Analysis of molecular HLA polymorphisms in Beninese populations

Diplôme Master Analysis of molecular HLA polymorphisms in Beninese populations eng 2020 author Faye Ndeye Khady 816513 director Sanchez-Mazas Alicia 22545 The variability of HLA genes provides a framework for the study of evolutionary processes and the genetic history of populations. We analyse the polymorphism of 19 African populations at 8 HLA loci. We describe the patterns of intra-population and inter-population polymorphism to make inferences on the mechanisms shaping HLA gene profiles, evaluate the efficiency of chip genotyping and imputation in capturing polymorphism compared to PacBio sequencing, and identify biases introduced by the typing method and their effect on population genetic analyses. We find that the density of variants identified by the Illumina Omni5 chip is insufficient to characterize the extent of HLA polymorphism, and that the chip under-estimates heterozygosity due to biases in SNP selection and typing errors. Imputation exacerbates the heterozygosity deficit and under-estimates population differentiation, likely due the bias present in the pre-imputation data and the reference panel rather than an endogenous bias in the imputation process. HLA Human Leucocyte Antigen Immunogenetics Population genetics Genotyping Benin Genotype imputation Dewey 590 44 Département de génétique et évolution 162 false 224ec522-fcca-47ef-8c20-574d7136c6cf Master thesis Restricted master_NDEYE_FAYE.pdf 3628006 application/pdf restrictedAccess Faculté des sciences / Section de biologie / Département de génétique et évolution

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Faye, Ndeye Khady

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