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    SYSTEMS AND METHODS FOR UNIVERSAL TAIL-BASED INDEXING STRATEGIES FOR AMPLICON SEQUENCING
    41.
    发明申请
    SYSTEMS AND METHODS FOR UNIVERSAL TAIL-BASED INDEXING STRATEGIES FOR AMPLICON SEQUENCING 审中-公开
    用于AMPLICON序列的通用基于尾段的指数策略的系统和方法

    公开(公告)号：WO2015070187A2

    公开(公告)日：2015-05-14

    申请号：PCT/US2014/064890

    申请日：2014-11-10

    Applicant: THE TRANSLATIONAL GENOMICS RESEARCH INSTITUTE

    Inventor： SCHUPP, James M. ,  COLMAN, Rebecca ,  ENGELTHALER, David ,  GILLECE, John ,  HICKS, Nathan ,  KEIM, Paul S.

    IPC: A61B3/10

    CPC classification number: C12Q1/686 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2525/155 ,  C12Q2525/191 ,  C12Q2537/143

    Abstract: Some embodiments of the invention include a method of preparing a sample for sequencing that includes receiving a sample and amplifying at least one marker within the sample. In some embodiments, amplification of the first marker may include mixing the sample with a first oligonucleotide that comprises a first universal tail sequence and a second oligonucleotide that comprises a second universal tail sequence. In some aspects of the invention, the first universal tail sequence and the second universal tail sequence are different sequences.

    Abstract translation: 本发明的一些实施方案包括制备用于测序的样品的方法，其包括接收样品并扩增样品中的至少一个标记物。 在一些实施方案中，第一标记的扩增可以包括将样品与包含第一通用尾部序列的第一寡核苷酸和包含第二通用尾部序列的第二寡核苷酸混合。 在本发明的一些方面，第一通用尾部序列和第二通用尾部序列是不同的序列。

    GENETIC ANALYSIS METHOD
    42.
    发明申请
    GENETIC ANALYSIS METHOD 审中-公开
    遗传分析方法

    公开(公告)号：WO2015067796A1

    公开(公告)日：2015-05-14

    申请号：PCT/EP2014/074155

    申请日：2014-11-10

    Applicant: CARTAGENIA N.V.

    Inventor： DEVOGELAERE, Benoit ,  VERRELST, Herman

    IPC: C12Q1/68

    CPC classification number: G06F19/18 ,  C12Q1/6869 ,  C12Q1/6874 ,  G06F19/24 ,  C12Q2521/301 ,  C12Q2525/191 ,  C12Q2535/122 ,  C12Q2545/101

    Abstract: A method of target DNA genome analysis is provided. The method comprises the steps of : - obtaining non-overlapping segments of target DNA stretches with segment boundaries defined by the presence of particular restriction enzyme recognition sites, whereby the assembly of said non-overlapping segments compose a reduced representation library of said target DNA genome; - obtaining for said segments, raw metrics from a sequencing process applied on said reduced representation library; - clustering non-overlapping, nearby segments with similar raw metrics to provide master segments; - providing metrics describing the master segments, - making a final discrete DNA call based on the master segments and its metrics.

    Abstract translation: 提供了靶DNA基因组分析的方法。 该方法包括以下步骤： - 获得具有由特定限制酶识别位点的存在限定的区段边界的靶DNA延伸的非重叠区段，由此所述非重叠区段的组装构成所述靶DNA基因组的缩小表示文库 ; - 对所述段获得应用于所述简化表示库的排序过程的原始度量; - 使用类似的原始度量来聚集不重叠的附近细分，以提供主分段; - 提供描述主节点的度量， - 根据主节点及其度量进行最终的离散DNA呼叫。

    METHODS AND SYSTEM FOR DETECTING SEQUENCE VARIANTS
    43.
    发明申请
    METHODS AND SYSTEM FOR DETECTING SEQUENCE VARIANTS 审中-公开
    检测序列变异的方法和系统

    公开(公告)号：WO2015048753A1

    公开(公告)日：2015-04-02

    申请号：PCT/US2014/058328

    申请日：2014-09-30

    Applicant: SEVEN BRIDGES GENOMICS INC.

