The CARTaGENE Genomics Project : Population structure, local ancestry contributions and relatedness analysis of the French Canadian founder population. H. Gauvin1,2, Y. Idaghdour1, J. Hussin1, J.-P. Goulet1, J.-C. Grenier1, M. Capredon1, A. Hodgkinson1, T. de Malliard1, V. Bruat1, E. Gbeha1, E. Hip-Ki1, P. Awadalla1,3 1) Sainte-Justine Hospital Research Center, Université de Montréal, Montreal, Canada; 2) Department of Social and Preventive Medicine, Université de Montréal, Montreal, Canada; 3) Department of Pediatrics, Université de Montréal, Montreal, Canada.

   The province of Quebec was colonized four hundred years ago by settlers coming from France. In the early settlement of Quebec, some First Nations populations were allied to French settlers and exchanged genetic material as the result of mixed unions between an aboriginal mother and a French father. After the British Conquest, the rapidly expanding French Canadian population generally grew in relative isolation with limited exchange with British, and other incoming populations such as Acadians and Loyalists. The colonization of the territory took place in successive waves leading to regional founder effects contributing to the uniqueness of the French Canadian population. Today, about 80% of the provinces 8 million inhabitants are French speaking. Starting in 2010, over 30,000 people from the province of Quebec were recruited to be a part of the CARTaGENE project. Genotyping data (Illumina Omni2.5M) was generated for ~1000 participants sampled in three distinct regions of the province: the Montreal area, the Quebec City area and the Saguenay region. We use the genotypes to study regional differentiation due to demographic history, admixture and migration patterns within Quebec. We analyze identity by descent (IBD) segments to infer relatedness between participants and trace back regional populations flow inside Quebec. Inferred IBD segments are also analyzed to attest their ancestral origin and their breakpoints are compared to recent and ancestral recombination breakpoints across the genome. We also investigate local ancestry of participants with a panel consisting of Native American and European populations. Specifically, we (i) identify regions of the genome shared between individuals and inherited from common ancestors; (ii) characterize IBD tracts in relation to recombination map and (iii) infer local ancestry across the genome to quantify the relative contributions of the different populations. This work refines previous analysis of population structure in Quebec, provides a more accurate picture of how the different populations contributed to the actual French Canadian genetic pool and gives insight on how their contribution is linked to mutations causing differences in disease prevalence throughout regions of Quebec.

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