Low-density DNA microarrays are versatile tools to screen for known mutations in hypertrophic cardiomyopathy

Familial hypertrophic cardiomyopathy (HCM or CMH) is a myocardial disorder caused by mutations that affect the contractile machinery of heart muscle cells. Genetic testing of HCM patients is hampered by the fact that mutations in at least eight different genes contribute to the disease. An affordable high-throughput mutation detection method is as yet not available. Since a significant number of mutations have been repeatedly found in unrelated families, we consider it feasible to pre-screen patients for known mutations, before more laborious techniques capable of detecting new mutations are applied. Here we demonstrate that the principle of hybridization of DNA to oligonucleotide probes immobilized on chips (glass slides) can be applied for this purpose. We have developed a low-density oligonucleotide probe array capable of detecting 12 different heterozygous mutations (in four different genes), among them single- and double-base exchanges, a single nucleotide insertion, and a trinucleotide deletion. The assay is simple and may be amenable to automation. Detection is achieved with a CCD camera-based fluorescence biochip reader. The technique turned out to be robust: Variations in either the relative position of a mutation, or the amount and size of target-DNA were compatible with mutation detection. Mutations could even be detected in amplicons as long as 800 bp, allowing the screening of more than one exon in one amplicon. Our data suggest that the development of a chip that covers all or most of known HCM-associated mutations is feasible and useful.