Table 1.
Summary of the 10 human TPH1 SNPs genotyped in this studya
| SNP name (Genomic localization)b | Position in the gene | SNP IDc | PCR primers and short-extension probee |
| 5'flankingSNP1 (T-1721G) | 5' flanking region | SNP000574351 | F: 5'-ctgttcttttggtgtcctc-3' R:5'-gctcctggcacttaacata-3' P: 5'-taatttctttcatgagtattttatagtt |
| 5'flankingSNP2 (A-1067G) | 5' flanking region | SNP000574353 | F: 5'-ctgttcttttggtgtcctc-3' R: 5'-gctcctggcacttaacata-3' P: 5'-ttttttgctgagtatggatgtactttaaagctcagga |
| 5'flankingSNP3 (G-347T) | 5' flanking region | SNP000574354 | F: 5'-cgataataggcgttatcttg-3' R: 5'-ctcaatctctgcgtgtatct-3' P: 5'-tcaggactgggctattaaatagcccagaagcacagaga |
| in1SNP1 (T3804A) | Intron 1 (exon 1c) | rs623580 | F: 5'-taattatcctccctccaagt-3' R: 5'-cttacccattcaattaccac-3' P: 5'-agagtatgggcgacgttgtccta |
| in2SNP1 (G7465A) | Intron 2 | rs684302 | F: 5'-tgctcttatatgtcttttcaagt-3' R: 5'-gagagatggagcaaaacac-3' P: 5'-ttaaataaaatacctgtatgtcttcttccatca |
| in3SNP1 (A12517C) | Intron 3 | rs211105 | F: 5'-tcaggaaaacagaagggta-3' R: 5'-ggtaaattgccctatttctaa-3' P: 5'-aggtggcaaagacaaatgatttctaagatcttttccatcggc |
| in6SNP1 (C18626G) | Intron 6 | rs2237907 | F: 5'-gggaagaaattatgtaagtgg-3' R: 5'-gaaatgttccatatctgtgc-3' P: 5'-ttgtaatgcacacaaaactgaaagctgatctcttagggtctggagc |
| in7SNP1 (A20004C)d | Intron 7 | rs1800532 | CF: 5'-acccacctacactttcctc-3' CR: 5'-taattgacaacctattaggttc-3' AR: 5'-agcacatgtgaagcatttag-3' AF: 5'-cctatgctcagaatagcagctct-3' |
| 3'UTRSNP1 (C27224T) | 3' UTR | rs2108977 | F: 5'-cacttgaatatcacagtccatc-3' R: 5'-gcttacagtagatttccttgc-3' P: 5'-tacatttgatggtaaatagatgctagctaatct |
| 3'UTRSNP2 (A27237G) | 3' UTR | New | F: 5'-cacttgaatatcacagtccatc-3' R: 5'-gcttacagtagatttccttgc-3' P: 5'-aactataaatcagataatcaata |
a. in7SNP1 was genotyped using ARMS, while the other SNPs were genotyped using MSBE.
b. Genomic localizations of SNPs are given in bp relative to the transcription start site (position 0).
c. The ID for 5'flankingSNP1, 5'flankingSNP2, and 5'flankingSNP3 are from HGVbase http://hgvbase.cgb.ki.se/. The ID for in1SNP1, in2SNP1, in3SNP1, in6SNP1, in7SNP1, 3'UTRSNP1, and 3'UTRSNP2 are from dbSNP http://www.ncbi.nlm.nih.gov/SNP/.
d. The A20004C is known as intron7 A218C polymorphism.
e. All PCR reactions were performed at the same annealing temperature (53°C). F: forward primer, R: reverse primer, P: short extension probe.