Table 5

 A comparison of mutation detection techniques for Usher syndrome

APEXRobustDetects only known variants
Versatile (addition of new variants with little extra costs)Low efficiency in early stages
Cheap (<€200)Less efficient for analysing patients of other ethnic backgrounds
Medium throughputRequires specialised expertise
Not highly dependent on DNA qualitySequence confirmation required
Sequence analysisRobustHigh costs (>€1000 for MYO7A or USH2A)
Easy set-up
Capillary-based heteroduplexRobustPolymorphic sequences difficult to analyse
analysisMedium throughputSequence analysis necessary for mutation identification
Relatively cheap
Resequencing (Affymetrix)Fully automatedHigh costs (∼€600)
Detects known and new nucleotide substitutionsNo detection of heterozygous deletions >1 nt and all duplications/insertions (47/292 (16%) pathologic USH variants)
Addition of tested genes requires new chip design