Le caryotype moléculaire permet d’identifier un CNV chez 10-14% des individus atteints de déficience intellectuelle et/ou de malformations congénitales. C’est pourquoi il s’agit maintenant de l’analyse de première intention chez ces patients. Toutefois, le rendement diagnostique n’est pas aussi bien défini en contexte prénatal et l’identification de CNVs de signification clinique incertaine y est particulièrement problématique à cause du risque d’interruption de grossesse. Nous avons donc testé 49 fœtus avec malformations majeures et un caryotype conventionnel normal avec une micropuce CGH pangénomique, et obtenu un diagnostic dans 8,2% des cas. Par ailleurs, des micropuces à très haute résolution combinant le caryotype moléculaire et le génotypage de SNPs ont récemment été introduites sur le marché. En plus d’identifier les CNVs, ces plateformes détectent les LOHs, qui peuvent indiquer la présence d’une mutation homozygote ou de disomie uniparentale. Ces anomalies pouvant être associées à la déficience intellectuelle ou à des malformations, leur détection est particulièrement intéressante pour les patients dont le phénotype reste inexpliqué. Cependant, le rendement diagnostique de ces plateformes n’est pas confirmé, et l’utilité clinique réelle des LOHs n’est toujours pas établie. Nous avons donc testé 21 enfants atteints de déficience intellectuelle pour qui les méthodes standards d’analyse génétique n’avaient pas résulté en un diagnostic, et avons pu faire passer le rendement diagnostique de 14,3% à 28,6% grâce à l’information fournie par les LOHs. Cette étude démontre l’utilité clinique d’une micropuce CGH pangénomique chez des fœtus avec malformations, de même que celle d’une micropuce SNP chez des enfants avec déficience intellectuelle. / Molecular karyotyping identifies a CNV in 10-14% of individuals affected with intellectual disability and/or congenital abnormalities. Therefore, it is now the first-tier analysis for these patients. However, the diagnostic yield is not as clear in the prenatal context, and the risk of pregnancy termination makes the detection of variants of uncertain clinical significance particularly problematic. We tested 49 fetuses with major malformations and a normal karyotype, using a pangenomic CGH array, and obtained a diagnosis in 8.2% of cases. Furthermore, high-resolution microarrays combining molecular karyotyping and SNP genotyping were recently introduced on the market. In addition to identifying CNVs, these platforms detect LOHs, which can indicate the presence of a homozygous mutation or of uniparental disomy. Since these abnormalities can be associated with intellectual disability or congenital abnormalities, their detection is of particular interest for patients whose phenotype remains unexplained. However, the diagnostic yield obtained with these platforms is not confirmed, and the real clinical value of LOH detection is not yet established. We tested 21 children affected with intellectual disability for whom standard genetic analyses failed to provide a diagnosis, and were able to increase the diagnostic yield from 14.3% to 28.6% as a result of the information provided by LOHs. This study shows the clinical usefulness of pangenomic CGH arrays in fetuses with malformation(s), as well as that of SNP arrays in children with intellectual disability.

