Identification of 96 single nucleotide polymorphisms in eight genes involved in iron metabolism: efficiency of bioinformatic extraction compared witha systematic sequencing approach

Single nucleotide polymorphisms (SNPs) can significantly contribute to the characterization of the genes predisposing to iron overloads or deficiencie s. We report an SNP survey of coding and non-coding regions of eight genes involved in iron metabolism, by two successive methods. First, we made use of the public domain sequence data, by using assembled expressed sequence t ags, non-redundant sequences, and SNP database screening. We extracted 77 p otential SNPs of which only 31 could be further validated by sequencing DNA from 44 unrelated multi-ethnic individuals. Our results indicate that a bi oinformatic approach may be effective only in those cases where candidate S NPs are extracted from two different data sources or in cases of experiment ally confirmed SNPs. Second, additional systematic sequencing of DNA from 2 4 unrelated Breton subjects increased the number of SNPs over a total lengt h of 86 kb to 96. The average distance between the SNPs and minor allele fr equencies were higher than reported by others authors; this discrepancy may reflect the nature of the genes studied and the ethnic homogeneity of our test population.