Other challenges of CNV detection include (a) size of the CNV, with smaller CNVs (<10 kb) being harder to detect, (b) number of CNV probes in the region of the CNV, with fewer probes resulting in greater noise, (c) the general quality of the data (including artifacts in the SNP data) and genomic waves (intensity variations in normalized GWAS data), (d) ethnic variations and (e) source of the sample that was genotyped – for instance, it now well known that deletions and duplications can arise in DNA drawn from cell lines (i.e. extracting cells from a DNA source and maintaining them in laboratory cultures to enhance longevity) and, thus CNV detection using cell cultures requires caution. Yet, if attention is paid to these challenges, CNVs represent a unique route for enquiry into the genetic architecture of alcohol dependence.
