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    METHODS AND SYSTEM FOR GENERATING AND COMPARING REDUCED GENOME DATA SETS
    1.
    发明申请
    METHODS AND SYSTEM FOR GENERATING AND COMPARING REDUCED GENOME DATA SETS 审中-公开
    用于生成和比较减少的基因组数据集的方法和系统

    公开(公告)号：WO2017210102A1

    公开(公告)日：2017-12-07

    申请号：PCT/US2017/034625

    申请日：2017-05-26

    Applicant: INSTITUTE FOR SYSTEMS BIOLOGY

    Inventor： GLUSMAN, Gustavo ,  ROBINSON, Robert, Maxwell

    IPC: C12Q1/68 ,  C40B20/00 ,  C40B40/06 ,  G06F19/10 ,  G06F19/22

    CPC classification number: C12N15/1089 ,  C12Q1/68 ,  C12Q1/6827 ,  C40B20/00 ,  C40B40/06 ,  G16B20/20 ,  G16B30/00 ,  G16B35/10 ,  G16B35/20 ,  G16B45/00 ,  G16B50/40

    Abstract: An ultra-fast solution to the problem of comparing genomes across sequencing technologies and genome freezes, while preserving privacy, is presented. A method for transforming a standard genome representation (i.e., a list of variants relative to a reference) into a "fingerprint" of the genome does not require knowledge of the technology, reference and encoding used, and yields fingerprints that can be readily compared to ascertain relatedness between two genome representations. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. This enables scaling up a variety of important genome analyses, including determinations of degree of relatedness, recognizing duplicative sequenced genomes in a set, and many others. Because the original genome representation cannot be reconstructed from its fingerprint, the method also has significant implications for privacy-preserving genome analytics.

    Abstract translation: 本文介绍了一种快速解决跨测序技术和基因组冻结的基因组比较问题，同时保护隐私的超快速解决方案。 用于将标准基因组表示（即，相对于参考的变体列表）转换为“指纹” 的基因组不需要关于所使用的技术，参考和编码的知识，并且产生可以容易地比较的指纹以确定两个基因组表示之间的相关性。 由于它们的尺寸减小，基因组指纹图谱的计算速度很快并且只需很少的记忆。 这使得可以扩大各种重要的基因组分析，包括确定亲缘关系程度，识别一组中重复测序的基因组以及许多其他基因组。 由于原始基因组表达无法通过其指纹重建，因此该方法对保护隐私的基因组分析也具有重要意义。

    GENOMIC DATA ANALYSIS SYSTEM AND METHOD
    3.
    发明申请
    GENOMIC DATA ANALYSIS SYSTEM AND METHOD 审中-公开

    公开(公告)号：WO2018183745A1

    公开(公告)日：2018-10-04

    申请号：PCT/US2018/025249

    申请日：2018-03-29

    Applicant: ILLUMINA, INC.

    Inventor： WARREN, Andrew

    IPC: G06F19/26

    CPC classification number: G16B45/00

    Abstract: Embodiments relate to methods and systems for analyzing genomic data, such as genetic variants. Some embodiments relate to the efficient analysis and presentation of certain genetic variants of an individual.

    USING K-MERS FOR RAPID QUALITY CONTROL OF SEQUENCING DATA WITHOUT ALIGNMENT
    6.
    发明申请
    USING K-MERS FOR RAPID QUALITY CONTROL OF SEQUENCING DATA WITHOUT ALIGNMENT 审中-公开

    公开(公告)号：WO2019091986A1

    公开(公告)日：2019-05-16

    申请号：PCT/EP2018/080376

    申请日：2018-11-07

    Applicant: KONINKLIJKE PHILIPS N.V.

    Inventor： WU, Jie ,  CHEUNG, Yee Him

    IPC: G16B30/10

    CPC classification number: G16B30/00 ,  C12Q1/68 ,  G16B20/00 ,  G16B45/00 ,  G16B50/30

    Abstract: A method (200) for evaluating nucleic acid sequencing data using a quality control analysis system (300), comprising: receiving (210) a plurality of reads of a nucleic acid sequence; extracting (220) a plurality of k-mers from the plurality of reads; identifying (230), using the plurality of extracted k-mers, one or more of a plurality of annotated k-mers found in the plurality of reads, wherein the plurality of extracted k-mers are stored in an annotation database (350), and further wherein the annotated k-mers are annotated with annotation information about the one or more nucleic acid sequences from which the annotated k-mers are generated; gathering (240), based on the identified annotated k-mers found in the plurality of reads, annotation information about the plurality of reads; and determining (250), based on the gathered annotation information, a quality control metric for at least some of the plurality of reads.

    DIGITAL IMAGE ANALYSIS OF INFLAMMATORY CELLS AND MEDIATORS OF INFLAMMATION
    8.
    发明申请
    DIGITAL IMAGE ANALYSIS OF INFLAMMATORY CELLS AND MEDIATORS OF INFLAMMATION 审中-公开
    炎症细胞和炎症介质的数字图像分析

    公开(公告)号：WO2017171720A1

    公开(公告)日：2017-10-05

    申请号：PCT/US2016/024598

    申请日：2016-03-29

    Applicant: FLAGSHIP BIOSCIENCES, INC.

    Inventor： PELJTO, Mirza ,  MILICI, Anthony J. ,  LANGE, Holger ,  KRUEGER, Joseph ,  AEFFNER, Famke ,  YOUNG, George David

    IPC: G01N33/567 ,  G01N33/50 ,  G06K9/34 ,  G06F19/26 ,  G06T1/00

    CPC classification number: G06K9/00147 ,  G06K9/0014 ,  G06T7/0012 ,  G06T2207/10024 ,  G06T2207/10056 ,  G06T2207/30024 ,  G16B45/00

    Abstract: This disclosure concerns methods for evaluating inflammatory cells and modulators of the inflammatory response in tumor tissue and other relevant tissue types. The methods entail: obtaining a tissue sample and processing said tissue sample to produce histologic slides of tissue sections; staining of the tissue sections to identify inflammatory cells and modulators of the inflammatory response; digitizing slides to produce an image of the stained tissue sections; digitally stratifying the tissue sample into tumor and other relevant tissue compartments; and using digital image analysis to quantify cell-based and cell population-based features. The quantification of cell-based and cell population-based features within a tissue compartment of interest is used to develop a summary score of the immune system-tissue compartment of interest interaction. Patient stratification and selection as candidates for a therapeutic approach is ultimately based on the summary score value.

    Abstract translation: 本公开涉及用于评估肿瘤组织和其他相关组织类型中炎性细胞和炎性应答调节剂的方法。 该方法需要：获得组织样本并处理所述组织样本以产生组织切片的组织切片; 对组织切片进行染色以鉴定炎性细胞和炎性应答的调节剂; 数字化幻灯片以产生染色组织切片的图像; 将组织样本数字分层到肿瘤和其他相关组织区室中; 并使用数字图像分析来量化基于细胞和细胞群体的特征。 定量感兴趣组织区间内的基于细胞和细胞群体的特征被用于开发免疫系统 - 感兴趣相互作用的组织区间的总结评分。 患者分层和选择作为治疗方案的候选者最终基于总分值。

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