Estimation and assessment of raw copy numbers at the single locus level.

Bioinformatics
Henrik BengtssonT P Speed

Abstract

Although copy-number aberrations are known to contribute to the diversity of the human DNA and cause various diseases, many aberrations and their phenotypes are still to be explored. The recent development of single-nucleotide polymorphism (SNP) arrays provides researchers with tools for calling genotypes and identifying chromosomal aberrations at an order-of-magnitude greater resolution than possible a few years ago. The fundamental problem in array-based copy-number (CN) analysis is to obtain CN estimates at a single-locus resolution with high accuracy and precision such that downstream segmentation methods are more likely to succeed. We propose a preprocessing method for estimating raw CNs from Affymetrix SNP arrays. Its core utilizes a multichip probe-level model analogous to that for high-density oligonucleotide expression arrays. We extend this model by adding an adjustment for sequence-specific allelic imbalances such as cross-hybridization between allele A and allele B probes. We focus on total CN estimates, which allows us to further constrain the probe-level model to increase the signal-to-noise ratio of CN estimates. Further improvement is obtained by controlling for PCR effects. Each part of the model is fitted robu...Continue Reading

References

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Citations

Jan 10, 2012·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Luís Muñoz-BellvisJ M Sayagués
May 21, 2013·Nature Genetics·Allen S HoTimothy A Chan
Oct 18, 2011·Proceedings of the National Academy of Sciences of the United States of America·Laura M HeiserPaul T Spellman
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Dec 27, 2012·Nucleic Acids Research·Samir Ben ChaabaneByeong-ha Lee
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Aug 5, 2009·The Journal of Clinical Investigation·Sophie Paquet-FifieldPritinder Kaur
Dec 25, 2010·The Journal of Clinical Investigation·Edwina SuttonPaul Thomas
Jun 2, 2011·BMC Bioinformatics·Jeanette E Eckel-PassowMariza de Andrade
Dec 29, 2012·BMC Bioinformatics·Melissa PronoldShahab Asgharzadeh
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