%0 Journal Article
%T Copy Number Studies in Noisy Samples
%A Philip Ginsbach
%A Bowang Chen
%A Yanxiang Jiang
%A Stefan T. Engelter
%A Caspar Grond-Ginsbach
%J Microarrays
%D 2013
%I MDPI AG
%R 10.3390/microarrays2040284
%X System noise was analyzed in 77 Affymetrix 6.0 samples from a previous clinical study of copy number variation (CNV). Twenty-three samples were classified as eligible for CNV detection, 29 samples as ineligible and 25 were classified as being of intermediate quality. New software (¡°noise-free-cnv¡±) was developed to visualize the data and reduce system noise. Fresh DNA preparations were more likely to yield eligible samples ( p < 0.001). Eligible samples had higher rates of successfully genotyped SNPs ( p < 0.001) and lower variance of signal intensities ( p < 0.001), yielded fewer CNV findings after Birdview analysis ( p < 0.001), and showed a tendency to yield fewer PennCNV calls ( p = 0.053). The noise-free-cnv software visualized trend patterns of noise in the signal intensities across the ordered SNPs, including a wave pattern of noise, being co-linear with the banding pattern of metaphase chromosomes, as well as system deviations of individual probe sets (per-SNP noise). Wave noise and per-SNP noise occurred independently and could be separately removed from the samples. We recommend a two-step procedure of CNV validation, including noise reduction and visual inspection of all CNV calls, prior to molecular validation of a selected number of putative CNVs.
%K copy number variation (CNV)
%K variance
%K wave noise
%K per-SNP noise
%K noise-free-cnv software
%K noise reduction
%K validation of CNV findings
%U http://www.mdpi.com/2076-3905/2/4/284