Robust regression analysis of copy number variation data based on a univariate score.

Published online

Journal Article

MOTIVATION: The discovery that copy number variants (CNVs) are widespread in the human genome has motivated development of numerous algorithms that attempt to detect CNVs from intensity data. However, all approaches are plagued by high false discovery rates. Further, because CNVs are characterized by two dimensions (length and intensity) it is unclear how to order called CNVs to prioritize experimental validation. RESULTS: We developed a univariate score that correlates with the likelihood that a CNV is true. This score can be used to order CNV calls in such a way that calls having larger scores are more likely to overlap a true CNV. We developed cnv.beast, a computationally efficient algorithm for calling CNVs that uses robust backward elimination regression to keep CNV calls with scores that exceed a user-defined threshold. Using an independent dataset that was measured using a different platform, we validated our score and showed that our approach performed better than six other currently-available methods. AVAILABILITY: cnv.beast is available at http://www.duke.edu/~asallen/Software.html.

Full Text

Duke Authors

Cited Authors

  • Satten, GA; Allen, AS; Ikeda, M; Mulle, JG; Warren, ST

Published Date

  • 2014

Published In

Volume / Issue

  • 9 / 2

Start / End Page

  • e86272 -

PubMed ID

  • 24516529

Pubmed Central ID

  • 24516529

Electronic International Standard Serial Number (EISSN)

  • 1932-6203

Digital Object Identifier (DOI)

  • 10.1371/journal.pone.0086272

Language

  • eng

Conference Location

  • United States