Table 4.
Evaluation of various genotyping platforms for molecular form diagnostic SNPs. The number of mismatches are calculated based on conventional DNA sequencing results for amplimers of the 28S IGS 540 and 649 SNPs, SINEX and the 2L and 3L SNPs described by White et al. (2010). All 79 individual samples were sequenced for each amplimer except SINEX (Santolamazza et al. 2008) method.
| Chromosome | X | 2L | 3L | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Marker sequence | 28S IGS-540 | SINEX | 28S IGS-649 | 04679-157 | 10313-052 | |||||
| Method | iPLEX | Favia PCR |
Fanello RFLP |
SINEX PCR |
iPLEX | White RFLP |
iPLEX | White RFLP |
iPLEX | White RFLP |
| failed amplification | 0 | 1 | 6 | 1 | 0 | 1 | 0 | 3 | 0 | 6 |
| DNA sequence mismatch |
3 | 15 | 20 | 12* | 4 | 9 | 2 | 12 | 4 | 19 |
| mismatch % | 3.8 | 19.0 | 25.3 | 13.9* | 5.1 | 11.4 | 2.5 | 15.2 | 5.1 | 24.1 |
*
SINEX PCR results were compared with molecular form diagnostic locus on 28S IGS for reasons provided in the Method - Comparison of molecular form diagnostic methods section. The percentage of mismatch on SINEX PCR was based on the comparison with consensus molecular form data.