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    USING DOUBLET INFORMATION IN GENOME MAPPING AND ASSEMBLY
    35.
    发明申请
    USING DOUBLET INFORMATION IN GENOME MAPPING AND ASSEMBLY 审中-公开
    在基因组映射和汇编中使用双重信息

    公开(公告)号：US20150317433A1

    公开(公告)日：2015-11-05

    申请号：US14701248

    申请日：2015-04-30

    Applicant: Complete Genomics, Inc.

    Inventor： Bahram Ghaffarzadeh Kermani ,  Somayeh Bakhtiari

    IPC: G06F19/22

    CPC classification number: G16B30/00

    Abstract: Systems, methods, and apparatuses are provided for determining a sequence of a heteropolymer molecule. For example, all or part of a chromosome or a protein can be determined using sequence data from a plurality of heteropolymer fragments corresponding to the heteropolymer molecule. As one example, a position in the sequence read of a DNA fragment can be identified where a single base call is not clear. A multiplet base call can then be used, where the multiplet base call includes two or more bases at the position, along with a score for each base. The scores can be carried through mapping and assembly procedures, where the scores can be used to determine a final base call for the position in a chromosome of a genome of an organism. Other examples can be used for other monomer units besides bases.

    Abstract translation: 提供了用于确定杂聚物分子序列的系统，方法和装置。 例如，染色体或蛋白质的全部或部分可以使用来自对应于杂聚物分子的多个杂聚物片段的序列数据来确定。 作为一个示例，可以在单个基本呼叫不清楚的地方识别DNA片段读取序列中的位置。 然后可以使用多重基数调用，其中多重基数调用在位置包括两个或更多个基数，以及每个基数的分数。 分数可以通过测绘和组装程序进行，其中分数可用于确定生物体基因组染色体中位置的最终基本调用。 其他实例也可用于除碱基之外的其它单体单元。

    PHASING AND LINKING PROCESSES TO IDENTIFY VARIATIONS IN A GENOME
    36.
    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。

    METHOD AND SYSTEM FOR ACCURATE ALIGNMENT AND REGISTRATION OF ARRAY FOR DNA SEQUENCING
    37.
    发明申请
    METHOD AND SYSTEM FOR ACCURATE ALIGNMENT AND REGISTRATION OF ARRAY FOR DNA SEQUENCING 有权
    用于DNA序列的精确对准和阵列注册的方法和系统

    公开(公告)号：US20150080231A1

    公开(公告)日：2015-03-19

    申请号：US14309049

    申请日：2014-06-19

    Applicant: Complete Genomics, Inc.

    Inventor： Bryan P. Staker

    IPC: C12Q1/68 ,  G06T7/00

    CPC classification number: C12Q1/6874 ,  G06K9/32 ,  G06K9/42 ,  G06K2209/07 ,  G06T7/0012 ,  G06T7/32 ,  G06T7/337 ,  G06T7/74 ,  G06T2207/10056 ,  G06T2207/30072

    Abstract: In a genome sequencing system and methodology, a protocol is provided to achieve precise alignment and accurate registration of an image of a planar array of nanoballs subject to optical analysis. Precise alignment correcting for fractional offsets is achieved by correcting for errors in subperiod x-y offset, scale and rotation by use of minimization techniques and Moiré averaging. In Moiré averaging, magnification is intentionally set so that the pixel period of the imaging element is a noninteger multiple of the site period. Accurate registration is achieved by providing for pre-defined pseudo-random sets of sites, herein deletion or reserved sites, where nanoballs are prevented from attachment to the substrate so that the sites of the array can be used in a pattern matching scheme as registration markers for absolute location identification. Information can be extracted with a high degree of confidence that it is correlated to a known location, while at the same time the amount of information that can be packed on a chip is maximized.

    Abstract translation: 在基因组测序系统和方法学中，提供了一种协议，以实现经受光学分析的纳米棒的平面阵列的图像的精确对准和精确配准。 通过使用最小化技术和莫尔平均来校正子周期x-y偏移，刻度和旋转中的误差来实现分数偏移的精确对准校正。 在莫尔平均中，有意地设置放大率，使得成像元件的像素周期是站点周期的非整数倍。 通过提供预定义的伪随机组的位点（这里是删除或保留位点）来实现精确的注册，其中防止了纳米线附着到基底，使得阵列的位点可以以模式匹配方案用作对准标记 用于绝对位置识别。 可以高信度地提取信息，使其与已知位置相关联，同时可将芯片上打包的信息量最大化。

    Genome Explorer System to Process and Present Nucleotide Variations in Genome Sequence Data
    39.
    发明申请
    Genome Explorer System to Process and Present Nucleotide Variations in Genome Sequence Data 审中-公开
    基因组探索系统来处理和表达基因组序列数据中的核苷酸变异

    公开(公告)号：US20140115515A1

    公开(公告)日：2014-04-24

    申请号：US14062234

    申请日：2013-10-24

    Applicant: Complete Genomics, Inc.

    Inventor： Julie Adams ,  Mirko Buholzer

    IPC: G06F19/22

    CPC classification number: G16B30/00 ,  G16B20/00 ,  G16B45/00 ,  G16B50/00

    Abstract: This disclosure provides a technology for users to gain first-hand knowledge and experience with interpreting whole genomes. The technology graphically depicts variations in genome sequences in an expandable display, and provides a platform whereby the user may find and research the biological significance of such variants. The technology also provides a unique collaborative environment designed to capture and improve the collective knowledge of the participating community.

    Abstract translation: 本公开提供了一种技术，使用户能够获得解释整个基因组的第一手知识和经验。 该技术图形地描绘了可扩展显示器中的基因组序列的变化，并且提供了一个平台，由此用户可以发现和研究这些变体的生物意义。 该技术还提供了独特的协作环境，旨在捕获和改进参与社区的集体知识。

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