CONTRA: copy number analysis for targeted resequencing

被引：270
作者：
Li, Jason [1 ]
Lupat, Richard [1 ,2 ]
Amarasinghe, Kaushalya C. [3 ]
Thompson, Ella R. [2 ]
Doyle, Maria A. [1 ]
Ryland, Georgina L. [2 ]
Tothill, Richard W. [4 ]
Halgamuge, Saman K. [3 ]
Campbell, Ian G. [2 ,5 ,6 ]
Gorringe, Kylie L. [2 ,5 ,6 ]
机构：
[1] Peter MacCallum Canc Ctr, Bioinformat Core Facil, Melbourne, Vic 3002, Australia
[2] Peter MacCallum Canc Ctr, Victorian Breast Canc Res Consortium, Canc Genet Lab, Melbourne, Vic 3002, Australia
[3] Univ Melbourne, Dept Mech Engn, Parkville, Vic 3010, Australia
[4] Peter MacCallum Canc Ctr, Mol Genom Core Facil, Melbourne, Vic 3002, Australia
[5] Univ Melbourne, Sir Peter MacCallum Dept Oncol, Parkville, Vic 3010, Australia
[6] Univ Melbourne, Dept Pathol, Parkville, Vic 3010, Australia
来源：
BIOINFORMATICS | 2012年 / 28卷 / 10期
基金：
澳大利亚研究理事会;
关键词：
IDENTIFICATION; CANCER; FRAMEWORK; ACCURATE; CAPTURE; GENE;
D O I：
10.1093/bioinformatics/bts146
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Results: We present a method for CNV detection for TR data, including whole-exome capture data. Our method calls copy number gains and losses for each target region based on normalized depth of coverage. Our key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. Our methods are made available via CONTRA (COpy Number Targeted Resequencing Analysis), a software package that takes standard alignment formats (BAM/SAM) and outputs in variant call format (VCF4.0), for easy integration with other next-generation sequencing analysis packages. We assessed our methods using samples from seven different target enrichment assays, and evaluated our results using simulated data and real germline data with known CNV genotypes.
引用
收藏
页码：1307 / 1313
页数：7
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