Modeling Read Counts for CNV Detection in Exome Sequencing Data

Love Michael I., Alena Myšičková, Sun Ruping, Kalscheuer Vera, Vingron Martin and Haas Stefan A.

Statistical Applications in Genetics and Molecular Biology, 2011, vol. 10, issue 1, 30

Abstract: Varying depth of high-throughput sequencing reads along a chromosome makes it possible to observe copy number variants (CNVs) in a sample relative to a reference. In exome and other targeted sequencing projects, technical factors increase variation in read depth while reducing the number of observed locations, adding difficulty to the problem of identifying CNVs. We present a hidden Markov model for detecting CNVs from raw read count data, using background read depth from a control set as well as other positional covariates such as GC-content. The model, exomeCopy, is applied to a large chromosome X exome sequencing project identifying a list of large unique CNVs. CNVs predicted by the model and experimentally validated are then recovered using a cross-platform control set from publicly available exome sequencing data. Simulations show high sensitivity for detecting heterozygous and homozygous CNVs, outperforming normalization and state-of-the-art segmentation methods.

Keywords: exorne sequencing; targeted sequencing; CNV; copy number variant; HMM; hidden Markov model (search for similar items in EconPapers)
Date: 2011
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (2)

Downloads: (external link)
https://doi.org/10.2202/1544-6115.1732 (text/html)
For access to full text, subscription to the journal or payment for the individual article is required.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:bpj:sagmbi:v:10:y:2011:i:1:n:52

Ordering information: This journal article can be ordered from
https://www.degruyter.com/journal/key/sagmb/html

DOI: 10.2202/1544-6115.1732

Access Statistics for this article

Statistical Applications in Genetics and Molecular Biology is currently edited by Michael P. H. Stumpf

More articles in Statistical Applications in Genetics and Molecular Biology from De Gruyter
Bibliographic data for series maintained by Peter Golla ().