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    ANCESTRAL-SPECIFIC REFERENCE GENOMES AND METHODS OF CONSTRUCTING
    6.
    发明申请
    ANCESTRAL-SPECIFIC REFERENCE GENOMES AND METHODS OF CONSTRUCTING 审中-公开
    管理特定参考基因和构建方法

    公开(公告)号：US20170017757A1

    公开(公告)日：2017-01-19

    申请号：US15249408

    申请日：2016-08-27

    Applicant: Inova Health System

    Inventor： Joseph Vockley ,  John Niederhuber

    IPC: G06F19/22 ,  C40B30/02 ,  G06F19/14

    CPC classification number: G16B20/00 ,  G16B10/00 ,  G16B30/00 ,  G16B35/00 ,  G16C20/60

    Abstract: Ancestry has a significant impact on the major and minor alleles found in each nucleotide position within the genome. Due to mechanisms of inheritance, ancestral-specific information contained within the genome is conserved within members of an ancestry. For this reason, individuals within a specific ancestry are more likely to share alleles in their genomes with other members of the same ancestry. Functionally, the combination of alleles at all positions within a group of individuals defines that group as having a common ancestry. Moreover, the aggregation of differences between alleles at all positions distinguishes one ancestry from another. The genomic similarities and differences between ancestries provides a mechanism to generate reference genomes that are specific for each ancestry. Reference genomes that are specific to an ancestry can be used to increase the accuracy of whole genome sequencing, DNA-based diagnostics and therapeutic marker discovery and in a variety of real-world DNA-based applications. Provided herein are methods for constructing an ancestral-specific reference genome database.

    Abstract translation: 祖先对基因组内每个核苷酸位置发现的主要和次要等位基因具有显着影响。 由于遗传机制，祖先特异性信息包含在基因组内，在祖先的成员中是保守的。 因此，特定祖先的个体更有可能与同一祖先的其他成员共享基因组中的等位基因。 功能上，一组个体内的所有位置上的等位基因的组合将该组定义为具有共同的祖先。 此外，所有位置的等位基因之间的差异的聚集将一个祖先与另一个祖先区分开。 祖先之间的基因组相似性和差异提供了生成对每个祖先特异的参考基因组的机制。 可以使用对祖先特异性的参考基因组来提高全基因组测序，基于DNA的诊断和治疗标记发现的准确性，以及各种真实的基于DNA的应用。 本文提供了构建祖先特异性参考基因组数据库的方法。

    Genetic Affinity of Microorganisms and Viruses
    7.
    发明申请
    Genetic Affinity of Microorganisms and Viruses 审中-公开
    微生物和病毒的遗传亲和力

    公开(公告)号：US20150324518A1

    公开(公告)日：2015-11-12

    申请号：US13532001

    申请日：2012-06-25

    Applicant: George E. Fox ,  Richard C. Willson, III ,  Zhengdong Zhang

    Inventor： George E. Fox ,  Richard C. Willson, III ,  Zhengdong Zhang

    IPC: G06F19/14 ,  H01J49/16

    CPC classification number: G16B10/00 ,  G16B20/00 ,  G16B25/00 ,  H01J49/164

    Abstract: Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism.

    Abstract translation: 选择核酸数据库（如16S rRNA）中的哪些子序列在基本系统发育树上是细菌，微生物，真菌等的特定分组的高度特征。 也适用于包含病毒基因组RNA或DNA的病毒。 组合通过该方法鉴定的高度特征性序列的目录，以确定未知生物体的遗传特性。 特征序列用于设计核酸杂交探针，其包括特征序列或其补体，或衍生自一个或多个特征序列。 在杂交中使用多个这些特征序列来确定样品中生物的系统发生树位置。 在原始序列数据库中表示的目标生物体和足够的特征序列可以鉴定物种或亚种水平。 许多探针的寡核苷酸阵列是特别优选的。 杂交信号可以包括荧光，化学发光或同位素标记等; 或样品中的序列可以通过直接方式检测，例如， 质谱。 该方法的特征序列也可用于设计特异性PCR引物。 该方法唯一地识别未知生物的系统发生亲和力，而不需要事先了解样品中存在的内容。 即使生物体以前没有遇到，该方法仍然提供关于哪个系统发生树分叉节点包含有机体的有用信息。

    Analysis of community structures in environmental samples
    8.
    发明授权
    Analysis of community structures in environmental samples 有权
    环境样本社区结构分析

    公开(公告)号：US09014987B2

    公开(公告)日：2015-04-21

    申请号：US13331557

    申请日：2011-12-20

    Applicant: Sharmila Shekhar Mande ,  Kuntal Kumar Bhusan ,  Tarini Shankar Ghosh

    Inventor： Sharmila Shekhar Mande ,  Kuntal Kumar Bhusan ,  Tarini Shankar Ghosh

    IPC: G06F19/26 ,  G06F19/14 ,  G06T11/20 ,  G06F19/20 ,  G06F19/28

    CPC classification number: G06F19/26 ,  G06F19/14 ,  G06F19/20 ,  G06F19/28 ,  G06T11/206

    Abstract: Systems and methods for analyzing community structures within a plurality of environmental samples are described herein. The method includes obtaining taxa data corresponding to taxonomic groups within the plurality of the environmental samples. Based on the taxa data, an abundance value for each of the taxonomic groups with respect to each of the plurality of environmental samples is determined. Further, based on abundance values, an interaction factor for each pair of the taxonomic groups in the plurality of environmental samples is computed. The interaction factor is indicative of a degree of interaction between a pair of taxonomic groups from among the taxonomic groups. Based in part on interaction factors and abundance values, the plurality of the environmental samples is clustered.

