A study of biases of DNA copy number estimation based on PICR model
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Affymetrix single-nucleotide polymorphism (SNP) arrays have been widely used for SNP genotype calling and copy number variation (CNV) studies, both of which are dependent on accurate DNA copy number estimation significantly. However, the methods for copy number estimation may suffer from kinds of difficulties: probe dependent binding affinity, crosshybridization of probes, and the whole genome amplification (WGA) of DNA sequences. The probe intensity composite representation (PICR) model, one former established approach, can cope with most complexities and achieve high accuracy in SNP genotyping. Nevertheless, the copy numbers estimated by PICR model still show array and site dependent biases for CNV studies. In this paper, we propose a procedure to adjust the biases and then make CNV inference based on both PICR model and our method. The comparison indicates that our correction of copy numbers is necessary for CNV studies.
Keywordssingle-nucleotide polymorphism (SNP) array copy number variation (CNV) cross-hybridization
MSC62P10 68U01 92D20
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- 17.Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A, Kurokawa M, Chiba S, Bailey D K, Kennedy G C, et al. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res, 2005, 65(14): 6071–6079CrossRefGoogle Scholar
- 27.Wan L, Xiao Y, Chen Q, Deng M, Qian M. The analysis of biases of copy numbers from Affymetrix SNP arrays. Communications in Information and Systems, 2010, 10(2): 81–96Google Scholar