La scoliose idiopathique est une déformation tridimensionnelle de la colonne vertébrale dont la pathogenèse reste obscure. Cette maladie affecte 2-4% des adolescents de 10-18 ans parmi les garçons et les filles. Il est à noter que les filles sont plus sévèrement affectées et ce en plus grand nombre que les garçons. Les études de jumeaux ont montré que les facteurs génétiques jouent un rôle important dans la scoliose idiopathique de l'adolescent (SIA). Depuis 2010, les études d'association pan génomiques ont été multipliées dans les recherches, visant à trouver des gènes candidats impliqués dans la SIA à travers des examens des polymorphismes nucléotidiques (SNPs). Un test génétique nommé "ScoliScore" a été publié pour essayer de prédire la progression de courbure dans la population caucasienne. Cependant, l'association n'a pas été reproduite dans une grande étude japonaise, soulignant l'importance d'une étude de réplication dans une population caucasienne indépendante. Dans ce contexte, mon projet de maîtrise a permis de génotyper plus de 1,4 millions de SNPs dans une cohorte canadienne-française dans le but: 1) de valider l'association de ScoliScoreTM; et 2) d’identifier les variants génomiques associées à la SIA dans la population québécoise. Notre étude a montré qu’aucun des variants constituant le test ScoliScoreTM n’était associé à la SIA. Ceci suggère que l'absence d'association dans une cohorte japonaise n'est pas due à l'appartenance ethnique. Aussi, nous avons identifié des variants génomiques associés significativement à l’initiation et/ou la progression de SIA dans la population québécoise, suggérant des gènes candidats impliqués dans la pathogenèse de SIA. / Idiopathic scoliosis is a common spinal deformation occurring without clear reason. This disease affects 2-4% adolescents aging from 10-18 years old in both genders. Of note, girls are more affected in number and severity than boys. Twin studies demonstrated that genetic factors play an important role in adolescent idiopathic scoliosis (AIS). Since 2010, Genome-wide association studies (GWAS) have been multiplied in AIS researches, aiming to find out candidate genes involved in the disease by an examination of single nucleotide polymorphisms (SNPs) throughout the entire genome. A genetic test named “ScoliScore” was released for the prediction of curvature progression in Caucasian AIS population using 53 SNPs. However, such association was not replicated in a larger Japanese-population study. Such a discrepancy could be explained by ethnicity, raising the importance of a replication study in an independent Caucasian population of European descent. In that context, we genotyped over 1.4 million SNPs in a French-Canadian cohort: 1) to validate the association in ScoliScoreTM test; and 2) to identify genomic variants associated with AIS in the population of Quebec. As a result, the association of ScoliScoreTM genomic markers could not be reproduced in French-Canadian AIS patients, suggesting that the lack of association of these SNPs in a Japanese cohort is not due to ethnicity. Meanwhile, we identified genome-wide significant variants associated with spinal curve initiation and/or progression in French-Canadian population, suggesting candidate genes involved in AIS pathogenesis.

O receptor scavenger classe B tipo I (SR-BI) media a captação seletiva do colesterol da lipoproteina de alta densidade (HDL) e participa no effluxo do colesterol livre para aceptores lipoprotéicos. A HDL tem um importante rol aterogênico associado com sua participação no transporte reverso do colesterol. Polimorfismos no gene que codifica para o SR-BI (SCARB1) foram relacionados com alterações do perfil lipídico sérico e outros fatores de risco associados com doença cardiovascular. As estatinas são inibidores da síntese do colesterol utilizados no tratamento da dislipidemia. Vários polimorfismos em genes envolvidos no metabolismo intermediario de lipideos foram relacionados com diferenças na resposta a hipolipemiantes. Com a finalidade de avaliar o efeito de polimorfismos do SCARB1 sobre o perfil lipídico sérico, expressão gênica e a resposta a estatinas, foram selecionados 185 indivíduos normolipidêmicos (NL) e 147 pacientes hipercolesterolêmicos (HC). Os pacientes HC foram tratados com atorvastatina (10 mg/dia/4 semanas). DNA e RNA foram extraídos de amostras de sangue periférico. Os polimorfismos de nucleotídeo único (SNP) G4A, In5C>T e Ex8C>T foram