Title |
Hybridization and amplification rate correction for affymetrix SNP arrays
|
---|---|
Published in |
BMC Medical Genomics, June 2012
|
DOI | 10.1186/1755-8794-5-24 |
Pubmed ID | |
Authors |
Quan Wang, Peichao Peng, Minping Qian, Lin Wan, Minghua Deng |
Abstract |
Copy number variation (CNV) is essential to understand the pathology of many complex diseases at the DNA level. Affymetrix SNP arrays, which are widely used for CNV studies, significantly depend on accurate copy number (CN) estimation. Nevertheless, CN estimation may be biased by several factors, including cross-hybridization and training sample batch, as well as genomic waves of intensities induced by sequence-dependent hybridization rate and amplification efficiency. Since many available algorithms only address one or two of the three factors, a high false discovery rate (FDR) often results when identifying CNV. Therefore, we have developed a new CNV detection pipeline which is based on hybridization and amplification rate correction (CNVhac). |
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