Table 1.
Sequence-specific primers PCR primers used for genotyping human genomic DNA samples
| SNP | Reaction | Gene region | ARMS primer sequence (forward and reverse) | Control primer conc to use (μM) | Annealing temperature (°C) | Elongation time (min) |
|---|---|---|---|---|---|---|
| rs1983526 G>C |
NKG2A V1 | 5' UTR (C) | GATCCTTTTACTAGGGCTTCTAGCAGAC AATCTCCACTCAAACTCCTCTCAACTGT |
1.25 short | 58 | 1 |
| NKG2A V2 | 5' UTR (G) | GATCCTTTTACTAGGGCTTCTAGCAGAG AATCTCCACTCAAACTCCTCTCAACTGT |
1.25 short | 58 | 1 | |
| rs7301582 C>T |
NKG2A V3 | Intron 5 (C) | TCAAAAGTACATTAGCAGTATATGAATTTTAAACC CTTGTCATCAACTATAAGTAAAATCACTATGCTT |
0.625 short | 58 | 1 |
| NKG2A V4 | Intron 5 (T) | TCAAAAGTACATTAGCAGTATATGAATTTTAAATT CTTGTCATCAACTATAAGTAAAATCACTATGCTT |
0.625 short | 55 | 1 | |
| rs2734440 C>T |
NKG2A V5 | Intron 4 (C) | GTTCACATATTTGCAAACATATAAACCTATTC CTACATTAATACAGAGGCACAACAATTCTTC |
1.25 long | 58 | 1 |
| NKG2A V6 | Intron 4 (T) | GTTCACATATTTGCAAACATATAAACCTATTT CTACATTAATACAGAGGCACAACAATTCTTC |
1.25 long | 58 | 1 | |
| rs2734414 A>T |
NKG2A V7 | 3' UTR (A) | GACACAAAGTAACGTTCTATCAGTTAAA GTGCATCAGATAAATTGTATATTTCTTAAAATAGAAATATAT |
1.25 long | 58 | 1 |
| NKG2A V8 | 3' UTR (T) | GACACAAAGTAACGTTCTATCAGTTAAT GTGCATCAGATAAATTGTATATTTCTTAAAATAGAAATATAT |
1.25 long | 58 | 1 | |
| rs3216778 AAGTTT> AAGTTTAAGTTT |
NKG2A V9 | Intron 3 | GTAACGATAGTTGTTATTCCCTGTAAGTC AAATTTGCATCTAAATCAATCATAATAATTTTAA |
0.833 long | 55 | 1 |
| NKG2A V10 | Intron 3 | GTAACGATAGTTGTTATTCCCTGTAAGTC AAATTTGCATCTAAATCAATCATAATAATTTTTT |
0.833 long | 55 | 1 | |
| rs1967432 T>C |
NKG2A V11 | Intron 1 (T) | CAGAGCCCATTGACTAAATGATTTAATTAGA TGGTCTTTTCTTAATGGCTGAAATGTTCT |
1.25 long | 55 | 1 |
| NKG2A V12 | Intron 1 (C) | CAGAGCCCATTGACTAAATGATTTAATTAAG TGGTCTTTTCTTAATGGCTGAAATGTTCT |
0.833 long | 55 | 1 | |
| rs1141715 A>G |
NKG2C V1 | Exon 3 (G) | CTATTACAGTCCTGGAGCAGAACAATCC ATCCACTCCTCAGGACAATGGCCACAGT |
0.72 short | 58 | 1 |
| NKG2C V2 | Exon 3 (A) | CTATTACAGTCCTGGAGCAGAACAATAT ATCCACTCCTCAGGACAATGGCCACATT |
0.72 short | 58 | 1 | |
| rs28403159 T>C |
NKG2C V3 | Exon 1 (C) | GTATTTCTAAATACAGTATTTTGATTGTTGAC CTCACTTCTGAGAAGGTTCCTCTTTGTTTTC |
0.833 long | 50 | 1 |
| NKG2C V4 | Exon 1 (T) | GTATTTCTAAATACAGTATTTTGATTGTTGAC CTCACTTCTGAGAAGGTTCCTCTTTGTTTTT |
0.833 long | 50 | 1 | |
