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Oxford University Press (OUP), Bioinformatics, 21(28), p. 2747-2754

DOI: 10.1093/bioinformatics/bts526

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A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

Journal article published in 2012 by Vincent Plagnol ORCID, James Curtis, Michael Epstein, Kin Y. Mok, Emma Stebbings, Sofia Grigoriadou, Nicholas W. Wood ORCID, Sophie Hambleton, Siobhan O. Burns, Adrian J. Thrasher, Dinakantha Kumararatne, Rainer Doffinger, Sergey Nejentsev
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Motivation: Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read depth strategy consists of using another sample (or a combination of samples) as a reference to control for the variability at the capture and sequencing steps. However, technical variability between samples complicates the analysis and can create spurious CNV calls.