Table 1. Genotyping of MYOC microsatellites and single nucleotide polymorphisms.
|
Marker |
Marker type/assay method |
Primer/probe/assay ID |
5'-3' Sequence/allele (probe signal) |
| NGA17 |
MS/Fragment analysis |
Myocpm-F |
FLU-GGCTGTTATTTTTCTCTGT |
| Myocpm-R |
TGCCAGCAAGATTCTTAGAA |
||
| NGA19 |
MS/Fragment analysis |
Myoc3pm-F |
FLU-GTTGGGAGATGTGATTGCAG |
| Myoc3pm-R |
AGATGGAGGTGGGAAAGTGT |
||
| rs7523603 |
SNP/TaqMan Assay-by-Design |
Myocil-F |
CGGACCCAGAGCGAAGTT |
| Myocil-R |
AGGGCTGTGGAAAGGTTATGG |
||
| A allele-specific probe |
VIC-CTGTGAGGTCAC[A]GAAG-MGB |
||
| G allele-specific probe |
FAM-TGTGAGGTCAC[G]GAAG-MGB |
||
| rs2075537 |
SNP/TaqMan Assay-on-Demand |
C_27532255_10 |
T (VIC) and G (FAM) |
| rs235920 |
SNP/TaqMan Assay-on-Demand |
C_558534_10 |
T (VIC) and C (FAM) |
| rs2421853 |
SNP/TaqMan Assay-on-Demand |
C_11335131_10 |
A (VIC) and G (FAM) |
| rs235858 | SNP/TaqMan Assay-on-Demand | C_2964922_10 | A (VIC) and G (FAM) |
Forward primers that amplified microsatellites (MS) were labeled with fluorescein (FLU). Four single nucleotide polymorphisms (SNPs) were genotyped by assay-on-demand TaqMan. Only assay identifications and allele-specific probe signals were provided by the manufacturer. All allele-specific probes were labeled with a reporter dye (either VIC or FAM) at the 5' end, and a quencher and a minor groove-binder (MGB) at the 3' end. Bases in square brackets indicate the positions of the bases defining the alleles of the SNPs that were to be detected by the probes.