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    METHODS FOR PREIMPLANTATION GENETIC DIAGNOSIS BY SEQUENCING
    101.
    发明申请
    METHODS FOR PREIMPLANTATION GENETIC DIAGNOSIS BY SEQUENCING 审中-公开
    通过序列预测遗传学诊断的方法

    公开(公告)号：WO2013052557A2

    公开(公告)日：2013-04-11

    申请号：PCT/US2012/058578

    申请日：2012-10-03

    Applicant: NATERA, INC. ,  RABINOWITZ, Matthew ,  HILL, Matthew ,  ZIMMERMANN, Bernhard ,  BANER, Johan ,  RYAN, Allison ,  GEMELOS, George

    Inventor： RABINOWITZ, Matthew ,  HILL, Matthew ,  ZIMMERMANN, Bernhard ,  BANER, Johan ,  RYAN, Allison ,  GEMELOS, George

    IPC: C12Q1/68 ,  G06F19/24 ,  G06F19/20

    CPC classification number: C12Q1/6858 ,  C12Q1/6883 ,  C12Q2600/156 ,  G06F19/18 ,  C12Q2535/122 ,  C12Q2545/114

    Abstract: The present disclosure provides methods for determining the ploidy status of an embryo at a chromosome from a sample of DNA from an embryo. The ploidy state is determined by sequencing the DNA from one or more cells biopsied from the embryo, and analyzing the relative amounts of each allele at a plurality of polymorphic loci on the chromosome. In an embodiment, the ploidy state is determined by comparing the observed allele ratios to the expected allele ratios for different ploidy states. In an embodiment, the DNA is selectively amplified at a plurality of polymorphic loci by targeted sequencing. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias.

    Abstract translation: 本公开提供了用于从胚胎的DNA样品测定染色体上胚胎的倍性状态的方法。 倍性状态通过对来自胚胎活检的一个或多个细胞的DNA进行测序，并分析染色体上多个多态性位点处的每个等位基因的相对量来确定。 在一个实施方案中，通过将观察到的等位基因比率与不同倍性状态的预期等位基因比率进行比较来确定倍性状态。 在一个实施方案中，通过靶向测序在多个多态位点选择性扩增DNA。 在一个实施方案中，DNA的混合样品可以以使等位基因偏倚最小化的方式优先富集在多个多态位点。

    DNA SAMPLE PREPARATION AND SEQUENCING
    102.
    发明申请
    DNA SAMPLE PREPARATION AND SEQUENCING 审中-公开
    DNA样品制备和测序

    公开(公告)号：WO2013049504A1

    公开(公告)日：2013-04-04

    申请号：PCT/US2012/057821

    申请日：2012-09-28

    Applicant: STC.UNM ,  EDWARDS, Jeremy ,  ZARKESH-HA, Payman ,  BRUECK, Steven, R.J.

    Inventor： EDWARDS, Jeremy ,  ZARKESH-HA, Payman ,  BRUECK, Steven, R.J.

    IPC: C12Q1/68 ,  C12N15/10 ,  C12N15/11

    CPC classification number: C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6874 ,  G01N27/414 ,  G01N27/4145 ,  Y10T436/143333 ,  C12Q2531/125 ,  C12Q2535/122

    Abstract: This disclosure describes, in one aspect, a method for preparing DNA molecule for sequencing. Generally, the method includes fragmenting the DNA molecule into double-stranded fragments; amplifying at least a portion of the double-stranded fragments; circularizing the fragments so that the first end of the fragment comprises a first loop connecting the strands and the second end of the fragment comprises a second loop connecting the strands; annealing a first sequencing primer to the first loop oriented to sequence at least a portion of one strand of the fragment; and annealing a second sequencing primer to the second loop oriented to sequence at least a portion of the other strand of the fragment. In another aspect, this disclosure describes a method for sequencing a DNA molecule. Generally, the method includes fragmenting the DNA molecule into double-stranded fragments; amplifying at least a portion of the double-stranded fragments; circularizing the fragments so that the first end of the fragment comprises a first loop connecting the strands and the second end of the fragment comprises a second loop connecting the strands; and sequencing at least one of the DNA strands.

