Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis

Marc K. Halushka, Jian Bing Fan, Kimberly Bentley, Linda Hsie, Naiping Shen, Alan Weder, Richard Cooper, Robert Lipshutz, Aravinda Chakravarti

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)239-247
Number of pages9
JournalNature genetics
Volume22
Issue number3
DOIs
StatePublished - Jul 1999

ASJC Scopus subject areas

  • Genetics

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