Journal Article

Power to detect selective allelic amplification in genome-wide scans of tumor data

Ninad Dewal, Matthew L. Freedman, Thomas LaFramboise and Itsik Pe'er

in Bioinformatics

Volume 26, issue 4, pages 518-528
Published in print February 2010 | ISSN: 1367-4803
Published online December 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp694
Power to detect selective allelic amplification in genome-wide scans of tumor data

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Motivation: Somatic amplification of particular genomic regions and selection of cellular lineages with such amplifications drives tumor development. However, pinpointing genes under such selection has been difficult due to the large span of these regions. Our recently-developed method, the amplification distortion test (ADT), identifies specific nucleotide alleles and haplotypes that confer better survival for tumor cells when somatically amplified. In this work, we focus on evaluating ADT's power to detect such causal variants across a variety of tumor dataset scenarios.

Results: Towards this end, we generated multiple parameter-based, synthetic datasets—derived from real data—that contain somatic copy number aberrations (CNAs) of various lengths and frequencies over germline single nucleotide polymorphisms (SNPs) genome-wide. Gold-standard causal sub-regions were assigned within these CNAs, followed by an assessment of ADT's ability to detect these sub-regions. Results indicate that ADT possesses high sensitivity and specificity in large sample sizes across most parameter cases, including those that more closely reflect existing SNP and CNA cancer data.

Availability: ADT is implemented in the Java software HADiT and can be downloaded through the SVN repository (via Develop→ Code→SVN Browse) at: http://sourceforge.net/projects/hadit/.

Contact: ninad.dewal@dbmi.columbia.edu

Supplementary Information: Supplementary data are available at Bioinformatics online.

Journal Article.  10039 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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