Hussman Institute Researchers Collaborate on First Genomic Survey of Multiple Hispanic Populations

A study co-led at the Miller School by Eden Martin, Ph.D., professor in the Dr. John T. Macdonald Foundation Department of Human Genetics, has identified a wide diversity of ancestry within and between Hispanic populations, findings that could lead to more targeted gene discovery for the group.

Published November 14 in PLOS Genetics, the study, “Reconstructing the Population Genetic History of the Caribbean,” is the first genomic survey to focus on multiple populations of Caribbean descent and underscores the importance of characterizing admixed populations in genetic studies at finer scales.

While genetic studies often regard Hispanics, the fastest growing and largest minority in the United States, as a single heterogeneous group, the population has origins in more than 20 countries throughout Latin America. In this study, researchers examined genetic diversity among and within different Hispanic groups from the Caribbean to learn more about their population history and determine how to best manage data from diverse, admixed Hispanics in studies looking for disease genes.

The researchers investigated the population genetic history by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, and Hispaniola), two mainland (Honduras and Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. They combined these data with a unique database of genomic variation in more than 3,000 individuals from diverse European, African, and Native American populations.

“Genome-wide data enables us to reconstruct population history at finer scales, shedding light on evolutionary processes shaping the genetic composition of peoples with complex demographic histories,” said Martin, who is also Director of the Center for Genetic Epidemiology and Statistical Genetics at the John P. Hussman Institute for Human Genomics. “This genetic reconstruction is especially relevant in recently admixed populations from the Americas.”

The researchers used local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region, and developed a new ancestry-specific principal component analysis method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. Their findings provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. In addition, the researchers found that two waves of African migrants in the island region, coinciding with the early and maximum activity stages of the transatlantic slave trade, appear to originate in different regions within West Africa. Surprisingly, they identified a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of a small European founder population size.

“The extensive population stratification within these sub-continental components suggests that medically relevant genetic variants may be geographically restricted,” said Martin. “There is definitely a need to look for more accurate and sensitive ways to adjust for differences in our disease gene mapping.”

The Hussman Institute’s Michael Cuccaro, Ph.D., associate professor of human genomics, and Jacob McCauley, Ph.D., assistant professor of human genomics, also contributed to the study, which was co-led by Carlos Bustamante, Ph.D., and first author Andres Moreno Estrada, M.D., Ph.D., at Stanford University School of Medicine.

The research was funded by an NIH grant (1R01GM090087) and an award from the Stanley J. Glaser Foundation.

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