Table 1.
Information on the polymorphisms under investigation
| Gene | GeneID | Chromosome | Polymorphism | Amino Acid Change | Reference SNP ID | Genotyping assay |
|---|---|---|---|---|---|---|
| GSTM1 | 2944 | 1p13.3 | Deletion | Multiplex PCRa | ||
| GSTT1 | 2952 | 22q11.23 | Deletion | Multiplex PCRa | ||
| GSTP1 | 2950 | 11q13.2 | Exon 5–24 A>G | Codon 105 Ile (I) → Val(V) | 947894 | MassCodeb |
| GSTP1 | 2950 | 11q13.2 | Exon 6+5 C>T | Codon 114 Ala (A) → Val (V) | 1799811 | MassCodeb |
| MGMT | 4255 | 10q26 | Exon 2–25 C>T | Codon 84 Leu (L) → Phe (F) | 12917 | MassCodeb |
| MGMT | 4255 | 10q26 | Exon 5+13 A>G | Codon 143 Ile (I) → Val (V) | 2308321 | PCR-SSCPa |
| XPD | 2608 | 19q13.3 | Exon10–16 G>A | Codon 312 Asp (D) → Asn (N) | 1799793 | MassCodeb |
| XPD | 2608 | 19q13.3 | Exon23+61 A>C | Codon 751 Lys (K) → Gln (Q) | 13181 | PCR-RFLPa |
| XRCC3 | 7517 | 14q32.3 | Exon 8–53 C>T | Codon 241 Thr (T) → Met (M) | 861539 | MassCodeb |
From the SNP500Cancer database of the U.S. National Cancer Institute. PCR, polymerase chain reaction; SSCP, single-strand conformation polymorphism; RFLP, restriction fragment length polymorphism. GST, glutathione-S-transferase; MGMT, O6-methylguanine-DNA-methyltransferase; XPD, xeroderma pigmentosum group D; XRCC3, X-ray repair cross-complementing group 3.
a
Methods are described in reference 12 (for the GSTM1 and GSTT1 polymorphisms), reference 13 (for the MGMT I143V polymorphism) and reference 14 (for the XPD K751Q polymorphism).
b
Masscode™ technology (BioServe Biotechnologies, Ltd., Laurel, MD).