| Genotyping methods to detect known SNP |
Instrument mean costs§ |
Approximate reagent costs per SNP$ |
Approxim time-labour per SNP# |
| D-HPLC |
++++ |
moderate |
very fast |
| SSCP |
+ |
Low |
very laborious |
| Allele Specific Amplification (ASA) |
+ |
very low |
moderate |
| Restriction Fragment Length Polymorphism (RFLP) |
+ |
very low |
very laborious |
| FRET probe Allelic Discrimination (Hyb Probe®TaqMan®, Beacons® Scorpions®) |
++ |
moderate |
moderate |
| Locked Nucleic Acid (LNA) probe |
++ |
moderate |
moderate |
| Oligo ligation assay (SNPlex®) |
+++ |
high |
Fast |
| PCR-Invader®Assay |
+++ |
high |
Fast |
| High resolution melting (HRM) |
++ |
low |
moderate |
| Pyrosequencing* |
+++ |
high |
Fast |
| Peptide nucleic acid-mediated Clamping PCR* |
+ |
moderate |
moderate |
| Gene Chip technology (LabOnChip)* |
+++/++++ |
very high |
moderate |
| Maldi-TOF |
++++ |
very high |
moderate |
| Conventional sequencing* |
++ |
low |
moderate |
§Approximate instrumentation list price were scored as + (<10000€); ++ (<50000€); +++ (<100000€), ++++ (>100000€).
$Reagent costs were scored as very low (<5€), low (<10€), moderate (<30€), high (<50€), very high (>50€).
#Time-labour refers input needed to perform a single test of multiple samples. It were scored as very fast (<1 hour), fast (<4 hours), moderate (<1 day), laborious (<2 day) very laborious (>2 working day).
*No address to allelic discrimination (mutant vs. wild type). |
