It is likely, therefore, that CNVs do significantly affect human phenotypes, and this is reflected by an increasing number of associations reported between CNVs and disease (Tables 1, 2). Several autoimmune disorders have been associated with CNVs, including systemic lupus erythematosus (Fanciulli et al. 2007 ), Crohn's disease (Fellermann et al. 2006; McCarroll et al. 2008 ) and psoriasis (Hollox et al. 2008) , and a range of other diseases have now been associated with CNVs (reviewed in Zhang et al. 2009 ). It has been postulated that CNVs could account for a large proportion of the missing heritability of common diseases that has emerged after the recent plethora of genome-wide Diskin et al. (2009) association studies (GWAS) (reviewed in Manolio et al. 2009 ), but this is the subject of heated controversy. In a recent large-scale genotyping survey of common CNVs, Conrad et al. (2010) found that the CNVs that they were able to genotype easily were only in linkage disequilibrium with 34 out of 1,554 trait-associated SNPs from GWAS, thus they suggest that common CNVs are unlikely to account for much of the missing heritability. There is, however, a particular challenge in analysis of amplified sequences (which may be remote from the original sequence copy (Conrad et al. 2010) ), multi-allelic variants (particularly VNTRs) and recurrent events, so further analysis of those CNV types is required before the full contribution of common CNVs to human disease can be assessed.