Research Article

Frontiers of Mathematics in China

, Volume 6, Issue 6, pp 1203-1216

First online:

A study of biases of DNA copy number estimation based on PICR model

  • Quan WangAffiliated withCenter for Theoretical Biology, Peking University
  • , Jianghan QuAffiliated withYuanpei College, Peking University
  • , Xiaoxing ChengAffiliated withSchool of Mathematical Sciences, Peking University
  • , Yongjian KangAffiliated withYuanpei College, Peking University
  • , Lin WanAffiliated withCenter for Theoretical Biology, Peking UniversitySchool of Mathematical Sciences, Peking UniversityMolecular and Computational Biology, University of Southern California
  • , Minping QianAffiliated withCenter for Theoretical Biology, Peking UniversitySchool of Mathematical Sciences, Peking University
  • , Minghua DengAffiliated withCenter for Theoretical Biology, Peking UniversitySchool of Mathematical Sciences, Peking UniversityCenter for Statistical Sciences, Peking University Email author 

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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.

Keywords

single-nucleotide polymorphism (SNP) array copy number variation (CNV) cross-hybridization

MSC

62P10 68U01 92D20