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    COMPOSITIONS AND METHODS FOR ASSESSING MICROBIAL POPULATIONS
    11.
    发明申请
    COMPOSITIONS AND METHODS FOR ASSESSING MICROBIAL POPULATIONS 有权

    公开(公告)号：US20220251669A1

    公开(公告)日：2022-08-11

    申请号：US17658493

    申请日：2022-04-08

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Shrutii SARDA ,  Anna MCGEACHY ,  Rajesh GOTTIMUKKALA ,  David MERRILL ,  Heesun SHIN ,  Aren EWING ,  Wing LEE ,  Birgit DREWS ,  Fiona HYLAND ,  Janice AU-YOUNG

    IPC: C12Q1/6888 ,  C12Q1/6874 ,  C12Q1/686 ,  G16B30/10

    Abstract: The present disclosure provides compositions and methods, as well as combinations, kits, and systems that include the compositions and methods, for amplification, detection, characterization, assessment, profiling and/or measurement of nucleic acids in samples, particularly biological samples. Compositions and methods provided herein include combinations of microbial species target-specific nucleic acid primers for selective amplification and/or combinations of primers for amplification of nucleic acids from a large group of taxonomically related microorganisms. In one aspect, amplified nucleic acids obtained using the compositions and methods can be used in various processes including nucleic acid sequencing and used to detect the presence of microbial species and assess microbial populations in a variety of samples. In accordance with the teachings and principles, new methods, systems and non-transitory machine-readable storage medium are provided to compress reference sequence databases used in mapping sequence reads for analysis and profiling of microbial populations.

    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS
    12.
    发明申请
    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS 有权

    公开(公告)号：US20210210164A1

    公开(公告)日：2021-07-08

    申请号：US17136800

    申请日：2020-12-29

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Zheng ZHANG ,  Fiona HYLAND ,  Sowmi UTIRAMERUR

    IPC: G16B30/00

    Abstract: Systems, methods, and computer program products for aligning a fragment sequence to a target sequencing. The alignment is allowed at most one gap, such as an insertion or a deletion. In some embodiments, both a gapped alignment and an ungapped alignment can be produced. A selection can be made between the gapped alignment and the ungapped alignment based on a quality value for each alignment.

    METHODS FOR DETECTING MUTATION LOAD FROM A TUMOR SAMPLE
    14.
    发明申请
    METHODS FOR DETECTING MUTATION LOAD FROM A TUMOR SAMPLE 审中-公开

    公开(公告)号：US20200075122A1

    公开(公告)日：2020-03-05

    申请号：US16550672

    申请日：2019-08-26

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Ruchi Chaudhary ,  Fiona HYLAND

    IPC: G16B20/20

    Abstract: A targeted panel with low sample input requirements from a tumor only sample may be processed to estimate mutation load in a tumor sample. The method may include: detecting variants in nucleic acid sequence reads corresponding to targeted locations in the tumor sample genome; annotating detected variants with an annotation information from a population database; filtering the detected variants, wherein the filtering retains the somatic variants and removes germline variants; calculating an initial TMB; and applying a calibration to the initial TMB level to produce a final TMB level for the mutation load of the tumor sample genome. The filtering may also include retaining nonsynonymous SNVs and indels for the analysis.

    SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION
    16.
    发明申请
    SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION 审中-公开
    用于识别序列变异的系统和方法

    公开(公告)号：US20130345066A1

    公开(公告)日：2013-12-26

    申请号：US13890923

    申请日：2013-05-09

    Applicant: Life Technologies Corporation

    Inventor： Dumitru BRINZA ,  Zheng ZHANG ,  Fiona HYLAND ,  Rajesh GOTTIMUKKALA

    IPC: C12Q1/68 ,  G06F19/12

    CPC classification number: C12Q1/6874 ,  G16B5/00 ,  G16B30/00

    Abstract: Systems and method for determining variants can receive mapped reads, align flow space information to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be evaluated in a context specific manner. A list of probable variants can be provided.

    Abstract translation: 用于确定变体的系统和方法可以接收映射读取，将流空间信息对准参考的对应部分的流空间表示。 可以以上下文特定的方式评估跨越具有潜在变体的位置的读数。 可以提供可能的变体列表。

    Systems and Methods for Annotating Biomolecule Data
    19.
    发明申请
    Systems and Methods for Annotating Biomolecule Data 审中-公开
    用于注释生物分子数据的系统和方法

    公开(公告)号：US20160078094A1

    公开(公告)日：2016-03-17

    申请号：US14859653

    申请日：2015-09-21

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Liviu Popescu ,  Fiona HYLAND

    IPC: G06F17/30 ,  G06F19/24 ,  G06F19/28

    CPC classification number: G06F16/24573 ,  G06F16/2455 ,  G06F16/248 ,  G16B40/00 ,  G16B50/00

    Abstract: Systems, methods, software and computer-usable media for annotating biomolecule-related data are disclosed. In certain exemplified embodiments, the biomolecules can be nucleic acids and the data can be sequence-related data. In various embodiments, systems can include one or more public or private biological attributes (e.g., annotation information databases, data storage devices and systems, etc.) sources, one or more genomic features data sources (e.g., genomic variant tools, genomic variant databases, genomic variant data storage devices and systems, etc.), a computing device (e.g., workstation, server, personal computer, mobile device, etc.) hosting an annotations module and/or a reporting module, and a client terminal.

    Abstract translation: 公开了用于注释生物分子相关数据的系统，方法，软件和计算机可用介质。 在某些示例性实施方案中，生物分子可以是核酸，并且数据可以是序列相关数据。 在各种实施例中，系统可以包括一个或多个公共或私人生物属性（例如，注释信息数据库，数据存储设备和系统等）源，一个或多个基因组特征数据源（例如，基因组变体工具，基因组变体数据库 ，基因组变体数据存储设备和系统等），托管注释模块和/或报告模块的计算设备（例如，工作站，服务器，个人计算机，移动设备等）和客户终端。

    SYSTEMS AND METHODS FOR PAIRED END SEQUENCING
    20.
    发明申请
    SYSTEMS AND METHODS FOR PAIRED END SEQUENCING 审中-公开
    配对终端序列的系统和方法

    公开(公告)号：US20130288902A1

    公开(公告)日：2013-10-31

    申请号：US13787221

    申请日：2013-03-06

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Sowmi UTIRAMERUR ,  Simon CAWLEY ,  Yongming SUN ,  Fiona HYLAND

    IPC: C12Q1/68

    CPC classification number: C12Q1/6869 ,  G16B30/00

    Abstract: Systems and methods for analyzing overlapping sequence information can obtain first and second overlapping sequence information for a polynucleotide, align the first and second sequence information, determine a degree of agreement between the first and second sequence information for a location along the polynucleotide, and determine a base call and a quality value for the location.

    Abstract translation: 用于分析重叠序列信息的系统和方法可以获得多核苷酸的第一和第二重叠序列信息，对齐第一和第二序列信息，确定沿着多核苷酸的位置的第一和第二序列信息之间的一致程度，并确定 基地电话和位置的质量值。

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