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    METHODS FOR HYBRIDIZATION BASED HOOK LIGATION
    24.
    发明申请
    METHODS FOR HYBRIDIZATION BASED HOOK LIGATION 审中-公开

    公开(公告)号：US20180245132A1

    公开(公告)日：2018-08-30

    申请号：US15903424

    申请日：2018-02-23

    Applicant: Complete Genomics, Inc.

    Inventor： Yuan Jiang ,  Radoje Drmanac

    IPC: C12Q1/6806

    CPC classification number: C12Q1/6806 ,  C12Q2521/501 ,  C12Q2525/161

    Abstract: Provided herein are compositions, methods, and kits for enriching for one or more nucleic acid sequences of interest in a sample. The methods include providing a circular ligase, one or more 5′ hook probes and/or one or more 3′ hook probes and contacting the sample comprising the nucleic acids with the circular ligase and one or more 5′ hook probes and/or one or more 3′ hook probes under conditions to allow the hook probes to selectively bind to the one or more nucleic acid sequences of interest, and under conditions to form one or more hook products, each hook product comprising the hook probes and the one or more nucleic acid sequences of interest.

    Identification of DNA fragments and structural variations
    28.
    发明授权
    Identification of DNA fragments and structural variations 有权
    鉴定DNA片段和结构变异

    公开(公告)号：US09514272B2

    公开(公告)日：2016-12-06

    申请号：US13649966

    申请日：2012-10-11

    Applicant: Complete Genomics, Inc.

    Inventor： Bahram Ghaffarzadeh Kermani ,  Radoje Drmanac ,  Oleg Alferov

    IPC: G01N33/50 ,  G06F19/22

    CPC classification number: G06F19/22

    Abstract: Various short reads can be grouped and identified as coming from a same long DNA fragment (e.g., by using wells with a relatively low-concentration of DNA). A histogram of the genomic coverage of a group of short reads can provide the edges of the corresponding long fragment (pulse). The knowledge of these pulses can provide an ability to determine the haploid genome and to identify structural variations.

    Abstract translation: 可以将各种短读数分组并鉴定为来自相同的长DNA片段（例如，通过使用具有相对低浓度DNA的孔）。 一组短读取的基因组覆盖的直方图可以提供对应的长片段（脉冲）的边缘。 这些脉冲的知识可以提供确定单倍体基因组并鉴定结构变化的能力。

    LONG FRAGMENT DE NOVO ASSEMBLY USING SHORT READS
    30.
    发明申请
    LONG FRAGMENT DE NOVO ASSEMBLY USING SHORT READS 审中-公开
    LONG FRAGMENT DE NOVO大会使用短篇小说阅读

    公开(公告)号：US20150057947A1

    公开(公告)日：2015-02-26

    申请号：US14467797

    申请日：2014-08-25

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac ,  Bahram Ghaffarzadeh Kermani

    IPC: G06F19/20

    Abstract: Techniques perform de novo assembly. The assembly can use labels that indicate origins of the nucleic acid molecules. For example, a representative set of labels identified from initial reads that overlap with a seed can be used. Mate pair information can be used. A sequence read that aligns to an end of a contig can lead to using the other sequence read of a mate pair, and the other sequence read can be used to determine which branch to use to extend, e.g., in an external cloud or helper contig. A kmer index can include labels indicating an origin of each of the nucleic acid molecules that include each kmer, memory addresses of the reads that correspond to each kmer in the index, and a position in each of the mate pairs that includes the kmer. Haploid seeds can also be determined using polymorphic loci identified in a population.

    Abstract translation: 技术执行从头装配。 该组件可以使用指示核酸分子起源的标记。 例如，可以使用从与种子重叠的初始读取中识别的代表性标签集合。 配对信息可以使用。 与对等体的末端对齐的序列读取可以导致使用配对对读取的其他序列，并且可以使用其他序列读取来确定用于扩展的分支，例如在外部云或辅助对象中 。 kmer指数可以包括指示每个核酸分子的来源的标签，其包括每个kmer，对应于索引中每个kmer的读取的存储器地址以及包括kmer的每个配对对中的位置。 单倍体种子也可以使用在群体中鉴定的多态性基因座来确定。

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