DNA sequence variation in a 3.7-kb noncoding sequence 5′ of the CYP1A2 gene

Implications for human population history and natural selection

S. P. Wooding, W. S. Watkins, M. J. Bamshad, D. M. Dunn, R. B. Weiss, L. B. Jorde

Research output: Contribution to journalArticle

65 Citations (Scopus)

Abstract

CYP1A2 is a cytochrome P450 gene that is involved in human physiological responses to a variety of drugs and toxins. To investigate the role of population history and natural selection in shaping genetic diversity in CYP1A2, we sequenced a 3.7-kb region 5′ from CYP1A2 in a diverse collection of 113 individuals from three major continental regions of the Old World (Africa, Asia, and Europe). We also examined sequences in the 90-member National Institutes of Health DNA Polymorphism Discovery Resource (PDR). Eighteen single-nucleotide polymorphisms (SNPs) were found. Most of the high-frequency SNPs found in the Old World sample were also found in the PDR sample. However, six SNPs were detected in the Old World sample but not in the PDR sample, and two SNPs found in the PDR sample were not found in the Old World sample. Most pairs of SNPs were in complete linkage disequilibrium with one another, and there was no indication of a decline of disequilibrium with physical distance in this region. The average ± SD nucleotide diversity in the Old World sample was 0.00043 ± 0.00026. The African population had the highest level of nucleotide diversity and the lowest level of linkage disequilibrium. Two distinct haplotype clusters with broadly overlapping geographical distributions were present. Of the 17 haplotypes found in the Old World sample, 12 were found in the African sample, 8 were found in Indians, 5 were found in non-Indian Asians, and 5 were found in Europeans. Haplotypes found outside Africa were mostly a subset of those found within Africa. These patterns are all consistent with an African origin of modern humans. Seven SNPs were singletons, and the site-frequency spectrum showed a significant departure from neutral expectations, suggesting population expansion and/or natural selection. Comparison with outgroup species showed that four derived SNPs have achieved high (>0.90) frequencies in human populations, a trend consistent with the action of positive natural selection. These patterns have a number of implications for disease-association studies in CYP1A2 and other genes.

Original languageEnglish (US)
Pages (from-to)528-542
Number of pages15
JournalAmerican Journal of Human Genetics
Volume71
Issue number3
DOIs
StatePublished - Sep 2002

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Cytochrome P-450 CYP1A2
Genetic Selection
Single Nucleotide Polymorphism
Population
Genes
Haplotypes
Linkage Disequilibrium
Nucleotides
National Institutes of Health (U.S.)
Cytochrome P-450 Enzyme System
DNA
Pharmaceutical Preparations

ASJC Scopus subject areas

  • Genetics

Cite this

DNA sequence variation in a 3.7-kb noncoding sequence 5′ of the CYP1A2 gene : Implications for human population history and natural selection. / Wooding, S. P.; Watkins, W. S.; Bamshad, M. J.; Dunn, D. M.; Weiss, R. B.; Jorde, L. B.

In: American Journal of Human Genetics, Vol. 71, No. 3, 09.2002, p. 528-542.

Research output: Contribution to journalArticle

Wooding, S. P. ; Watkins, W. S. ; Bamshad, M. J. ; Dunn, D. M. ; Weiss, R. B. ; Jorde, L. B. / DNA sequence variation in a 3.7-kb noncoding sequence 5′ of the CYP1A2 gene : Implications for human population history and natural selection. In: American Journal of Human Genetics. 2002 ; Vol. 71, No. 3. pp. 528-542.
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