Approaches to assess copy number variation have advanced rapidly and are being incorporated into genetic studies. While the technology exists for CNV genotyping, a further understanding and discussion of how to use the CNV data for association analyses is warranted. We present the options available for processing and analysing CNV data. We break these steps down into choice of genotyping platform, normalisation of the array data, calling algorithm, and statistical analysis.
Keywords: CBS; DNA; GWAS; array CGH; calling algorithm; circular binary segmentation; complex disorders; copy number; genome-wide association study; hidden Markov model; microarray; normalization; whole genome amplification.