Table 2 PCR primer sequences and allele specific probe sequences used to genotype the five haplotypes tagging SNPs
Single nucleotide polymorphism | Primer/Probe sequence |
|---|---|
Primers used for PCR | |
SNP1, F1 | 5'-AGCATAGCCGGGTCCAATAA-3' |
SNP1, R1 | 5'-CCCGGCTTGTATTGGGTAAG-3' |
SNP2, F2 | 5'-CAGAAGAGTATTTAGAAGGGCTGCTT-3' |
SNP2, R2 | 5'-AGGTCACAGATGACAAACATCAAAA-3' |
SNP3, F5 | 5'-GGAAGACTTTATTTTTTTTCTTACCAGGTA-3' |
SNP3, R5 | 5'-AGCAGTGCTCTTCACATCAGTGA-3' |
SNP4, F3 | 5'-GGAGGACACTCAAAACAGCATTAAA-3' |
SNP4, R3 | 5'-TTAGCAGATTTAGTTTCAGGACACGTA-3' |
SNP5, F4 | 5'-CCAGAGCAGTTAGCTGTTCTGAACT-3' |
SNP5, R4 | 5'-GAGCAAGTAGCTTTAGGTCGTAAATTTT-3' |
FAM-labeled allele-specific probes | |
SNP1 | CCTCCATCCCGCG |
SNP2 | TGTCAGCGTATTAAA |
SNP3 | TTCCTGATGAGATACAC |
SNP4 | AATAGAGAGATTTTGGTTCT |
SNP5 | CATGATGAATTTCTG |
VIC-labeled allele-specific probes | |
SNP1 | CCCTCCTTCCCGC |
SNP2 | TGTCAGAGTATTAAAAAT |
SNP3 | TTCCTGACGAGATACA |
SNP4 | AATAGAGCGATTTTGG |
SNP5 | CATGAGGAATTTC |