    Inventor： KURAL, Deniz

    IPC: G06F19/22 ,  C12Q1/68 ,  C40B40/06 ,  C40B60/12

    CPC classification number: G06F19/22 ,  C12Q1/6874 ,  C12Q2535/122 ,  C12Q2537/165

    Abstract: The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.

    Abstract translation: 本发明提供用于鉴定遗传序列中结构变异附近的罕见变体的方法，例如在取自受试者的核酸样品中。 本发明还包括用于将读取（例如，核酸读取）与构成结构变异的参考序列构型对齐的方法，构建结构变异或结构变异的参考序列构建的方法和稀有变体，以及系统， 使用对齐方法来识别稀有变体。 该方法是可扩展的，并且可以用于将数百万次读取与数千个基准长或更长的时间对齐。

    HIGH-THROUGHPUT RNA-SEQ
    47.
    发明申请
    HIGH-THROUGHPUT RNA-SEQ 审中-公开
    高通量RNA-SEQ

    公开(公告)号：WO2014201273A1

    公开(公告)日：2014-12-18

    申请号：PCT/US2014/042159

    申请日：2014-06-12

    Applicant: THE BROAD INSTITUTE, INC. ,  PRESIDENT AND FELLOWS OF HARVARD COLLEGE ,  MIKKELSEN, Tarjei ,  SOUMILLON, Magali

    Inventor： MIKKELSEN, Tarjei ,  SOUMILLON, Magali

    IPC: C12Q1/68

    CPC classification number: C12N15/1065 ,  C12Q1/6844 ,  C12Q1/6874 ,  C12Q2521/107 ,  C12Q2525/101 ,  C12Q2525/191 ,  C12Q2563/179

    Abstract: The present invention relates generally to methods for single-cell nucleic acid profiling, and nucleic acids useful in those methods. For example, it concerns using barcode sequences to track individual nucleic acids at single-cell resolution, utilizing template switching and sequencing reactions to generate the nucleic acid profiles. These methods and compositions are also applicable to other starting materials, such as cell and tissue lysates or extracted/purified RNA.

    Abstract translation: 本发明一般涉及用于单细胞核酸分析的方法，以及在这些方法中有用的核酸。 例如，它涉及使用条形码序列来以单细胞分辨率跟踪单个核酸，利用模板切换和测序反应来产生核酸谱。 这些方法和组合物也适用于其它原料，例如细胞和组织裂解物或提取/纯化的RNA。

    METHODS AND SYSTEMS FOR LOCAL SEQUENCE ALIGNMENT
    48.
    发明申请
    METHODS AND SYSTEMS FOR LOCAL SEQUENCE ALIGNMENT 审中-公开
    用于本地序列比对的方法和系统

    公开(公告)号：WO2014159495A1

    公开(公告)日：2014-10-02

    申请号：PCT/US2014/023918

    申请日：2014-03-12

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： KOLLER, Christian ,  ZHANG, Zheng

    IPC: G06F19/22

    CPC classification number: C12Q1/6874 ,  G06F19/22

    Abstract: A method for nucleic acid sequencing includes: (a) disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith; (b) exposing the template polynucleotide strands with the sequencing primer and a polymerase operably bound therewith to a series of flows of nucleotide species flowed according to a predetermined ordering; (c) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands; and (d) aligning the plurality of sequencing reads using an alignment process comprising a first set of alignment criteria or penalties that are based on biological changes in sequence and a second set of alignment criteria or penalties that are based on a sequencing error mode.

    Abstract translation: 用于核酸测序的方法包括：（a）将多个模板多核苷酸链设置在设置在传感器阵列上的多个限定的空间中，至少一些模板多核苷酸链具有测序引物和与之可操作地结合的聚合酶; （b）用测序引物和可操作地与其结合的聚合酶将模板多核苷酸链暴露于根据预定顺序流过的一系列核苷酸物质流; （c）基于核苷酸物种的流量确定多个定义空间中的模板多核苷酸链的序列信息，以产生对应于模板多核苷酸链的多个测序读数; 并且（d）使用包括基于顺序的生物变化的第一组对准标准或惩罚的对准过程对齐多个测序读数，以及基于排序错误模式的第二组对准标准或惩罚。

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