Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

ABSTRACT:

Background

The recent discovery of widespread copy number variation in humans has forced a shift away from the assumption of two copies per locus per cell throughout the autosomal genome. In particular, a SNP site can no longer always be accurately assigned one of three genotypes in an individual. In the presence of copy number variability, the individual may theoretically harbor any number of copies of each of the two SNP alleles.

Results

To address this issue, we have developed a method to infer a "generalized genotype" from raw SNP microarray data. Here we apply our approach to data from 48 individuals and uncover thousands of aberrant SNPs, most in regions that were previously unreported as copy number variants. We show that our allele-specific copy numbers follow Mendel

SUBMITTER: Macconaill LE 

PROVIDER: S-EPMC1934372 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature