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Case–control study in basal cell carcinoma of the skin: single nucleotide polymorphisms in three interleukin promoters pre‐analysed in pooled DNA
Author(s) -
Wilkening S.,
Hemminki K.,
Rudnai P.,
Gurzau E.,
Koppova K.,
Kumar R.,
Försti A.
Publication year - 2006
Publication title -
british journal of dermatology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.304
H-Index - 179
eISSN - 1365-2133
pISSN - 0007-0963
DOI - 10.1111/j.1365-2133.2006.07440.x
Subject(s) - single nucleotide polymorphism , genotype , biology , odds ratio , genotyping , genetics , allele , snp , polymerase chain reaction , promoter , microbiology and biotechnology , genomic dna , gene , medicine , gene expression
Summary Background Basal cell carcinoma (BCC) is one of the most common neoplasms in the world. Development of BCC is associated with environmental factors (especially sun exposure) as well as heritable factors. Objectives To analyse three single nucleotide polymorphisms (SNPs) in the promoter regions of interleukin (IL) genes in genomic DNA from 527 cases of BCC and 530 matched controls and to examine if DNA pooling is a useful method on which to base decisions regarding further SNP analysis. Methods The SNPs analysed were IL6 –597, IL10 –1082 and IL1B –511. The SNPs were first analysed from pooled DNA and afterwards from individual samples. The DNA pools resulted from a division of the samples into cases and controls, female and male, and three age groups. In these pools the allele frequencies were estimated by two methods, real‐time polymerase chain reaction with allele‐specific primers, and quantitative sequencing. Results No significant association was found when the allele frequencies in cases and controls were compared. However, by analysis of the individual genotypes we found SNP IL6 –597 G/A to be significantly associated with BCC risk ( P =0·007). Hereby the heterozygous genotype ‘GA’ had a protective effect (odds ratio 0·64, 95% confidence interval 0·49–0·84). No significant association was found for IL10 –1082 and IL1B –511. Conclusions The association of SNP IL6 –597 with BCC could be found only by individual genotyping, but would have been missed if only data from the pooling analysis had been known.