    Abstract translation: 本文描述了用于分析多个环境样品中的社区结构的系统和方法。 该方法包括获得与多个环境样品中的分类群相对应的分类数据。 基于分类单元数据，确定每个分类群相对于多个环境样本中的每一个的丰度值。 此外，基于丰度值，计算多个环境样本中每对分类群的相互作用因子。 相互作用因子表明分类群中一对分类群之间的相互作用程度。 部分基于相互作用因子和丰度值，将多个环境样本聚类。

    Algorithm for Modification of Somatic Cancer Evolution
    9.
    发明申请
    Algorithm for Modification of Somatic Cancer Evolution 审中-公开
    体细胞癌变化修改算法

    公开(公告)号：US20150072865A1

    公开(公告)日：2015-03-12

    申请号：US14374924

    申请日：2012-02-13

    Applicant: Albert RÜBBEN

    Inventor： Albert Rubben

    IPC: G06F19/18 ,  G06F19/00 ,  G01N33/574 ,  G06F19/14 ,  G06F19/24

    CPC classification number: G06F19/18 ,  G01N33/574 ,  G06F19/00 ,  G06F19/12 ,  G06F19/14 ,  G06F19/24 ,  G16H50/30

    Abstract: Most clinically distinguishable malignant tumors are characterized by specific mutations, specific patterns of chromosomal rearrangements and a predominant mechanism of genetic instability. It has been suggested that the internal dynamics of genomic modifications as opposed to the external evolutionary forces have a significant and complex impact on Darwinian species evolution. A similar situation can be expected for somatic cancer evolution as the key mechanisms encountered in species evolution such as duplications, rearrangements or deletions of genes also constitute prevalent mutation mechanisms in cancers with chromosomal instability. The invention is an algorithm which is based on a systems concept describing the putative constraints of the cancer genome architecture on somatic cancer evolution. The algorithm allows the identification of therapeutic target genes in individual cancer patients which do not represent oncogenes or tumor suppressor genes but have become putative therapeutic targets due to constraints of the cancer genome architecture on individual somatic cancer evolution. Target genes or regulatory elements may be identified by their designation as essential genes or regulatory elements in cancer cells of the patient but not in normal tissue cells or they may be identified by their impact on the process of somatic cancer evolution in individual patients based on phylogenetic trees of somatic cancer evolution and on the constructed multilayered cancer genome maps. The algorithm can be used for delivering personalized cancer therapy as well as for the industrial identification of novel anti-cancer drugs. The algorithm is essential for designing software programs which allow the prediction of the natural history of cancer disease in individual patients.

    Abstract translation: 大多数临床上可区分的恶性肿瘤的特征是特异性突变，染色体重排的特定模式和遗传不稳定的主要机制。 有人提出，基因组修饰的内在动力与外部进化力相反，对达尔文物种进化有重要和复杂的影响。 对于体细胞癌进展来说，类似的情况可以预期，因为在物种进化中遇到的关键机制，如基因重复，重排或缺失，也构成了具有染色体不稳定性的癌症中的普遍突变机制。 本发明是一种基于描述癌症基因组构架对体细胞癌进化的推定约束的系统概念的算法。 该算法允许在不代表致癌基因或肿瘤抑制基因的个体癌症患者中鉴定治疗靶基因，但是由于癌症基因组结构对个体体细胞癌进展的限制，已经成为推定的治疗靶标。 目标基因或调节元件可以通过它们的名称被鉴定为患者的癌细胞中的必需基因或调节元件，但不能在正常组织细胞中鉴定，或者它们可以通过其对基于系统发生的个体患者体细胞癌进展过程的影响来鉴定 体细胞癌进化树和构建的多层癌基因组图谱。 该算法可用于提供个性化的癌症治疗以及新型抗癌药物的工业鉴定。 该算法对于设计允许预测个体患者的癌症疾病自然史的软件程序至关重要。

    GRANULAR ELECTION OF PREDICTIVE POLYGENIC MODELS
    10.
    发明申请
    GRANULAR ELECTION OF PREDICTIVE POLYGENIC MODELS 审中-公开

    公开(公告)号：US20200019674A1

    公开(公告)日：2020-01-16

    申请号：US16033983

    申请日：2018-07-12

    Applicant: Helix OpCo, LLC

    Inventor： Ryan P. Trunck ,  Rani K. Powers ,  Christopher M. Glode

    IPC: G06F19/14 ,  G06F19/24

    Abstract: Systems and methods are provided for selecting from among polygenic models that predict characteristics of individuals. One embodiment is a genetic prediction server that includes a memory that stores polygenic models which predict characteristics of individuals based on genetic variants of the individuals, including a set of polygenic models for a characteristic that each perform a different analysis of genetic variants when making a prediction. The server also includes a controller that receives an indication of genetic variants of an individual, determines that the individual belongs to a demographic, and selects, based on the demographic, a polygenic model from the set to predict the characteristic for the individual.

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