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

Publication ,  Journal Article
Satten, GA; Allen, AS; Ikeda, M; Mulle, JG; Warren, ST
Published in: PLoS One
2014

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.

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Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2014

Volume

9

Issue

2

Start / End Page

e86272

Location

United States

Related Subject Headings

  • Software
  • Regression Analysis
  • Humans
  • Genomics
  • Genome-Wide Association Study
  • Genome, Human
  • General Science & Technology
  • DNA Copy Number Variations
 

Citation

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Satten, G. A., Allen, A. S., Ikeda, M., Mulle, J. G., & Warren, S. T. (2014). Robust regression analysis of copy number variation data based on a univariate score. PLoS One, 9(2), e86272. https://doi.org/10.1371/journal.pone.0086272
Satten, Glen A., Andrew S. Allen, Morna Ikeda, Jennifer G. Mulle, and Stephen T. Warren. “Robust regression analysis of copy number variation data based on a univariate score.PLoS One 9, no. 2 (2014): e86272. https://doi.org/10.1371/journal.pone.0086272.
Satten GA, Allen AS, Ikeda M, Mulle JG, Warren ST. Robust regression analysis of copy number variation data based on a univariate score. PLoS One. 2014;9(2):e86272.
Satten, Glen A., et al. “Robust regression analysis of copy number variation data based on a univariate score.PLoS One, vol. 9, no. 2, 2014, p. e86272. Pubmed, doi:10.1371/journal.pone.0086272.
Satten GA, Allen AS, Ikeda M, Mulle JG, Warren ST. Robust regression analysis of copy number variation data based on a univariate score. PLoS One. 2014;9(2):e86272.

Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2014

Volume

9

Issue

2

Start / End Page

e86272

Location

United States

Related Subject Headings

  • Software
  • Regression Analysis
  • Humans
  • Genomics
  • Genome-Wide Association Study
  • Genome, Human
  • General Science & Technology
  • DNA Copy Number Variations