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    EFFICIENT SHOTGUN SEQUENCING METHODS
    91.
    发明申请
    EFFICIENT SHOTGUN SEQUENCING METHODS 审中-公开
    有效的射击测序方法

    公开(公告)号：US20130059737A1

    公开(公告)日：2013-03-07

    申请号：US13647338

    申请日：2012-10-08

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac ,  Clifford Reid

    IPC: C40B20/00

    CPC classification number: C12Q1/6869 ,  C12Q1/6874 ,  C12Q2549/119 ,  C12Q2537/149 ,  C12Q2565/137

    Abstract: Methods are provided for efficient shotgun sequencing to allow efficient selection and sequencing of nucleic acids of interest contained in a library. The nucleic acids of interest can be defined any time before or after preparation of the library. One example of nucleic acids of interest is missing or low confidence genome sequences resulting from an initial sequencing procedure. Other nucleic acids of interest include subsets of genomic DNA, RNA or cDNAs (exons, genes, gene sets, transciptomes). By designing an efficient (simple to implement, speedy, high specificity, low cost) selection procedure, a more complete sequence is achieved with less effort than by using highly redundant shotgun sequencing in an initial sequencing procedure

    Abstract translation: 提供了有效的霰弹枪测序的方法，以允许文库中包含的感兴趣的核酸的有效选择和测序。 感兴趣的核酸可以在文库制备之前或之后的任何时间进行定义。 感兴趣的核酸的一个实例是由初始测序程序产生的缺失或低置信基因组序列。 感兴趣的其他核酸包括基因组DNA，RNA或cDNAs（外显子，基因，基因组，转录本）的子集。 通过设计一种高效（简单实施，快速，高特异性，低成本）选择程序，通过在初始测序程序中使用高度冗余的霰弹枪测序，以更少的努力实现更完整的顺序

    Methods for hybridization based hook ligation
    96.
    发明授权
    Methods for hybridization based hook ligation 有权

    公开(公告)号：US11091791B2

    公开(公告)日：2021-08-17

    申请号：US15903424

    申请日：2018-02-23

    Applicant: Complete Genomics, Inc.

    Inventor： Yuan Jiang ,  Radoje Drmanac

    IPC: C12Q1/68 ,  C12Q1/6806

    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.

    METHODS FOR IDENTIFYING NUCLEOTIDES IN TARGET SEQUENCES
    98.
    发明申请
    METHODS FOR IDENTIFYING NUCLEOTIDES IN TARGET SEQUENCES 审中-公开

    公开(公告)号：US20200318183A1

    公开(公告)日：2020-10-08

    申请号：US16882461

    申请日：2020-05-23

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac

    IPC: C12Q1/6874 ,  C12Q1/6876 ,  C12Q1/6869 ,  C12Q1/686

    Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.

    Long fragment de novo assembly using short reads
    99.
    发明授权
    Long fragment de novo assembly using short reads 有权

    公开(公告)号：US10726942B2

    公开(公告)日：2020-07-28

    申请号：US14467797

    申请日：2014-08-25

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac ,  Bahram Ghaffarzadeh Kermani

    IPC: G16B30/00 ,  G16B30/20

    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.

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