公开(公告)号：US20160117444A1

公开(公告)日：2016-04-28

申请号：US14960996

申请日：2015-12-07

Applicant: Complete Genomics, Inc.

Inventor： Aaron Halpern ,  Krishna Pant

IPC: G06F19/22 ,  G06F19/28 ,  C40B30/02 ,  G06F19/26

CPC classification number: G16B30/00 ,  C12Q1/6827 ,  G16B20/00 ,  G16B35/00 ,  G16B40/00 ,  G16B45/00 ,  G16B50/00 ,  G16C20/60 ,  C12Q2537/16 ,  C12Q2537/165

Abstract: Methods for interpreting absolute copy number of complex tumors and for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. In certain aspects, genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.

公开(公告)号：US20140229117A1

公开(公告)日：2014-08-14

申请号：US14253642

申请日：2014-04-15

Applicant: COMPLETE GENOMICS, INC.

Inventor： Aaron Halpern ,  Krishna Pant

IPC: G06F19/18

CPC classification number: G16B20/00 ,  C12Q1/6809 ,  C12Q1/6827 ,  G16B25/00 ,  G16B30/00 ,  G16B40/00 ,  C12Q2537/16 ,  C12Q2537/165

Abstract: Methods for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. Genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.

Abstract translation: 公开了用于确定样品中靶序列的检测位置处的基因组区域的拷贝数的方法。 对样品中靶序列的基因组区域进行测序，并获得序列覆盖度的测量数据。 校正序列覆盖偏差并且可以相对于基线样本进行归一化。 执行隐马尔科夫模型（HMM）分割，评分和输出，并且在一些实施例中，也可以执行基于群体的无呼叫和低置信区域的识别。 然后估计多个区域的总拷贝数值和区域特定拷贝数值。