A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6
Henrik Bengtsson, Pratyaksha Wirapati, Terence P Speed
BIOINFORMATICS | OXFORD UNIV PRESS | Published : 2009
MOTIVATION: High-resolution copy-number (CN) analysis has in recent years gained much attention, not only for the purpose of identifying CN aberrations associated with a certain phenotype, but also for identifying CN polymorphisms. In order for such studies to be successful and cost effective, the statistical methods have to be optimized. We propose a single-array preprocessing method for estimating full-resolution total CNs. It is applicable to all Affymetrix genotyping arrays, including the recent ones that also contain non-polymorphic probes. A reference signal is only needed at the last step when calculating relative CNs. RESULTS: As with our method for earlier generations of arrays, thi..View full abstract
Awarded by NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
Wenner-Gren Foundation (to H. B.); the American-Scandinavian Foundation (to H. B.); the Solander Foundation (to H. B.).