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A genome wide SNP genotyping study in the Tunisian population: specific reporting on a subset of common breast cancer risk loci

Abstract : Background: Breast cancer is the most common cancer in women worldwide. Around 50% of breast cancer familial risk has been so far explained by known susceptibility alleles with variable levels of risk and prevalence. The vast majority of these breast cancer associated variations reported to date are from populations of European ancestry. In spite of its heterogeneity and genetic wealth, North-African populations have not been studied by the HapMap and the 1000Genomes projects. Thus, very little is known about the genetic architecture of these populations. Methods : This study aimed to investigate a subset of common breast cancer loci in the general Tunisian population and to compare their genetic composition to those of other ethnic groups. We undertook a genome-wide haplotype study by genotyping 135 Tunisian subjects using the Affymetrix 6.0-Array. We compared Tunisian allele frequencies and linkage disequilibrium patterns to those of HapMap populations and we performed a comprehensive assessment of the functional effects of several selected variants. Results : Haplotype analyses showed that at risk haplotypes on 2p24, 4q21, 6q25, 9q31, 10q26, 11p15, 11q13 and 14q32 loci are considerably frequent in the Tunisian population (> 20%). Allele frequency comparison showed that the frequency of rs13329835 is significantly different between Tunisian and all other HapMap populations. LD-blocks and Principle Component Analysis revealed that the genetic characteristics of breast cancer variants in the Tunisian, and so probably the North-African populations, are more similar to those of Europeans than Africans.
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Submitted on : Thursday, January 17, 2019 - 11:40:07 AM
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Yosr Hamdi, Mariem Ben Rekaya, Shan Jingxuan, Majdi Nagara, Olfa Messaoud, et al.. A genome wide SNP genotyping study in the Tunisian population: specific reporting on a subset of common breast cancer risk loci. BMC Cancer, BioMed Central, 2018, 18 (1), pp.1295. ⟨10.1186/s12885-018-5133-8⟩. ⟨pasteur-01984744⟩

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