Diagnostic mutation analysis in hypertrophic cardiomyopathy by DNA resequencing array

Purpose: Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease (1/500) characterized by a remarkable clinical and genetic heterogeneity. More than 450 different pathogenic mutations in at least 20 genes have been identified so far. Genetic testing for HCM has a growing impact on the medical management of patients and their families, however routine diagnostic mutation analysis by classical methods remains very time-consuming and expensive. Methods: We have developed a 30 Kbp HCM-DNA-resequencing-array (CustomSeq Affymetrix) for all exons (n=160), splice-sites and 5'-UTR of 12 HCM genes, which we currently use for mutation analysis in clinical practice. This HCM-array is very efficient to detect single nucleotide substitutions accounting for up to 86% of all HCM mutations. Actually it does not detect small indels. Results: We analysed 115 patients from 5 different centres. Overall, we identified 30 different single nucleotide substitutions in the coding regions or splice sites of MYH7, MYBPC3, TNNT2, TNNI3, TPM1 and MYL3 in 42 patients (37%). Twelve variants were reported as known mutations and 14 were novel changes not found in a control population study (>200 chromosomes). Furthermore, we identified 4 known SNPs/variants previously reported as mutations for HCM. Conclusions: Our DNA resequencing array appears to date as the most rapid and cost-effective technology for mutation screening in HCM. Further improvement of the software may detect small insertions/deletions in the future. The HCM-array provides a first attempt of high throughput sequencing methodology which will further develop and probably become the method of choice for routine molecular diagnosis of heterogeneous disorders such as HCM.