Rare variants and founder effect in the Beauce region of Quebec

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Abstract: Founder events influenced the genetic diversity within the province of Quebec, increasing the frequency of certain rare pathogenic variants in regional populations. Some regions, such as Beauce, remain understudied despite evidence of a regional founder effect. Leveraging extensive genealogical data, we observe a specific regional structure emerging in Beauce following the initial settlement. It is characterised by a gradual increase in inbreeding and kinship coefficients and a low diversity of ancestors. Taking advantage of the region’s genetic distinctiveness, we describe 36 rare pathogenic variants with higher carrier rates in Beauce than in urban regions, likely due to the regional founder effect. This provides the first in-depth study of Beauce’s genetic and genealogical landscape, revealing a distinct structure and suggesting that other overlooked regions, in Quebec and elsewhere, could benefit from fine-scale population structure studies to improve the understanding and management of rare diseases.