Karen Makar, PhD, Senior Staff Scientist, Public Health Sciences, FHCRC
Multiple projects within the PUEDO initiative will analyze traits that show significant inter-ethnic differences in distribution (such as body mass index) or frequency (such as hormone receptor negative breast cancer). With such traits, one of the key questions is the degree to which genetics and environment contribute to the correlation in Hispanic Americans. To help Center investigators measure the contribution of ancestry, the Genetics Core will coordinate the collection of genotype data on ancestry informative markers (AIMs) for participants in the appropriate projects. AIMs are genetic polymorphisms with striking allele frequency differences between geographic populations that can be used to estimate an individual’s ancestry. While markers with strong geographic correlations are rare overall, recent large genetic studies have allowed identification of small panels of AIMs that can provide an estimate of the geographic ancestry of individuals from admixed populations. Particularly in the Mexican American population, the distribution of European ancestry is widely variable between individuals, ranging from individuals who are indistinguishable from European populations to individuals who are indistinguishable from Mayan or Pima populations. The Genetics Core will genotype participants and generate ancestry estimates using a panel of AIMs, such as the 128 marker panel described by Kosoy et al1 that has been shown to provide reasonably precise estimates of the continental ancestry of Hispanic Americans. These estimates will be used as a proxy for the genetic background of the individual, and allow Center researchers to directly assess correlations between genetic ancestry and a given trait.
The Genetics Core will both lead the selection of the AIMs, to provide maximal information in the Latina populations studied, as well as actually generate the ancestry estimates. Analysis of genetic ancestry is associated with significant ethical issues, so the Genetics Core will coordinate with the Ethics and Policy Core at all levels of the project, from developing the panel of AIMs to data analysis and presentation of results.
1. Kosoy, R. et al Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Human Mutation 2009. 30(1):69-78.