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    HIGH THROUGHPUT GENOME SEQUENCING ON DNA ARRAYS
    62.
    发明申请
    HIGH THROUGHPUT GENOME SEQUENCING ON DNA ARRAYS 审中-公开

    公开(公告)号：US20190010542A1

    公开(公告)日：2019-01-10

    申请号：US15940771

    申请日：2018-03-29

    Applicant: Complete Genomics Inc.

    Inventor： Radoje Drmanac ,  Matthew J. Callow ,  Snezana Drmanac

    IPC: C12Q1/6874 ,  C12N15/66 ,  C12N15/64

    Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.

    Preparing a DNA fragment library for sequencing using tagged primers
    63.
    发明授权
    Preparing a DNA fragment library for sequencing using tagged primers 有权

    公开(公告)号：US10125392B2

    公开(公告)日：2018-11-13

    申请号：US13971797

    申请日：2013-08-20

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac

    IPC: C12Q1/68 ,  C12Q1/6874 ,  C12Q1/682 ,  C12Q1/6837 ,  C12Q1/6869 ,  C07H21/04 ,  C07K1/04 ,  G01N15/14 ,  C12Q1/6806

    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.

    High Throughput Genome Sequencing on DNA Arrays
    64.
    发明申请
    High Throughput Genome Sequencing on DNA Arrays 审中-公开

    公开(公告)号：US20170226577A1

    公开(公告)日：2017-08-10

    申请号：US15267514

    申请日：2016-09-16

    Applicant: Complete Genomics Inc.

    Inventor： Radoje Drmanac ,  Matthew J. Callow ,  Snezana Drmanac

    IPC: C12Q1/68

    CPC classification number: C12Q1/6874 ,  C12N15/64 ,  C12N15/66 ,  Y10T436/143333 ,  C12Q2521/313 ,  C12Q2525/191 ,  C12Q2525/151 ,  C12Q2525/131 ,  C12Q2565/518 ,  C12Q2533/107 ,  C12Q2531/125

    Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.

    PHASING AND LINKING PROCESSES TO IDENTIFY VARIATIONS IN A GENOME
    68.
    发明申请
    PHASING AND LINKING PROCESSES TO IDENTIFY VARIATIONS IN A GENOME 审中-公开
    相关和链接过程识别基因组中的变化

    公开(公告)号：US20150094961A1

    公开(公告)日：2015-04-02

    申请号：US14503872

    申请日：2014-10-01

    Applicant: Complete Genomics, Inc.

    Inventor： Bahram Ghaffarzadeh Kermani ,  Radoje Drmanac ,  Brock A. Peters

    IPC: G06F19/22

    CPC classification number: G16B30/00 ,  G16B20/00

    Abstract: Long fragment read techniques can be used to identify deletions and resolve base calls by utilizing shared labels (e.g., shared aliquots) of a read with any reads corresponding to heterozygous loci (hets) of a haplotype. For example, the linking of a locus to a haplotype of multiple hets can increase the reads available at the locus for determining a base call for a particular haplotype. For a hemizygous deletion, a region can be linked to one or more hets, and the labels for a particular haplotype can be used to identify which reads in the region correspond to which haplotype. In this manner, since the reads for a particular haplotype can be identified, a hemizygous deletion can be determined. Further, a phasing rate of pulses can be used to identify large deletions. A deletion can be identified with the phasing rate is sufficiently low, and other criteria can be used.

    Abstract translation: 可以使用长片段读取技术来识别缺失并通过利用与单倍型的杂合位点（hets）相对应的任何读取的共享标签（例如共享等分试样）来解析基本调用。 例如，将一个基因座与多个单倍型的单倍型的连接可以增加在该位点处可用的读数，以确定特定单体型的碱基调用。 对于半合子缺失，区域可以连接到一个或多个疱疹，并且特定单元型的标签可用于鉴定区域中哪个读取对应于哪个单倍型。 以这种方式，由于可以鉴定特定单体型的读数，所以可以确定半合子缺失。 此外，可以使用脉冲的相位速率来识别大的缺失。 可以通过相位速率来确定删除，并且可以使用其他标准。

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