Level II to generate a comprehensive analysis, interpretation, and/or diagnostic report. The report may be used to direct the appropriate treatment of human or animal patients as well as the informative study of microbial systems within bodily flora that are not currently in a pathogenic state. Improved thereby are accuracy, speed, and sensitivity of microbial diagnostics; microbial detection and/or quantification (i.e., identification); and patient or disease specific treatment, enhancement, or remediation.

    Abstract translation: 使用方法（I级）评估样本的微生物生态学，其使用具有特异性基因引物的核酸扩增的方法（I级），其将鉴定产生诊断报告的微生物群和抗生素抗性因子（任选地定量每种微生物或抗生素抗性因子 ）和一种方法（II级），其使用通用或半通用引物来扩增在一般或特定分类水平上的保守基因，其特异性地使用其衍生的样品特异的遗传或化学标记来标记样品， 然后用高度平行，高通量技术对扩增产物进行测序，以提供样品中微生物群体的综合序列，然后分析该序列信息和来自I级和/或II级的特异性靶向信息以产生综合分析， 口译和/或诊断报告。 该报告可用于指导人或动物患者的适当治疗以及目前处于致病状态的体内菌群内的微生物系统的信息性研究。 因此改进了微生物诊断的准确性，速度和敏感性; 微生物检测和/或定量（即鉴定）; 和患者或疾病特异性治疗，增强或补救。

    NUCLEIC ACID ANALYSIS BY RANDOM MIXTURES OF NON-OVERLAPPING FRAGMENTS
    120.
    发明申请
    NUCLEIC ACID ANALYSIS BY RANDOM MIXTURES OF NON-OVERLAPPING FRAGMENTS 审中-公开
    非叠加片段随机混合物的核酸分析

    公开(公告)号：WO2006138284A2

    公开(公告)日：2006-12-28

    申请号：PCT/US2006/022950

    申请日：2006-06-13

    Applicant: CALLIDA GENOMICS, INC. ,  DRMANAC, Radoje

    Inventor： DRMANAC, Radoje

    IPC: C12Q1/68

    CPC classification number: C12Q1/6874 ,  C07H21/04 ,  C07K1/047 ,  C12Q1/6806 ,  C12Q1/682 ,  C12Q1/6837 ,  C12Q1/6869 ,  C12Q2525/151 ,  C12Q2525/313 ,  C12Q2531/125 ,  C12Q2565/513 ,  G01N15/1404 ,  G01N15/1434 ,  Y10S977/778 ,  Y10S977/789 ,  Y10S977/792 ,  Y10S977/88 ,  Y10S977/882 ,  C12Q2521/307 ,  C12Q2525/161 ,  C12Q2535/122 ,  C12Q2563/179 ,  C12Q2565/514

    Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like.

    Abstract translation: 本发明提供了用于排序从一个或多个目标多核苷酸衍生的序列信息的方法和试剂盒。 在一个方面，产生一个或多个分层或等级的碎片和等分，之后从最终级别或层级的片段获得序列信息。 这样的最后一层中的每个片段都来自特定的等分试样，反过来，这些等分试样来自先前层的特定等分试样，依此类推。 对于最后一层中的等分试样的每个片段，从每个先前层得到的等分试样是已知的，或者可以被辨别出来。 因此，来自不同等分试样的重叠片段的相同序列可以被区分并分组为从与先前层相同或不同的片段衍生的。 当最终层中的片段被排序时，使用不同等分试样的片段的重叠序列区域来对片段进行寄存以使非重叠区域被排序。 在一个方面，该方法以分级方式进行，直到一个或多个目标多核苷酸被表征为例如。 通过其核酸序列，或通过序列片段的排序，或通过单核苷酸多态性（SNP）等的排序。

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