CONTRA: copy number analysis for targeted resequencing
Jason Li, Richard Lupat, Kaushalya C Amarasinghe, Ella R Thompson, Maria A Doyle, Georgina L Ryland, Richard W Tothill, Saman K Halgamuge, Ian G Campbell, Kylie L Gorringe
BIOINFORMATICS | OXFORD UNIV PRESS | Published : 2012
MOTIVATION: In light of the increasing adoption of targeted resequencing (TR) as a cost-effective strategy to identify disease-causing variants, a robust method for copy number variation (CNV) analysis is needed to maximize the value of this promising technology. 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 met..View full abstract
Awarded by Australian Research Council
Peter MacCallum Cancer Foundation Endowment Fund, the Victorian Breast Cancer Research Consortium and Australian Research Council (grant DP1096296).