detectados por PCR-RFLP. A expressão de RNAm do SCARB1 em células mononucleares de sangue periférico (CMSP) foi analisada por PCR em tempo real usando o gene da Ubiquitina c (UBC) como referência endógena. Nos indivíduos HC, as freqüências dos alelos raros G4A (12%), In5C>T (7%) e Ex8C>T (40%), no grupo HC, foram similares às encontradas no grupo NL (4A: 15%, In5T: 7%, e Ex8T: 35%, p>0,05). O alelo SCARB1 4A (genótipos GA + AA) foi associado com valores diminuídos de apoAI no grupo NL. O alelo In5T foi associado com maior concentração LDL-C sérico (p=0,029), em NL, e com apoB e razão apoB/apoAI elevadas (p>0,05) no grupo HC. O SNP SCARB1 Ex8C>T não foi relacionado com o perfil lipídico sérico basal, embora os portadores do genótipo Ex8CC foram associados com resposta reduzida ao tratamento com atorvastatina mostrando menor variação de colesterol total, LDL-C, apoB e razão apoB/apoAI. O SNP Ex8C>T foi associado com maior probabilidade (OR=3,1; 95% IC: 1,00-9,5; p=0,044) de ter uma resposta à atorvastatina diminuída. Os SNPs SCARB1 In5C>T e Ex8C>T estão em desequilíbrio de ligação. O haplótipo G1C5C8/G1T5C8 foi associado com concentrações basais elevadas de triglicérides e VLDL-C em NL e diminuídas de HDL-C e apoAI em HC. Os haplótipos G1C5C8/A1C5C8 e C5C8/C5C8 tiveram variação diminuída da apoB quando comparados com os outros haplótipos, G1C5C8/A1C5C8 e o diplótipo C5C8/C5C8 também apresentou uma variação reduzida da razão apoB/apoAI. Os SNPs G4A e In5C>T estão associados com diminuição da expressão gênica do SCARB1 em NL. O tratamento com atorvastatina não modifica a expressão de RNAm do SCARB1 em CMSP nos HC. Esses resultados são sugestivos de que os polimorfismos no SCARB1 estão associados com valores basais do perfil lipídico sérico e de expressão de RNAm do SCARB1, assim como de resposta à atorvastatina. / The scavenger receptor class B type I (SR-BI) mediates the selective uptake of the high density lipoprotein (HDL) cholesterol and it participates in the free cholesterol efflux to lipoprotein acceptors. HDL has an important antiatherogenic role associated with important activity in the cholesterol reverse transport. Polymorphisms in the SR-BI gene (SCARB1) have been related to variations on plasma lipoprotein profile and other risk factors for cardiovascular disease. Statins are potent inhibitors of cholesterol synthesis prescribed for treatment of the dislipidemia. Several polymorphisms in genes involved in intermediary metabolism of lipids have been related to differences in response to lowering-cholesterol drugs. In order to evaluate the effect of SCARB1 polymorphisms on serum lipids, gene expression and lipid-lowering response to atorvastatin, 185 normolipidemic (NL) and 147 hypercholesterolemic (HC) individuals were selected. HC individuals were treated with atorvastatin (10 mg/day/4 weeks). DNA and RNA were extracted from peripheric blood mononuclear cells (PBMC). SCARB1 mRNA expression was analyzed by real time PCR using ubiquitin c gene (UBC) as endogenous reference. The frequencies of the rare alleles in HC group (G4A: 12%; In5C>T: 7%, and ExC>T: 39%) were similar to those found in NL individuals (4A: 15%, In5T: 7%, and Ex8T: 35%, p>0.05). The SCARB1 4A allele (GA+AA genotypes) was associated with lower apoAI concentration in NL. The In5T allele was associated with higher serum LDL-C (p=0,029) in NL individuals, and with higher apoB and apoB/apoAI ratio (p>0,05) in HC group. SCARB1 Ex8C>T SNP was not related to serum lipids profile, however Ex8CC genotype carriers had lower variation of total cholesterol, LDL-C, apoB and apoB/apoAI ratio in response to atorvastatin. SCARB1 Ex8C>T was associated with higher chance to have a lower atorvastatin response (OR=3.1, 95% CI: 1.00-9.5; p=0.044). SCARB1 In5C>T and ExC>T were in linkage disequilibrium. G1C5C8/G1T5C8 SCARB1 haplotype was associated with higher level of triglycerides and VLDL-C in NL and lower HDL-C and apoAI levels in HC individuals. G1C5C8/A1C5C8 haplotype and C5C8/C5C8 diplotype had lower variations on apoB than the other haplotypes, and G1C5C8/A1C5C8 had also lower variation on apoB/apoAI ratio. G4A and In5C>T SNPs are associated with lower SCARB1 mRNA expression in PBMC of NL individuals. Atorvastatin therapy did not modify the expression level of the SCARB1 transcript in HC. Our results suggest that SCARB1 polymorphisms are associated with basal serum lipids profile, mRNA SCARB1 expression and atorvastatin response.

