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    BASECALLER FOR DNA SEQUENCING USING MACHINE LEARNING
    13.
    发明申请
    BASECALLER FOR DNA SEQUENCING USING MACHINE LEARNING 审中-公开
    使用机器学习的DNA序列的基础知识

    公开(公告)号：US20150169824A1

    公开(公告)日：2015-06-18

    申请号：US14571022

    申请日：2014-12-15

    Applicant: Complete Genomics, Inc.

    Inventor： Bahram Ghaffarzadeh Kermani ,  Radoje Drmanac

    IPC: G06F19/24

    CPC classification number: G06F19/24 ,  G06F19/22

    Abstract: Methods, systems, and apparatuses are provided for creating and using a machine-leaning model to call a base at a position of a nucleic acid based on intensity values measured during a production sequencing run. The model can be trained using training data from training sequencing runs performed earlier. The model is trained using intensity values and assumed sequences that are determined as the correct output. The training data can be filtered to improve accuracy. The training data can be selected in a specific manner to be representative of the type of organism to be sequenced. The model can be trained to use intensity signals from multiple cycles and from neighboring nucleic acids to improve accuracy in the base calls.

    Abstract translation: 提供了方法，系统和装置，用于创建和使用机器倾斜模型，以基于在生产测序运行期间测量的强度值来调用核酸位置处的碱基。 可以使用训练数据训练模型，训练数据来自前面进行的训练排序运行。 使用强度值和假定序列来训练该模型，该序列被确定为正确的输出。 训练数据可以被过滤以提高准确度。 可以以特定方式选择训练数据以代表待测序的生物体的类型。 可以训练该模型以使用来自多个周期和相邻核酸的强度信号来提高基本呼叫的准确性。

    METHOD FOR IMAGING HIGH DENSITY BIOCHEMICAL ARRAYS WITH SUB-PIXEL ALIGNMENT
    14.
    发明申请
    METHOD FOR IMAGING HIGH DENSITY BIOCHEMICAL ARRAYS WITH SUB-PIXEL ALIGNMENT 审中-公开
    用子像素对准成像高密度生物化学阵列的方法

    公开(公告)号：US20150160451A1

    公开(公告)日：2015-06-11

    申请号：US14594979

    申请日：2015-01-12

    Applicant: Complete Genomics, Inc.

    Inventor： Bryan P. Staker ,  Craig E. Uhrich

    IPC: G02B21/36 ,  G02B21/00 ,  G01B11/27

    CPC classification number: G02B21/365 ,  G01B11/272 ,  G02B21/002 ,  G02B21/025 ,  G02B21/361 ,  H04N5/37206 ,  H04N7/18

    Abstract: A method and associated system for imaging high density biochemical arrays comprises one or more imaging channels that share a common objective lens and a corresponding one or more time delay integration-type imaging cameras with optical alignment mechanisms that permit independent inter-channel and intra-channel adjustment of each of four degrees: X, Y, rotation and scale. The imaging channels are configured to independently examine different spectra of the image of the biochemical arrays.

    Abstract translation: 用于高密度生物化学阵列成像的方法和相关系统包括共享共同物镜的一个或多个成像通道和具有光学对准机构的相应的一个或多个时间延迟积分型成像相机，其允许独立的通道间和通道内 四度调整：X，Y，旋转和刻度。 成像通道被配置为独立地检查生物化学阵列的图像的不同光谱。

    METHODS FOR ESTIMATING GENOME-WIDE COPY NUMBER VARIATIONS
    16.
    发明申请
    METHODS FOR ESTIMATING GENOME-WIDE COPY NUMBER VARIATIONS 审中-公开
    估计基因型复制数变化的方法

    公开(公告)号：US20140229117A1

    公开(公告)日：2014-08-14

    申请号：US14253642

    申请日：2014-04-15

    Applicant: COMPLETE GENOMICS, INC.

