prediction of a deletion copy number variant by a dense snp panel预测删除拷贝数变异的一个密集的snp面板.pdfVIP

Kadri et al. Genetics Selection Evolution 2012, 44:7 Ge n e t i c s /content/44/1/7 Se l e c t i o n Evolution RESEARCH Open Access Prediction of a deletion copy number variant by a dense SNP panel 1 2 1* Naveen K Kadri , Patrick D Koks and Theo H E Meuwissen Abstract Background: A newly recognized type of genetic variation, Copy Number Variation (CNV), is detected in mammalian genomes, e.g. the cattle genome. This form of variation can potentially cause phenotypic variation. Our objective was to determine whether dense SNP (single nucleotide polymorphisms) panels can capture the genetic variation due to a simple bi-allelic CNV, with the prospect of including the effect of such structural variations into genomic predictions. Methods: A deletion type CNV on bovine chromosome 6 was predicted from its neighboring SNP with a multiple regression model. Our dataset consisted of CNV genotypes of 1,682 cows, along with 100 surrounding SNP genotypes. A prediction model was fitted considering 10 to 100 surrounding SNP and the accuracy obtained directly from the model was confirmed by cross-validation. Results and conclusions: The accuracy of prediction increased with an increasing number of SNP in the model and the predicted accuracies were similar to those obtained by cross-validation. A substantial increase in accuracy was observed when the number of SNP increased from 10 to 50 but thereafter the increase was smaller, reaching the highest accuracy (0.94) with 10