公开(公告)号：US09193992B2

公开(公告)日：2015-11-24

申请号：US13894886

申请日：2013-05-15

Applicant: Agilent Technologies, Inc.

Inventor： Bo U. Curry ,  Jayati Ghosh ,  Brian Jon Peter ,  Arjun Vadapalli

IPC: C12Q1/68 ,  C07H21/00 ,  G06F19/18

CPC classification number: C12Q1/6827 ,  C12Q1/6883 ,  C12Q2600/156 ,  C12Q2600/158 ,  G06F19/18

Abstract: A method for determining the ploidy of a test genome is provided. In some embodiments, the method may comprises: a) obtaining a plurality of ratios for polymorphisms that are distributed throughout a test genome, wherein each of the ratios is a ratio of the measured copy number of uncut allele in a polymorphic site relative to the measured copy number of the uncut allele in the reference sample; b) taking the log of the ratios and plotting a distribution of the reference corrected log ratios of the SNP probes; and c) determining the ploidy of said the genome based on the number of peaks in that distribution.

Abstract translation: 提供了测定基因组倍性的方法。 在一些实施方案中，所述方法可以包括：a）获得分布在整个测试基因组中的多态性的多个比率，其中每个比率是多态性位点中未切割等位基因的测定拷贝数相对于测量的 参考样品中未切割等位基因的拷贝数; b）记录比率对数，并绘制SNP探针的参考校正对数比的分布; 和c）基于该分布中的峰的数目确定所述基因组的倍性。

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：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。