DNA sequence variation in a 3.7-kb noncoding sequence 5' of the CYP1A2 gene: implications for human population history and natural selection

Natural selection and molecular evolution in PTC, a bitter-taste receptor gene

The ability to taste phenylthiocarbamide (PTC) is a classic phenotype that has long been known to vary in human populations. This phenotype is of genetic, epidemiologic, and evolutionary interest because the ability to taste PTC is correlated with the ability to taste other bitter substances, many of which are toxic. Thus, variation in PTC perception may reflect variation in dietary preferences throughout human history and could correlate with susceptibility to diet-related diseases in modern populations. To test R. A. Fisher's long-standing hypothesis that variability in PTC perception has been maintained by balancing natural selection, we examined patterns of DNA sequence variation in the recently identified PTC gene, which accounts for up to 85% of phenotypic variance in the trait. We analyzed the entire coding region of PTC (1,002 bp) in a sample of 330 chromosomes collected from African (n=62), Asian (n=138), European (n=110), and North American (n=20) populations by use of new statistical tests for natural selection that take into account the potentially confounding effects of human population growth. Two intermediate-frequency haplotypes corresponding to "taster" and "nontaster" phenotypes were found. These haplotypes had similar frequencies across Africa, Asia, and Europe. Genetic differentiation between the continental population samples was low (FST=0.056) in comparison with estimates based on other genes. In addition, Tajima's D and Fu and Li's D and F statistics demonstrated a significant deviation from neutrality because of an excess of intermediate-frequency variants when human population growth was taken into account (P<.01). These results combine to suggest that balancing natural selection has acted to maintain "taster" and "nontaster" alleles at the PTC locus in humans.

Locus-specific genetic diversity between human populations: an analysis of the literature

The debate over classification of the human species according to racial or continental lines has involved reports on genetic differences in allele frequencies of a number of loci with important biomedical functions. Such differences are in contrast with the fact that, for human beings, intrapopulation genetic diversity is larger than that seen between populations. In an attempt to address the hypothesis that certain genes show high interpopulation diversity due to selective pressure, the literature was surveyed to quantify such diversity using Wrights Fst statistic. The gene-specific Fst values were then compared to pairwise population values of Fst taken over a large number of genes, which presumably reflect mostly neutral mechanisms of genetic diversity such as drift. The results showed that the majority of pairwise population values of Fst for over 30 genes of biomedical significance were either below or within the expected limits of Fst based on published values. These results do not support the idea that positive or diversifying natural selection plays an important role in increasing genetic diversity, even in genes that might be expected to be subject to selection pressure. Balancing selection, whereby the degree of genetic diversity is actually lower than that expected, appears to occur more frequently for these genes. The fact that allele frequency differences between populations might be "statistically significant" does not therefore necessarily imply a degree of genetic diversity greater than would be expected due to nonselective mechanisms.

Catalog of 162 single nucleotide polymorphisms (SNPs) in a 4.7-kb region of the HLA-DP loci in southern Chinese ethnic groups

HLA class-II proteins are cell-surface molecules that present antigens to T cells, and their expressional regulation is crucial to the immune reaction. Sequence variation at the regulatory region can directly affect the gene expression level. We cloned and sequenced a 4.7-kb region containing the regulatory region, exon1, and partial intron1 of both HLA-DPA1 and DPB1 genes in 25 variable sequences from southern Chinese ethnic groups and got a high-density map of 162 single nucleotide polymorphisms (SNPs): seven in 5'-flanking regions, four in 5'-untranslated regions, and four in the coding regions. By comparing these data with SNPs in dbSNP database in the NCBI, 145 SNPs (89.5%) were novel. In addition, eight genetic variations of insertion-deletion polymorphisms (INDELs) were discovered within the 4.7-kb region. These high-resolution maps can be used as resources of markers for association studies of complex diseases, assessment of individuals' predisposition to diseases, and tailoring of therapies, as well as research markers for population genetics and evolution.

Patterns of human genetic diversity: implications for human evolutionary history and disease

Since the completion of the human genome sequencing project, the discovery and characterization of human genetic variation is a principal focus for future research. Comparative studies across ethnically diverse human populations and across human and nonhuman primate species is important for reconstructing human evolutionary history and for understanding the genetic basis of human disease. In this review, we summarize data on patterns of human genetic diversity and the evolutionary forces (mutation, genetic drift, migration, and selection) that have shaped these patterns of variation across both human populations and the genome. African population samples typically have higher levels of genetic diversity, a complex population substructure, and low levels of linkage disequilibrium (LD) relative to non-African populations. We discuss these differences and their implications for mapping disease genes and for understanding how population and genomic diversity have been important in the evolution, differentiation, and adaptation of humans.

Race, ancestry, and genes: implications for defining disease risk

Geneticists are interested in finding genes associated with disease. Because of widespread health disparities, race is a variable that is often said to be relevant in this context. The idea is that members of a preconceived "race" share common ancestry that may include genetic risk factors. Human variation has been shaped by the long-term processes of population history, and population samples that reflect that history carry statistical information about shared genetic variation or "ancestry." But race is an elusive concept and a term difficult even to define rigorously. Unfortunately, these problems are neither new nor related to recent genetic knowledge. Race is also one of the most politically charged subjects in American life because its associated sociocultural component has notoriously led to categorical treatment that has been misleading and politically misused. There are ways in which the concept of race (whether or not the term is used) can be a legitimate tool in the search for disease-associated genes. But in that context race reflects deeply confounded cultural as well as biological factors, and a careful distinction must be made between race as a statistical risk factor and causal genetic variables.

Genetic polymorphism of CYP1A2 in Ethiopians affecting induction and expression: characterization of novel haplotypes with single-nucleotide polymorphisms in intron 1

CYP1A2 polymorphism has been well studied in white persons and Asians but not in Africans. We performed CYP1A2 genotype and phenotype analysis using caffeine in Ethiopians living in Ethiopia (n = 100) or in Sweden (n = 73). We sequenced the CYP1A2 gene using genomic DNA from 12 subjects, which revealed a novel intron 1 single-nucleotide polymorphism (SNP), -730C>T. We developed SNP-specific polymerase chain reaction-restriction fragment length polymorphism genotyping and molecular haplotyping methods for the intron 1 SNPs, and four different haplotypes were identified: CYP1A2*1A (wild-type for all SNPs), CYP1A2*1F (-164A), CYP1A2*1J (-740G and -164A), and CYP1A2*1K (-730T, -740G, and -164A), having frequencies of 39.9, 49.6, 7.5, and 3.0%, respectively. The frequency of CYP1A2*1J and CYP1A2*1K among Saudi Arabians (n = 136) was 5.9% and 3.6%, and among Spaniards (n = 117) 1.3% and 0.5%, respectively. Functional significance of the different intron 1 haplotypes was analyzed. Subjects with CYP1A2*1K had significantly decreased CYP1A2 activity in vivo, and reporter constructs with this haplotype had significantly less inducibility with 2,3,7,8-tetrachlorodibenzo-p-dioxin in human B16A2 hepatoma cells. Electrophoretic mobility shift assay using nuclear extracts from B16A2 cells revealed a specific DNA binding protein complex to an Ets element. Efficient competition was obtained using oligonucleotide probes carrying the wt sequence and Ets consensus probe, whereas competition was abolished using probes with the -730C>T SNP alone or in combination with -740T>G (CYP1A2*1K). The results indicate a novel polymorphism in intron 1 of importance for Ets-dependent CYP1A2 expression in vivo and inducibility of the enzyme, which might be of critical importance for determination of interindividual differences in drug metabolism and sensitivity to carcinogens activated by CYP1A2.