A study of biases of DNA copy number estimation based on PICR model |
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Authors: | Quan Wang Jianghan Qu Xiaoxing Cheng Yongjian Kang Lin Wan Minping Qian Minghua Deng |
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Institution: | 1. Center for Theoretical Biology, Peking University, Beijing 100871, China; 2. Yuanpei College, Peking University, Beijing 100871, China; 3. School of Mathematical Sciences, Peking University, Beijing 100871, China; 4. Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; 5. Center for Statistical Sciences, Peking University, Beijing 100871, China |
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Abstract: | 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. |
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Keywords: | single-nucleotide polymorphism (SNP) array copy number variation (CNV) cross-hybridization |
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