A nefropatia diabética (ND) decorre da hiperglicemia crônica, de fatores de risco como a hipertensão arterial e a dislipidemia e de uma susceptibilidade genética já evidenciada em inúmeros estudos clínicos. Uma das características histológicas da ND é o acúmulo de proteínas de matriz extracelular no mesângio, para o qual contribuem várias vias bioquímicas. O GLUT-1, codificado pelo gene SLC2A1, é o principal transportador de glucose da célula mesangial e sua expressão está aumentada no glomérulo de animais diabéticos, o que constitui uma alça de feedback positivo pela qual a glicose extracelular aumentada estimula ainda mais sua própria captação, piorando a lesão mesangial. O GLUT-2, codificado pelo gene SLC2A2, é expresso nas células tubulares e nos podócitos e sua expressão também está aumentada na ND. A expressão deste transportador de glicose é regulada pelo fator de transcrição HNF-1. Participa, ainda, da lesão renal induzida pela hiperglicemia o fator de crescimento transformante - (TGF-), que exerce vários efeitos deletérios, tais como diminuir a atividade de metaloproteinases de matriz e promover fibrose renal. Esse fator de crescimento determina a ativação transcricional de genes-alvo, mas necessita de outros ativadores e co-ativadores da transcrição, tais como a proteína SMIF, codificada pelo gene DCP1A. Tendo em vista a participação das proteínas mencionadas acima na patogênese da ND, o presente estudo teve o objetivo de avaliar a associação de polimorfismos de um único nucleotídeo (SNPs) nos genes SLC2A1, SLC2A2, HNF1A, TGFB1 e DCP1A com a doença renal em portadores de diabetes mellitus tipo 1 (DM1). Um total de 449 pacientes (56,4% do sexo feminino, idade média de 36,0±11,0 anos) com mais de 10 anos de doença foram incluídos e classificados de acordo com o estágio de ND: (1) Ausência de ND: excreção urinária de albumina (EUA) normal (< 30 mg/24h ou < 20 g/min) e creatinina plasmática < 1,7 mg/dL sem tratamento anti-hipertensivo; (2) ND incipiente: microalbuminúria (EUA de 30 299 mg/24h ou 20 199 g/min) e creatinina plasmática < 1,7 mg/dL sem tratamento anti-hipertensivo e (3) ND Franca: macroalbuminúria (EUA > 300 mg/24h ou > 200 g/min) ou proteinúria ou tratamento para reposição renal. Também foram avaliadas as associações dos SNPs com o ritmo de filtração glomerular estimado (RFGe). Os SNPs foram genotipados pela metodologia de reação em cadeia da polimerase em tempo real, com o uso de sondas fluorescentes. As associações dos SNPs com a ND foram avaliadas por análise de regressão logística e os odds ratios (OR) e respectivos intervalos de confiança (IC) de 95% foram calculados após ajuste para possíveis confundidores, que foram incluídos como co-variáveis no modelo de regressão. Valores de P < 0.05 (bicaudal) foram considerados estatisticamente significantes. As seguintes associações foram observadas: (1) gene SLC2A1: genótipos CT+TT do SNP rs841848 conferiram risco para a ND incipiente na população global (OR 1,88; CI95% 1,06-3,34; P= 0,03) e nos pacientes do sexo masculino (OR 2,67; CI95% 1,13-6,35; P=0,0247) e para a ND franca (OR 2,70; CI95% 1,18-6,31; e P= 0,0197) apenas nos pacientes do sexo masculino; genótipos GA+AA do SNP rs1385129 conferiram risco para a ND franca na população do sexo masculino (OR 3,09; CI95% 1,34-7,25; P=0,0085); genótipos AT + TT do SNP rs3820589, conferiram proteção contra a ND incipiente na população global (OR 0,36; CI95% 0,16-0,78; P=0,0132) e na população do sexo feminino (OR 0,14; CI95% 0,02-0,52; P=0,0122). (2) gene SLC2A2: genótipos GA+GG do SNP rs5396 conferiram proteção contra ND franca nos pacientes do sexo masculino (OR 0,29; CI95% 0,12-0,69; P=0,0052); os genótipos AG+GG do SNP rs6800180 conferiram proteção contra a ND franca nos pacientes do sexo masculino (OR 0,16; CI95% 0,14-0,90; P=0,0324). (3) gene