    Abstract translation: 本公开一方面描述了用于测序的DNA分子的制备方法。 通常，该方法包括将DNA分子分成双链片段; 扩增至少一部分双链片段; 使片段环化，使得片段的第一端包含连接线束的第一环和片段的第二端包括连接线的第二环; 将第一测序引物退火至所述第一环以定向以序列所述片段的一条链的至少一部分; 以及将第二测序引物退火至所述第二环，其定向为序列所述片段的另一条链的至少一部分。 在另一方面，本公开描述了用于测序DNA分子的方法。 通常，该方法包括将DNA分子分成双链片段; 扩增至少一部分双链片段; 使片段环化，使得片段的第一端包含连接线束的第一环和片段的第二端包括连接线的第二环; 并测序至少一个DNA链。

    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING
    104.
    发明申请
    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING 审中-公开
    方法，系统和计算机可读介质，用于在核酸序列中进行基准测量

    公开(公告)号：WO2013025998A1

    公开(公告)日：2013-02-21

    申请号：PCT/US2012/051361

    申请日：2012-08-17

    Applicant: LIFE TECHNOLOGIES CORPORATION ,  SIKORA, Marcin ,  DAVEY, Melville ,  KOLLER, Christian ,  CAWLEY, Simon ,  WILLIAMS, Alan ,  KULP, David

    Inventor： SIKORA, Marcin ,  DAVEY, Melville ,  KOLLER, Christian ,  CAWLEY, Simon ,  WILLIAMS, Alan ,  KULP, David

    IPC: G01N33/48 ,  G06F19/10

    CPC classification number: G06F19/22 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2565/607

    Abstract: A method for nucleic acid sequencing includes receiving a plurality of observed or measured signals indicative of a parameter observed or measured for a plurality of defined spaces; determining, for at least some of the defined spaces, whether the defined space comprises one or more sample nucleic acids; processing, for at least some of the defined spaces, the observed or measured signal to improve a quality of the observed or measured signal; generating, for at least some of the defined spaces, a set of candidate sequences of bases for the defined space using one or more metrics adapted to associate a score or penalty to the candidate sequences of bases; and selecting the candidate sequence leading to a highest score or a lowest penalty as corresponding to the correct sequence for the one or more sample nucleic acids in the defined space.

    Abstract translation: 一种用于核酸测序的方法包括：接收多个观察或测量的指示针对多个限定空间观察或测量的参数的信号; 对于至少一些所定义的空间，确定所定义的空间是否包含一个或多个样品核酸; 对于至少一些所定义的空间，处理观察或测量的信号以改善所观察或测量的信号的质量; 为所述定义的空间中的至少一些为所述定义的空间生成一组用于使用一个或多个适于将所述候选序列的分数或惩罚相关联的度量的候选序列的序列集合; 以及选择与所述定义空间中的一个或多个样品核酸的正确序列相对应的最高分数或最低分数的候选序列。

    SAFE SEQUENCING SYSTEM
    105.
    发明申请
    SAFE SEQUENCING SYSTEM 审中-公开
    安全排序系统

    公开(公告)号：WO2012142213A3

    公开(公告)日：2013-01-24

    申请号：PCT/US2012033207

    申请日：2012-04-12

    Applicant: UNIV JOHNS HOPKINS ,  VOGELSTEIN BERT ,  KINZLER KENNETH W ,  PAPADOPOULOS NICKOLAS ,  KINDE ISAAC

    Inventor： VOGELSTEIN BERT ,  KINZLER KENNETH W ,  PAPADOPOULOS NICKOLAS ,  KINDE ISAAC

    IPC: C12Q1/68 ,  C12N15/11

    CPC classification number: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6876 ,  C12Q2563/179 ,  C12Q2600/158 ,  C12Q2535/122 ,  C12Q2565/514

    Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called "Safe-SeqS" for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant ("super-mutants") if =95% of them contain the identical mutation. We illustrate the utility of this approach for determining the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells.

