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.

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：US20160125130A1

公开(公告)日：2016-05-05

申请号：US14533743

申请日：2014-11-05

Applicant: Agilent Technologies, Inc.

Inventor： Christian A. Le Cocq ,  Magnus Isaksson ,  Ashutosh ,  Linus Forsmark

IPC: G06F19/22

CPC classification number: G16B30/00

Abstract: Provided herein, among other things, is a computer-implemented method for assigning a sequence read to a genomic location, the method including: a) accessing a file containing a sequence read, wherein the sequence read is obtained from a nucleic acid sample that has been enriched by hybridization to a plurality of capture sequences; and b) assigning the sequence read to a genomic location by: i) identifying a capture sequence as being a match with the sequence read if the sequence read contains one or more subsequences of the capture sequence; ii) calculating, using a computer, a score indicating the degree of sequence similarity between each of the matched capture sequences and the sequence read; and iii) assigning the sequence read to the genomic location if the calculated score for a matched capture sequence is above a threshold.

Abstract translation: 本文提供了一种用于将读取的序列分配给基因组位置的计算机实现的方法，所述方法包括：a）访问包含读取序列的文件，其中读取的序列是从具有 通过与多个捕获序列的杂交而富集; 和b）通过以下操作将读取的序列分配到基因组位置：i）如果读取的序列包含捕获序列的一个或多个子序列，则将捕获序列识别为与读取的序列匹配; ii）使用计算机计算指示每个匹配捕获序列与读取的序列之间的序列相似度的分数; 以及iii）如果匹配捕获序列的计算得分高于阈值，则将读取的序列分配给基因组位置。