Methods for SNP Analysis
| Method | Allele discrimination by | Format | Instrumentation | References |
| MASDA | ASO | format 1 array + gel | none | Shuber et al. (1997) |
| Whitehead– Affymetrix SNP microarray | ASO | format 2 array | array scanner | D.G. Wang et al. (pers. comm.) |
| TaqMan | ASO | homogeneous closed tube[i] | TaqMan instrument | Livak et al. (1995) |
| Molecular beacons | ASO | homogeneous closed tube[i] | TaqMan instrument | Tyagi et al. (1998) |
| MADGE | Restriction cleavage | gel | none | Day and Humphries (1994) |
| Allele-specific PCR | 3′ matched/mismatched primer | gel | none | Liu et al. (1997) |
| OLA | ligation | solid-phase microtiter readout | fluorospectrophotometer | Samiotaki et al. (1994); Tobe et al. (1996) |
| OLA multiplex gel | ligation | gel | automated sequencer | Grossman et al. (1994); Day et al. (1995) |
| DOL | ligation | homogeneous closed tube[i] | TaqMan instrument | Chen et al. (1998) |
| Solid-phase minisequencing | nucleotide incorporation | solid-phase microtiter readout | scinitillation counter | Syvänen et al. (1993) |
| Minisequencing on array | nucleotide incorporation | format 2 array | PhosphorImager | Shumaker et al. (1996); Pastinen et al. (1997) |
| Minisequencing multiplex gel | nucleotide incorporation | solid phase + gel | automated sequencer | Pastinen et al. (1996) |
| Minisequencing with FRET | nucleotide incorporation | homogeneous reagent addition[ii] | TaqMan instrument | Chen et al. (1997) |
| Pyrominisequencing | nucleotide incorporation | homogenous reagent addition[ii] | luminometer | P. Nyrén and M. Ronaghi (pers. comm.) |
[i] Reagents for amplification and allele distinction are mixed together at the start, and results are recorded without opening the reaction vessel.
[ii] After amplification, detection reagents are added to the reaction vessel, but no separations are required before recording the results.