Table 2.
Polymorphisms evaluated in this study and their primers for genotyping
| GENE | Polymorphism | Type of change | Location | MAF* | dbSNP ID | PCR & Pyrosequencing Primers |
|---|---|---|---|---|---|---|
| CDKN2A | C to G | NA | C540G, 3’UTR | 0.14 | rsll515 | F Bio 5’7GTGCCACACATCTTTGACCTCAG3’ |
| R 5’TACGAAAGCGGGGTGGGT3’ | ||||||
| S 5’GACTGATGATCTAAGTTTCC3’ | ||||||
| C to T | NA | C580T, 3’UTR | 0.12 | rs3088440 | Same F & R as above | |
| S 5’TGTGGCGGGGGCAGT3’ | ||||||
| CDKN2B | C to A | NA | Intron 1 | 0.10 | rs2069426 | F Bio 5’7CCTCTGCACTGGGTGAAAACTT3’ |
| R 5’ATCATGACCTGCCAGAGAGAGC3’ | ||||||
| S 5’GAGAGCAGAGTGGTCAG3’ | ||||||
| TP53 | G to C | Arg to Pro | Codon 72 | 0.25 | rs1042522 | F Bio 5’7AGACCCAGGTCCAGATGAAGC3’ |
| R 5’CCGGTGTAGGAGCTGCTGG3’ | ||||||
| S 5’GGTGCAGGGGCCACG3’ | ||||||
| CCNDl | G to A | Pro to Pro, alternate | Codon 242 | 0.40 | rs603965 | F Bio 5’7TCCTACTACCGCCTGACACGC3’ |
| splicing | R 5’GCACTAGGTGTCTCCCCCTGTAA3’ | |||||
| S 5’GCACATCACCCTCACTTA3’ | ||||||
| AURKA | T to A | Phe to lie | Codon 31 | 0.21 | rs2273535 | F 5’CCATTCTAGGCTACAGCTCCA3’ |
| R Bio 5’7 ATTCTGAACCGGCTTGTGAC3’ | ||||||
| S 5’TCTCGTGACTCAGCAA3’ | ||||||
| MDM2 | T to G | NA | Promoter SNP309 | 0.38 | rs2279744 | F 5’GGGGTGGTTCGGAGGTCT3’ |
| R Bio 5’7GTGACCCGACAGGCACCT3’ | ||||||
| S 5’GGGCTGCGGGGCCGCT3’ | ||||||
| E2F2 | G to T | Gln to His | Codon 226 | 0.45 | rs2075995 | F Bio 5’7AGGAGCTGATGAACACGGAG3’ |
| R 5’ACTTGTCCTCAGTCAGGTGCTTGA3’ | ||||||
| S 5’AGCAGCTCTGGATGAG3’ | ||||||
| TP73 | G to A | NA | 5’UTR Ex2+4 | 0.21 | rs2273953 | F 5’AGTTCCCAGGGTGCTCAGGT3’ |
| R Bio 5’7GGTGGACTGGGCCATCTTC3’ | ||||||
| S 5’CCTTCCTTCCTGCAGA3’ | ||||||
| IGFl | CA repeat | NA | 5’UTR | † | F 5’6 -GCTAGCCAGCTGGTGTTATT−3’ | |
| R 5’ACCACTCTGGGAGAAGGGTA−3’ |
*
MAP = minor allele frequency.
†
No dbSNP ID for the IGFl polymorphism because it is composed of CA repeats, not single nucleotide polymorphism.
F = Forward, R = Reverse, S = Sequencing Primer, Bio = Biotinylated