Genetic diversity among human genomes comes in many forms, including single nucleotide polymorphisms (SNPs) and small insertions and deletions on the order of one to several basepairs. More recently, large, >1 kb copy number changes have been identified as an important source of normal genomic variation as well as disease-causing variation. The ability to perform genome-wide discovery of large copy number variants (CNVs) has been facilitated by advances in two technologies – array comparative genomic hybridization and SNP genotyping platforms. Here, we discuss the general principles and strategies underlying CNV detection with SNP genotyping platforms, which are widely used and capable of providing both SNP and CNV genotyping information.