    Inventor： Aaron Halpern ,  Krishna Pant

    IPC: G06F19/18

    CPC classification number: G16B20/00 ,  C12Q1/6809 ,  C12Q1/6827 ,  G16B25/00 ,  G16B30/00 ,  G16B40/00 ,  C12Q2537/16 ,  C12Q2537/165

    Abstract: Methods for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. Genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.

    Abstract translation: 公开了用于确定样品中靶序列的检测位置处的基因组区域的拷贝数的方法。 对样品中靶序列的基因组区域进行测序，并获得序列覆盖度的测量数据。 校正序列覆盖偏差并且可以相对于基线样本进行归一化。 执行隐马尔科夫模型（HMM）分割，评分和输出，并且在一些实施例中，也可以执行基于群体的无呼叫和低置信区域的识别。 然后估计多个区域的总拷贝数值和区域特定拷贝数值。

    EFFICIENT BASE DETERMINATION IN SEQUENCING REACTIONS
    17.
    发明申请
    EFFICIENT BASE DETERMINATION IN SEQUENCING REACTIONS 审中-公开
    顺序反应中有效的碱基测定

    公开(公告)号：US20140213461A1

    公开(公告)日：2014-07-31

    申请号：US13965166

    申请日：2013-08-12

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac ,  Matthew J. Callow

    IPC: C12Q1/68

    CPC classification number: C12Q1/6874 ,  C12Q1/6855 ,  C12Q2531/125 ,  C12Q2521/313 ,  C12Q2521/125 ,  C12Q2537/163 ,  C12Q2525/191 ,  C12Q2521/531 ,  C12Q2521/501 ,  C12Q2525/307 ,  C12Q2525/151

    Abstract: The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.

    Abstract translation: 本发明涉及用于核酸鉴定和检测的组合物和方法。 本发明的组合物和方法包括从样品中提取和分离靶核酸，使用片段化的靶核酸产生靶核酸模板，并使这些靶核酸模板进行扩增方法以形成核酸纳米棒。 本发明还包括使用各种测序应用检测和鉴定序列的方法，包括通过连接方法测序。

    HIGH-DENSITY ARRAY CHIPS WITH SYNCHRONOUS TRACKS
    18.
    发明申请
    HIGH-DENSITY ARRAY CHIPS WITH SYNCHRONOUS TRACKS 有权
    高密度阵列与同步轨迹

    公开(公告)号：US20140085457A1

    公开(公告)日：2014-03-27

    申请号：US14090529

    申请日：2013-11-26

    Applicant: Complete Genomics, Inc.

    Inventor： Bryan P. Staker ,  Paul Heilman

    IPC: G01N21/01 ,  H04N7/18

    CPC classification number: G01N21/01 ,  G01N21/6456 ,  H04N7/18

    Abstract: An array chip design is provided where the chip includes a field region arranged with sites according to a first pitch and at least one track region having a one-dimensional site pattern arranged according to a second pitch that is less dense and is an integer multiple of the first pitch so that observation through pixel-based sensors using one-dimensional quad-cell averaging can be applied in the track region, thereby to attain alignment of the chip to pixel-based optical instrumentation with a higher density of sites.

    Abstract translation: 提供了一种阵列芯片设计，其中芯片包括具有根据第一间距设置的位置的场区域和至少一个具有根据第二间距排列的一维位置图案的轨道区域，所述第二间距不太密集，并且是至少一个 第一音调，使得通过使用一维四单元平均的基于像素的传感器的观察可以应用于轨道区域，从而实现基片与基于像素的光学仪器与较高密度位置的对准。

    LABELING STRATEGY FOR USE IN DNA SEQUENCING TO FACILITATE ASSEMBLY OF SEQUENCE READS INTO LONGER FRAGMENTS OF A GENOME
    19.
    发明申请
    LABELING STRATEGY FOR USE IN DNA SEQUENCING TO FACILITATE ASSEMBLY OF SEQUENCE READS INTO LONGER FRAGMENTS OF A GENOME 有权

    公开(公告)号：US20220411865A1

    公开(公告)日：2022-12-29

    申请号：US17864913

    申请日：2022-07-14

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac

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

    Abstract: This disclosure provides technology 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.

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