Identification of 96 single nucleotide polymorphisms in eight genes involved in iron metabolism: efficiency of bioinformatic extraction compared with a systematic sequencing approach.
Single nucleotide polymorphisms (SNPs) can significantly contribute to the characterization of the genes predisposing to iron overloads or deficiencies. 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 tags, non-redundant sequences, and SNP database screening. We extracted 77 potential SNPs of which only 31 could be further validated by sequencing DNA from 44 unrelated multi-ethnic individuals. Our results indicate that a bioinformatic approach may be effective only in those cases where candidate SNPs are extracted from two different data sources or in cases of experimentally confirmed SNPs. Second, additional systematic sequencing of DNA from 24 unrelated Breton subjects increased the number of SNPs over a total length of 86 kb to 96. The average distance between the SNPs and minor allele frequencies 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.
Douabin-Gicquel
V
V
Département de Biochimie et Biologie Moléculaire, et UMR6061 CNRS, Faculté de Médecine, 2 Avenue du Pr Léon Bernard CS34317, 35043 Rennes cédex, France.
Soriano
N
N
Ferran
H
H
Wojcik
F
F
Palierne
E
E
Tamim
S
S
Jovelin
T
T
McKie
A T
AT
Le Gall
J Y
JY
David
V
V
Mosser
J
J
D027682:Cation Transport Proteins / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D005006:Ethnicity / Q000235:genetics; D005091:Exons / Q000235:genetics; D020224:Expressed Sequence Tags; D005293:Ferritins / Q000235:genetics; D005787:Gene Frequency; D006680:HLA Antigens / Q000235:genetics; D000071020:Hemochromatosis Protein; D015395:Histocompatibility Antigens Class I / Q000235:genetics; D006801:Humans; D007501:Iron / Q000378:metabolism*; D019189:Iron Metabolism Disorders / Q000235:genetics* / Q000378:metabolism; D019190:Iron Overload / Q000235:genetics / Q000378:metabolism; D033862:Iron-Binding Proteins; D008565:Membrane Proteins / Q000235:genetics; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D044469:Racial Groups / Q000235:genetics; D011990:Receptors, Transferrin / Q000235:genetics; D014168:Transferrin / Q000235:genetics; D000099236:Solute Carrier Family 11, Member 2
D027682:Cation Transport Proteins; D005293:Ferritins; D006680:HLA Antigens; D000071020:Hemochromatosis Protein; D015395:Histocompatibility Antigens Class I; D007501:Iron; D033862:Iron-Binding Proteins; D008565:Membrane Proteins; D011990:Receptors, Transferrin; D014168:Transferrin; D000099236:Solute Carrier Family 11, Member 2; C492164:HEPH protein, human; C103673:HFE protein, human