title: Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis.
abstract: Sequence variation in human genes is largely confined to single-nucleotide polymorphisms (SNPs) and is valuable in tests of association with common diseases and pharmacogenetic traits. We performed a systematic and comprehensive survey of molecular variation to assess the nature, pattern and frequency of SNPs in 75 candidate human genes for blood-pressure homeostasis and hypertension. We assayed 28 Mb (190 kb in 148 alleles) of genomic sequence, comprising the 5' and 3' untranslated regions (UTRs), introns and coding sequence of these genes, for sequence differences in individuals of African and Northern European descent using high-density variant detection arrays (VDAs). We identified 874 candidate human SNPs, of which 22% were confirmed by DNA sequencing to reveal a discordancy rate of 21% for VDA detection. The SNPs detected have an average minor allele frequency of 11%, and 387 are within the coding sequence (cSNPs). Of all cSNPs, 54% lead to a predicted change in the protein sequence, implying a high level of human protein diversity. These protein-altering SNPs are 38% of the total number of such SNPs expected, are more likely to be population-specific and are rarer in the human population, directly demonstrating the effects of natural selection on human genes. Overall, the degree of nucleotide polymorphism across these human genes, and orthologous great ape sequences, is highly variable and is correlated with the effects of functional conservation on gene sequences.
authors.affiliation: Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Ohio 44106, USA.
authors.forename: M K
authors.initials: MK
authors.lastname: Halushka
authors.forename: J B
authors.initials: JB
authors.lastname: Fan
authors.forename: K
authors.initials: K
authors.lastname: Bentley
authors.forename: L
authors.initials: L
authors.lastname: Hsie
authors.forename: N
authors.initials: N
authors.lastname: Shen
authors.forename: A
authors.initials: A
authors.lastname: Weder
authors.forename: R
authors.initials: R
authors.lastname: Cooper
authors.forename: R
authors.initials: R
authors.lastname: Lipshutz
authors.forename: A
authors.initials: A
authors.lastname: Chakravarti
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000483:Alleles; D000818:Animals; D001483:Base Sequence; D001794:Blood Pressure / Q000235:genetics*; D004247:DNA / Q000235:genetics; D019143:Evolution, Molecular; D005787:Gene Frequency; D014644:Genetic Variation; D006706:Homeostasis / Q000235:genetics; D006801:Humans; D006973:Hypertension / Q000235:genetics; D002679:Pan troglodytes / Q000235:genetics; D011110:Polymorphism, Genetic; D011506:Proteins / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D011506:Proteins; D004247:DNA