Prevalence of Rare Variants Associated with Monogenic Diseases in Pre-contact Caribbean Communities

Abstract

Genomic technologies in archaeology have been used to study migration patterns, origin of and genetic similarity between ancient populations. Researchers are, however, just beginning to employ these technologies to evaluate the genomic health of ancient communities. In this study we screen publicly available whole-genome sequencing data of pre-contact Caribbean individuals for the presence of pathogenic mutations causing monogenic diseases. Our results show that Caribbean communities from the Ceramic Age (3100–400 BP) had an unusually high frequency of pathogenic variants associated with three monogenic conditions, Classical Phenylketonuria, Hypohidrotic Ectodermal Dysplasia and LRRK2-Related Parkinson’s disease. The estimated frequency of these variants from the analyzed ancient samples is severalfold higher than that in contemporary populations. Three conditions classified today as rare diseases thus might have had much higher prevalence in the past. Studying the history of monogenic diseases from ancient communities will expand the list of rare diseases with larger prevalence in the past.