| N/A | NKG2C Neg | GTAGGATATACTTCGGATTTCTATTTGATGC GCTAAAATTAAATACAAGTGATGTATAAGAAAAAG |
1.25 long | 58 | 1 | |
| rs2246809 A>G |
NKG2D V1 | 5' UTR (A) | GCCTGTTTAAATTTATTAATGCACAGGAGATTCT GCAATACAACAAACAGAAATCTGAGTAACCTC |
5 long | 58 | 1 |
| NKG2D V2 | 5' UTR (G) | GCCTGTTTAAATTTATTAATGCACAGGAGATTCC GCAATACAACAAACAGAAATCTGAGTAACCTC |
5 long | 58 | 1 | |
| rs11053781 C>T |
NKG2D V3 | Intron 2 (C) | CATAAAATCTTTGCCTAGACTAATGTCCGG ATCACGTTACCTGACTTCAATATATACGA |
1.25 long | 57 | 1 |
| NKG2D V4 | Intron 2 (T) | CATAAAATCTTTGCCTAGACTAATGTCCAA ATCACGTTACCTGACTTCAATATATACGA |
1.25 long | 57 | 1 | |
| rs1049174 G>C |
NKG2D V5 | 3' UTR (G) | AGTGAAGGAAGAGAAGGCCAGCAGATCTC ACAAGTACAAATCATAGCAAAGGAAACGTCCTAAGATC |
2.5 long | 60 | 1 |
| NKG2D V6 | 3' UTR (C) | AGTGAAGGAAGAGAAGGCCAGCAGATCCG ACAAGTACAAATCATAGCAAAGGAAACGTCCTAAGATC |
2.5 long | 60 | 1 | |
| rs2302489 A>T |
CD94 V1 | Exon 1 (A) | GAACATCATTTAAATACACAATTTTTCATTCTCAA CAATGAAGAATCAGGAAAATATAATGAATGTGG |
1.25 long | 56 | 1 |
| CD94 V2 | Exon 1 (T) | GAACATCATTTAAATACACAATTTTTCATTCTCCT CAATGAAGAATCAGGAAAATATAATGAATGTGG |
2.5 long | 56 | 1 | |
| rs3759272 G>T |
CD94 V3 | 5' UTR (G) | ATTACCTGACTTTAGGGCTGAGACTGCAG TTCCATGTACTGTATCTCTCCCACTCAT |
2.5 long | 56 | 1 |
| CD94 V4 | 5' UTR (T) | ATTACCTGACTTTAGGGCTGAGACTGCAT TTCCATGTACTGTATCTCTCCCACTCAT |
5 long | 56 | 1 | |
| rs1264457 G>A |
HLA-E 01:01 | Exon 2 (A) | ATGCATGGCTGCGAGCTGGGGCCCGATA GCATGTGTCTTCCAGGTAGGCTCTCTCG |
10 long | 63 | 1 |
| HLA-E 01:03 | Exon 2 (G) | ATGCATGGCTGCGAGCTGGGGCCCGATG GCATGTGTCTTCCAGGTAGGCTCTCTCG |
10 long | 63 | 1 | |
| rs17408553 G>T |
HLA-C1 | Exon 2 (G) | TTGGGAGGGAAACGGCCTCTGCGAA TTGGGAGGGAAACGGCCTCTGGGAA GCTCTGGTTGTAGTAGCCGCGCATG |
10 long | 63 | 1 |
| HLA-C2 | Exon 2 (T) | TTGGGAGGGAAACGGCCTCTGCGAA TTGGGAGGGAAACGGCCTCTGGGAA GCTCTGGTTGTAGTAGCCGCGCAAT |
10 long | 63 | 1 | |
| N/A | Long control | CCAAGCCCAACCTTAAGAAGAAAATTGGAG CCAAACCCACGGTACGCATGGGAACACTGC |
- | |||
| N/A | Short control | CCCACCTTCCCCTCTCTCCAGGCAAATGGG GGGCCTCAGTCCCAACATGGCTAAGAGGTG |
- |
Each is listed with the SNP, its associated reaction name or variant (referred to throughout this study), targeted gene region, primer sequences, control primer concentration, annealing temperature, and elongation time.
ARMS, amplification-refractory mutation system; conc, concentration.