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IBD Mapping Uncovers Haplotype with Large Effect on Height in Hispanics and Latinos

COLD SPRING HARBOR, NY (GenomeWeb) – By delving into patient data, researchers in New York City have identified a haplotype that greatly affects height.

At the Biology of Genomes meeting yesterday, Eimear Kenny, an assistant professor at the Icahn School of Medicine at Mount Sinai, described how she and her colleagues drew on data housed in the BioMe biobank to examine patterns of ancestry and map trait-associated loci, like height.

The BioMe bank is an opt-in biobank started at Mount Sinai in 2007 that currently houses data from some 30,000 patients mostly living in northern Manhattan, she said. It includes not only data from linked electronic health records alongside genetic data from genotyping chips, whole-exome sequencing, and whole-genome sequencing, but also information regarding self-reported ancestry, family history, and socioeconomic status.

The patients included in the bank represent a swathe of ancestral backgrounds, Kenny noted, and as 35 percent were not born in the US and 64 percent have grandparents born outside the US, it includes a number of diaspora populations. More than a third of patients whose data are included in the biobank are African American, 29 percent are from the Caribbean, 13 percent have an Ashkenazi Jewish background, and 10 percent have Central or South American ancestry.

"Population diversity in large urban populations can be really broad," Kenny said, noting that census categories don't often capture that diversity. But, she added, "genetics can reveal fine-scale populations."

Hispanic and Latino individuals included in this data have varying degrees of European, Native American, and African ancestry. They also have a high degree of cryptic relatedness and identity-by-descent or long-range genomic tract sharing, Kenny reported, though not to the extent seen in Ashkenazi Jewish populations.

This, she added, provides an opportunity to examine population-based linkage.

Kenny noted that there is about a 2-inch difference in the height between people descended from Afro-Caribbean populations and those from South American populations, with the Afro-Caribbean population being the taller of the two — though Kenny noted this was a trend and didn't reach significance.

Though a genome-wide association study examining height in these populations had no signals reaching significance, a genome-wide haplotype association study based on IBD haplotypes did tease out loci related to height. The strongest signal was located at 9q31.3/9q32, Kenny said, noting that it was validated using a separate platform.

Additionally, this signal is linked to a strong difference in height. According to Kenny, the researchers identified a haplotype conferring short stature — a difference of some six to 10 inches.

These signals were shared, she added, among unrelated individuals. However, she noted that the haplotypes were enriched for local Native-American ancestry. She hypothesized that this version of the haplotype could be traced to Afro-Caribbean populations from Puerto Rico and the Dominican Republic.

This finding, she said, indicates that an IBD mapping approach can be used to reveal genetic architecture and uncover variants that aren't captured elsewhere.