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    BASECALLER FOR DNA SEQUENCING USING MACHINE LEARNING
    12.
    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。

    EFFICIENT BASE DETERMINATION IN SEQUENCING REACTIONS
    14.
    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。

    Nucleic acid analysis by random mixtures of non-overlapping fragments
    16.
    发明授权
    Nucleic acid analysis by random mixtures of non-overlapping fragments 有权

    公开(公告)号：US11414702B2

    公开(公告)日：2022-08-16

    申请号：US16730829

    申请日：2019-12-30

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac

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

    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.

    METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING
    17.
    发明申请
    METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING 有权

    公开(公告)号：US20220186309A1

    公开(公告)日：2022-06-16

    申请号：US17407935

    申请日：2021-08-20

    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.

    SELF-ASSEMBLED SINGLE MOLECULE ARRAYS AND USES THEREOF
    20.
    发明申请
    SELF-ASSEMBLED SINGLE MOLECULE ARRAYS AND USES THEREOF 审中-公开

    公开(公告)号：US20190316190A1

    公开(公告)日：2019-10-17

    申请号：US16189469

    申请日：2018-11-13

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac ,  Matthew J. Callow ,  Brian K. Hauser ,  George Yeung

    IPC: C12Q1/6837 ,  C12N15/10 ,  C12Q1/682 ,  C12Q1/6869 ,  C12Q1/6874

    Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.

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