    Abstract translation: 存在于DNA模板的一小部分中的突变的鉴定对于在几个生物医学研究领域的进展是必不可少的。 尽管大规模并行测序仪器原则上非常适合于此任务，但是这些仪器中的错误率通常太高，无法确定罕见的变体。 我们在这里描述了一种可以显着增加大规模并行测序仪器对此目的的灵敏度的方法。 这种方法的一个例子是（Safe-Sequencing System），称为“Safe-SeqS”，包括（i）将唯一标识符（UID）分配给每个模板分子; （ii）每个唯一标记的模板分子的扩增以产生UID家族; 和（iii）扩增产物的冗余测序。 具有相同UID的PCR片段是真正的突变体（“超突变体”），如果其中95％含有相同的突变。 我们说明了这种方法用于确定聚合酶的保真度，体外合成的寡核苷酸的准确性以及正常细胞的核和线粒体基因组中突变的流行率的效用。

    SEQUENCE BASED GENOTYPING BASED ON OLIGONUCLEOTIDE LIGATION ASSAYS
    106.
    发明申请
    SEQUENCE BASED GENOTYPING BASED ON OLIGONUCLEOTIDE LIGATION ASSAYS 审中-公开
    基于寡核苷酸测序的基于序列的基因分析

    公开(公告)号：WO2013009175A1

    公开(公告)日：2013-01-17

    申请号：PCT/NL2012/050493

    申请日：2012-07-09

    Applicant: KEYGENE N.V. ,  VAN EIJK, Michael Josephus Theresia ,  HOGERS, René Cornelis Josephus

    Inventor： VAN EIJK, Michael Josephus Theresia ,  HOGERS, René Cornelis Josephus

    IPC: C12Q1/68

    CPC classification number: C12Q1/6874 ,  C12Q1/6827 ,  C12Q1/683 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2561/125 ,  C12Q2525/131 ,  C12Q2525/155

    Abstract: The invention relates to a method for the detection of a target nucleotide sequence in a sample based on an oligonucleotide ligation assay wherein probes are used that contain (a combination of) sequence-based identifiers that can identify the sample and the target sequence (i.e. locus and/or allele combination) wherein after the ligation step, the ligated probes, or after amplification, the amplified ligated probes, are restricted using restriction enzymes to cut of part of the probes and continue with those parts (identifiers and target sequence) that contain the relevant information in the sequencing step.

    Abstract translation: 本发明涉及一种基于寡核苷酸连接测定法检测样品中目标核苷酸序列的方法，其中使用探针，其含有可鉴定样品和靶序列（即基因座）的基于序列的标识符（的组合） 和/或等位基因组合），其中在连接步骤之后，连接的探针或扩增后的扩增的连接的探针被限制使用限制性内切酶切割部分探针，并且继续使用含有 测序步骤中的相关信息。

    NORMALIZING CHROMOSOMES FOR THE DETERMINATION AND VERIFICATION OF COMMON AND RARE CHROMOSOMAL ANEUPLOIDIES
    110.
    发明申请
    NORMALIZING CHROMOSOMES FOR THE DETERMINATION AND VERIFICATION OF COMMON AND RARE CHROMOSOMAL ANEUPLOIDIES 审中-公开
    正常化染色体用于确定和验证常见和罕见的染色体异常

    公开(公告)号：WO2012141712A1

    公开(公告)日：2012-10-18

    申请号：PCT/US2011/032554

    申请日：2011-04-14

    Applicant: VERINATA HEALTH, INC. ,  RAVA, Richard, P.

    Inventor： RAVA, Richard, P.

    IPC: C12Q1/68

    CPC classification number: C12Q1/6809 ,  G06F19/18 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2539/113

    Abstract: The present invention provides a method capable of detecting single or multiple fetal chromosomal aneuploidies in a maternal sample comprising fetal and maternal nucleic acids, and verifying that the correct determination has been made. The method is applicable to determining copy number variations (CNV) of any sequence of interest in samples comprising mixtures of genomic nucleic acids derived from two different genomes, and which are known or are suspected to differ in the amount of one or more sequence of interest. The method is applicable at least to the practice of noninvasive prenatal diagnostics, and to the diagnosis and monitoring of conditions associated with a difference in sequence representation in healthy versus diseased individuals.

    Abstract translation: 本发明提供了一种能够检测包含胎儿和母体核酸的母体样品中的单胎或多胎胎儿染色体非整倍体的方法，并验证是否进行了正确的确定。 该方法适用于确定样品中的任何感兴趣的序列的拷贝数变异（CNV），其包含衍生自两个不同基因组的基因组核酸的混合物，其已知或被怀疑在一个或多个感兴趣序列的量上不同 。 该方法至少适用于无创产前诊断的实践，以及与健康与患病个体中序列表现差异相关的病症的诊断和监测。

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