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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.

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Figure 1: Distribution of nucleotide diversity in human genes in coding and non-coding segments.
Figure 2: Distribution of minor allele frequency of SNPs classified by their occurrence among individuals of either African or European descent (population specific) or their presence in both (shared).
Figure 3: Schematic summary of all sequence changes between 75 human and 3 chimpanzee samples.

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Acknowledgements

We acknowledge the assistance of N. Bringht-Twumasi and R. Keefer for technical assistance in sample preparation, PCR analyses and sequencing; M. Mittmann and E. Hubbell for chip design; A. Berno for chip data analyses; N. Patil and C. Marjoribanks for cDNA samples; M. Zwick, H. Willard, C. Langley, E. Eichler and anonymous reviewers for comments on the manuscript; and M. Chee for his efforts at the initiation of this gene screening project. This study was supported by research funds from Case Western Reserve University, University Hospitals of Cleveland, National Heart, Lung & Blood Institute (U10 HL54466) and National Human Genome Research Institute (RO1 HG01847) to A.C. This study is a component of the GenNet network of the NHLBI Family Blood Pressure Program.

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Correspondence to Aravinda Chakravarti.

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Halushka, M., Fan, JB., Bentley, K. et al. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet 22, 239–247 (1999). https://doi.org/10.1038/10297

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