公开(公告)号：US20150073724A1

公开(公告)日：2015-03-12

申请号：US14288299

申请日：2014-05-27

Applicant: Agilent Technologies, Inc

Inventor： Ashutosh ,  Devendra Joshi ,  Christian A. Le Cocq

IPC: G06F19/22 ,  C12Q1/68

CPC classification number: G16B30/00 ,  C12Q1/6869 ,  C12Q1/6886 ,  C12Q2600/156

Abstract: Provided herein is a method for identifying a sequence variant in an enriched sample. In certain embodiments, this method may comprise: (a) obtaining: (i) a plurality of sequence reads from a sample that has been enriched for a genomic region and (ii) a reference sequence for the genomic region; (b) assembling the sequence reads to obtain a plurality of discrete sequence assemblies that correspond to potential variants; (c) determining which of the potential variants are true and which are artifacts by examining the sequence reads that make up each of the discrete sequence assemblies; (d) optionally determining whether each of the true potential variants contains a mutation that is known to be associated with the reference sequence; and (e) outputting a report indicating whether the sample comprises a sequence variant.

Abstract translation: 本文提供了用于鉴定富集样品中的序列变体的方法。 在某些实施方案中，该方法可以包括：（a）获得：（i）来自富集基因组区域的样品的多个序列读数和（ii）基因组区域的参考序列; （b）组合序列读取以获得对应于潜在变体的多个离散序列组件; （c）通过检查构成每个离散序列组件的序列读数来确定哪些潜在变体是真实的，哪些是伪影; （d）任选地确定每个真实潜在变体是否包含已知与参考序列相关的突变; 和（e）输出指示样本是否包括序列变体的报告。

公开(公告)号：US20160300013A1

公开(公告)日：2016-10-13

申请号：US14684242

申请日：2015-04-10

Applicant: Agilent Technologies, Inc.

Inventor： Ashutosh ,  Devendra Joshi ,  Arjun Vadapalli ,  Jayati Ghosh

IPC: G06F19/22 ,  C12Q1/68

CPC classification number: G16B30/00 ,  C12Q1/6869 ,  G16B20/00

Abstract: Provided herein are methods for simultaneously identifying genomic copy number variations (CNVs) and sequence variations in an enriched genomic sample and compositions, systems, and kits for performing such methods. In some aspects, the methods include: (a) obtaining a plurality of sequence reads from an enriched genomic sample that includes a plurality of genomic backbone regions and a plurality of genomic mutation regions of interest in a genomic locus of a subject; (b) obtaining a plurality of sequence reads from corresponding genomic backbone regions and genomic mutation regions of at least one reference genomic sample; (c) assembling the plurality sequence reads from the enriched genomic sample and the at least one reference genomic sample; and (d) determining, based on computational analysis of the assembly, whether the genomic locus has a copy number variation (CNV) and/or a sequence variation. The present disclosure further includes aspects in which the methods are performed by a computer and provide an output to a user identifying a genomic CNV and/or sequence variation.

Abstract translation: 本文提供了用于同时鉴定富集的基因组样品和用于进行此类方法的组合物，系统和试剂盒中的基因组拷贝数变异（CNV）和序列变异的方法。 在一些方面，所述方法包括：（a）从富集的基因组样品中获得多个序列读数，所述富集的基因组样品包括多个基因组骨架区域和在受试者的基因组区域中的多个感兴趣的基因组突变区域; （b）从至少一个参考基因组样品的相应基因组骨架区域和基因组突变区域获得多个序列读数; （c）从富集的基因组样品和至少一个参考基因组样品组装多个序列读数; 和（d）基于组装的计算分析来确定基因组轨迹是否具有拷贝数变异（CNV）和/或序列变异。 本公开还包括其中方法由计算机执行并向用户识别基因组CNV和/或序列变异提供输出的方面。

公开(公告)号：US20210174901A1

公开(公告)日：2021-06-10

申请号：US17133998

申请日：2020-12-24

Applicant: Agilent Technologies, Inc.

Inventor： Ashutosh ,  Devendra Joshi ,  Arjun Vadapalli ,  Jayati Ghosh

IPC: G16B30/00 ,  C12Q1/6869 ,  G16B20/00

Abstract: Provided herein are methods for simultaneously identifying genomic copy number variations (CNVs) and sequence variations in an enriched genomic sample and compositions, systems, and kits for performing such methods. In some aspects, the methods include: (a) obtaining a plurality of sequence reads from an enriched genomic sample that includes a plurality of genomic backbone regions and a plurality of genomic mutation regions of interest in a genomic locus of a subject; (b) obtaining a plurality of sequence reads from corresponding genomic backbone regions and genomic mutation regions of at least one reference genomic sample; (c) assembling the plurality sequence reads from the enriched genomic sample and the at least one reference genomic sample; and (d) determining, based on computational analysis of the assembly, whether the genomic locus has a copy number variation (CNV) and/or a sequence variation. The present disclosure further includes aspects in which the methods are performed by a computer and provide an output to a user identifying a genomic CNV and/or sequence variation.