Nucleic Acids Research Publication 2008
This research found that Phi29-based whole genome amplification systematically introduces hundreds of potentially confounding copy number variant artifacts that can obscure detection of bona fide copy number variants (NCVs) and that these artifacts are correlated with proximity to chormosome ends and GC content. Pair-wise comparison of amplified products considerably reduced the number of apparent artifacts and partially restored the ability to detect real CNVs.
Pugh TJ, Delaney AD, Farnoud N, Flibotte S, Griffith M, Li I, Qian H, Farinha P, Gascoyne RD and Marra MA. Nucleic Acids Research 2008. 36(13):e80