Characteristics of the PCR primers and ASO probes used to genotype the selected pSNPs
| Gene (chromosome), DNA variant . | SNP ID . | PCR primers . | Product size, bp . | Alleles (ASO probe) . | Washing temperature, °C . | |
|---|---|---|---|---|---|---|
| Forward . | Reverse . | |||||
| CDKN2A (9p21) | ||||||
| −222T>A | None | tgttaaaaagaaatccgccc | aatgtacacgrctgagaaaccc | 368 | T-222(ggcagttAggaaggt); | 45/40* |
| A-222(ggcagttTggaaggt) | ||||||
| CDKN2B (9p21) | ||||||
| −1270C>T | None | gcaacgttttccctaccc | caacagagctgaaatccacc | 428 | C-1270(tggacaggGaagggaac); | 55 |
| T-1270(tggacaggAaagggaac) | ||||||
| −593A>T,C | rs2069416 | ctgtacaaatatgatgaaactggg | ttcactgtggagacgttgg | 408 | A-593(gattcttaAagtataat); | 30 |
| T-593(gattcttaTagtataat); | ||||||
| C-593(gattcttaCagtataat) | ||||||
| −287G>C | rs2069418 | ctgtacaaatatgatgaaactggg | ttcactgtggagacgttgg | 408 | G-287(ttaagaaaCacggagtt); | 45 |
| C-287(ttaagaaaGacggagtt) | ||||||
| CDKN1A (6p21.2) | ||||||
| −1284T>C | rs733590 | ttggatgtataggagcgaagg | aaaaagggcaacctgatctc | 897 | T-1284(atcccactAaaaaacag); | 45 |
| C-1284(atcccactGaaaaacag) | ||||||
| −899T>G | rs762624 | ttggatgtataggagcgaagg | aaaaagggcaacctgatctc | 897 | T-899(ggggaaacTggggctca); | 65 |
| G-899(ggggaaacGggggctca) | ||||||
| −791T>C | rs2395655 | ttggatgtataggagcgaagg | aaaaagggcaacctgatctc | 897 | T-791(gaagaaaTccctgtg); | 40 |
| C-791(gaagaaaCccctgtg) | ||||||
| CDKN1B (12p13.1–p12) | ||||||
| −1857C>T | rs3759217 | gcattttactggaaaccaacc | tgagacctcttgcttgatcc | 663 | C-1857(ctcaagaCagctgca); | 40 |
| T-1857(ctcaagaTagctgca) | ||||||
| −1608G>A | None | gcattttactggaaaccaacc | tgagacctcttgcttgatcc | 663 | G-1680(tgtccaggGacatgcat); | 52 |
| A-1680(tgtccaggAacatgcat) | ||||||
| −373G>T | None | gacaaacaaactagccaaacg | gcagaaacttctgggttaagg | 356 | G-373(ttcccgggCgaggagc); | 60 |
| T-373(ttcccgggAgaggagc) | ||||||
| Gene (chromosome), DNA variant . | SNP ID . | PCR primers . | Product size, bp . | Alleles (ASO probe) . | Washing temperature, °C . | |
|---|---|---|---|---|---|---|
| Forward . | Reverse . | |||||
| CDKN2A (9p21) | ||||||
| −222T>A | None | tgttaaaaagaaatccgccc | aatgtacacgrctgagaaaccc | 368 | T-222(ggcagttAggaaggt); | 45/40* |
| A-222(ggcagttTggaaggt) | ||||||
| CDKN2B (9p21) | ||||||
| −1270C>T | None | gcaacgttttccctaccc | caacagagctgaaatccacc | 428 | C-1270(tggacaggGaagggaac); | 55 |
| T-1270(tggacaggAaagggaac) | ||||||
| −593A>T,C | rs2069416 | ctgtacaaatatgatgaaactggg | ttcactgtggagacgttgg | 408 | A-593(gattcttaAagtataat); | 30 |
| T-593(gattcttaTagtataat); | ||||||
| C-593(gattcttaCagtataat) | ||||||
| −287G>C | rs2069418 | ctgtacaaatatgatgaaactggg | ttcactgtggagacgttgg | 408 | G-287(ttaagaaaCacggagtt); | 45 |
| C-287(ttaagaaaGacggagtt) | ||||||
| CDKN1A (6p21.2) | ||||||
| −1284T>C | rs733590 | ttggatgtataggagcgaagg | aaaaagggcaacctgatctc | 897 | T-1284(atcccactAaaaaacag); | 45 |
| C-1284(atcccactGaaaaacag) | ||||||
| −899T>G | rs762624 | ttggatgtataggagcgaagg | aaaaagggcaacctgatctc | 897 | T-899(ggggaaacTggggctca); | 65 |
| G-899(ggggaaacGggggctca) | ||||||
| −791T>C | rs2395655 | ttggatgtataggagcgaagg | aaaaagggcaacctgatctc | 897 | T-791(gaagaaaTccctgtg); | 40 |
| C-791(gaagaaaCccctgtg) | ||||||
| CDKN1B (12p13.1–p12) | ||||||
| −1857C>T | rs3759217 | gcattttactggaaaccaacc | tgagacctcttgcttgatcc | 663 | C-1857(ctcaagaCagctgca); | 40 |
| T-1857(ctcaagaTagctgca) | ||||||
| −1608G>A | None | gcattttactggaaaccaacc | tgagacctcttgcttgatcc | 663 | G-1680(tgtccaggGacatgcat); | 52 |
| A-1680(tgtccaggAacatgcat) | ||||||
| −373G>T | None | gacaaacaaactagccaaacg | gcagaaacttctgggttaagg | 356 | G-373(ttcccgggCgaggagc); | 60 |
| T-373(ttcccgggAgaggagc) | ||||||
SNP ID indicates reference SNP identifier number from the NCBI dbSNP database.37 In the ASO probe sequences, uppercase characters indicate the polymorphic site.
45°C for the T-222 allele, 40°C for the A-222 allele.