A comparison of mutation detection techniques for Usher syndrome
| Advantages | Disadvantages | |
|---|---|---|
| APEX | Robust | Detects 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 throughput | Requires specialised expertise | |
| Not highly dependent on DNA quality | Sequence confirmation required | |
| Sequence analysis | Robust | High costs (>€1000 for MYO7A or USH2A) |
| Versatile | ||
| Easy set-up | ||
| Capillary-based heteroduplex | Robust | Polymorphic sequences difficult to analyse |
| analysis | Medium throughput | Sequence analysis necessary for mutation identification |
| Relatively cheap | ||
| Resequencing (Affymetrix) | Fully automated | High costs (∼€600) |
| Detects known and new nucleotide substitutions | No detection of heterozygous deletions >1 nt and all duplications/insertions (47/292 (16%) pathologic USH variants) | |
| Addition of tested genes requires new chip design |