ARS | Publication request: Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 14, 2009
Publication Date: August 14, 2009
Citation: Mattei, J., Parnell, L.D., Lai, C., Garcia-Bailo, B., Adiconis, X., Shen, J., Arnett, D., Demissie, S., Tucker, K., Ordovas, J.M. 2009. Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites. BioMed Central (BMC) Genetics. 10:45.

Interpretive Summary: Variations in frequencies of different gene variants can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection, the evolutionary process by which certain gene variants are favored in a population, can be a force that modulates the frequencies of certain gene variants across a population. Puerto Ricans, as a population group and the second largest Hispanic ethnic group in the US, have not thoroughly been studied in terms of changes in frequencies of gene variants across the population as influenced by natural selection pressures emanating from the environment. We determined frequencies of gene variants and the changes in frequencies of those variants across the population for 101 single base polymorphisms (SNPs) mapping to 30 different genes involved in major metabolic and disease-relevant pathways in 969 Puerto Ricans persons and compared the values to similarly aged non-Hispanic whites (NHW). The distribution of the frequencies of the less common variant of 46 of the 101 assessed SNPs were significantly different from those of NHW. Puerto Ricans more often carried gene variants that confer risk of disease and more seldom harbored gene variants confer protection of disease than NHW. The changes in frequencies of the 101 variants across the population that we noted tended to map in Puerto Ricans to non-protein coding portions of genes or to gene control regions or altered amino acid sequence of encoded proteins. In the NHW population such changes in frequencies of the 101 variants across the population mapped to non-protein coding portions of genes or to gene control regions only. In conclusion, these observations may explain and broaden studies on the impact of gene variants on chronic diseases affecting Puerto Ricans.

Technical Abstract: Background: Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST) can evidence environmental selection pressures. Such genetic information is limited in Puerto Ricans, the second largest Hispanic ethnic group in the US, and a group with high prevalence of chronic disease. We determined allele frequencies and population differentiation for 101 single nucleotide polymorphisms (SNPs) in 30 genes involved in major metabolic and disease-relevant pathways in Puerto Ricans (n=969, ages 45-75 years) and compared them to similarly aged non-Hispanic whites (NHW) (n=597). Results: Minor allele frequency (MAF) distributions for 45.5% of the SNPs assessed in Puerto Ricans were significantly different from those of NHW. Puerto Ricans carried risk alleles in higher frequency and protective alleles in lower frequency than NHW. Patterns of population differentiation showed that Puerto Ricans had SNPs with exceptional FST values in intronic, non-synonymous and promoter regions. NHW had exceptional FST values in intronic and promoter region SNPs only. Conclusions: These observations may serve to explain and broaden studies on the impact of gene polymorphisms on chronic diseases affecting Puerto Ricans.