The use of long PCR to confirm three common alleles at the CYP2A6 locus and the relationship between genotype and smoking habit

Long PCR followed by nested PCR has previously been used to determine CYP2A6 160H alleles, but the method proved unreliable. We have optimized this approach in a DNA bank of 1032 subjects (age range 59–74 years) to give reliable results, yielding indirect molecular evidence and very strong statistical evidence of hitherto unrecognized common alleles (designated O) recalcitrant to the long PCR. Coding three alleles (160L, 160H and O) and an approach to association analysis originally developed to deal with null alleles implicit in ABO blood group phenotyping, the contribution of 160H (functionally null) to reduced smoking habit has been clearly measured for the first time, unconfounded by alleles null to the long PCR. The most significant findings (p < 0.01) are that the possession of a 160H allele, compared with not possessing a 160H allele, is associated with a mean age of starting regular smoking 3 years later (95% CI±1.93 years, average start age 20–21 years rather than 17–18 years); and that the average likelihood of quitting smoking at any time is 1.75 fold (95% CI. 1.17–2.61) for those possessing an 160H allele compared with those who have no 160H allele. This suggests that a smoking subject with a genotype predicted to confer 50% of the ability to eliminate nicotine via the CYP2A6 pathway has almost twice the likelihood of quitting smoking.