HNF1A: genótipos AC + CC do SNP rs1169288 conferiram risco para ND franca na população global (OR 2,23; CI95% 1,16-4,38; P=0,0175); genótipos CG+GG do SNP rs1169289 conferiram risco para ND franca na população global (OR 3,43; CI95% 1,61-7,73; P=0,002); (4) Gene TGFB1: genótipos CT + TT do SNP 1800468 conferiram risco para ND incipiente na população total (OR 2,99; CI95% 1,26-7,02; P 0,0116) e o alelo polimórfico T do SNP rs1800469 conferiu risco para um menor RFGe (p=0,0271). (5) gene DCP1A: o alelo polimórfico A do SNP rs11925433 também se associou com um menor RFGe (p=0,0075). Em conclusão, SNPs em genes que codificam as proteínas envolvidas na patogênese da ND GLUT-1, GLUT-2, HNF-1, TGF- e SMIF conferem susceptibilidade para essa complicação crônica nos portadores de DM1 avaliados no presente estudo / Diabetic nephropathy (DN) results from chronic hyperglycemia, risk factors such as hypertension and dyslipidemia as well as from genetic susceptibility, already demonstrated in numerous clinical studies. A histological feature of DN is the accumulation of extracellular matrix proteins in the mesangium after activation of multiple biochemical pathways. GLUT-1, encoded by gene SLC2A1, is the major glucose transporter in mesangial cell and its expression is increased in the glomeruli of diabetic animals, comprising a positive feedback loop whereby high extracellular glucose stimulates its own uptake and worsening mesangial injury. GLUT-2, encoded by SLC2A2 gene, is expressed in podocytes and tubular cells and its expression is also increased in DN. The expression of this glucose transporter is regulated by the transcription factor HNF-1. Transforming growth factor - (TGF-) also participates in renal injury induced by hyperglycemia, exerting several deleterious effects, such as to decrease the activity of matrix metalloproteinases and to promote renal fibrosis. This growth factor determines the transcriptional activation of target genes, but needs other activators and co-activators, such as the protein named SMIF, encoded by the gene DCP1A. Given the involvement of the aforementioned proteins in the pathogenesis of DN, the present study aimed to evaluate the association of single nucleotide polymorphisms (SNPs) in the genes SLC2A1, SLC2A2, HNF1A, TGFB1 e DCP1A with renal disease in patients with type 1 diabetes mellitus (T1DM). A total of 449 patients (56.4% female, mean age 36.0±11.0 years) with disease duration > 10 years were included and grouped according to DN stages: (1) absence of DN: normal urinary albumin excretion (UAE) (< 30 mg/24h or < 20 g/min) and plasmatic creatinine < 1.7 mg/dL without antihypertensive treatment; (2) incipient DN: microalbuminuria (UAE 30 299 mg/24h or 20 199 g/min) and plasmatic creatinine < 1.7 mg/dL without antihypertensive treatment and (3) overt DN: macroalbuminúria (UAE > 300 mg/24h or > 200 g/min) or proteinuria or renal replacement therapy. Associations of SNPs with estimated glomerular filtration rate (eGFR) were also evaluated. All SNPs were genotyped by real time polymerase chain reaction using fluorescent-labelled probes. Associations of the SNPs with DN were assessed by logistic regression analyses and odds ratios (OR) were calculated after adjustments for possible confounders included as covariables in the regressive model. P values <0.05 (two-tails) were considered significant. The following associations were observed: (1) SLC2A1: genotypes CT+TT from rs841848 conferred risk to incipient DN in the overall population (OR 1.88; 95%IC 1.06-3.34; P= 0.03) and in the male patients (OR 2.67; CI95% 1.13-6.35; P=0.0247) and to overt DN (OR 2.70; CI95% 1.18-6.31; e P= 0.0197) only in the male patients; genotypes GA+AA from rs1385129 conferred risk to overt DN in the male population (OR 3.09; CI95% 1.34-7.25; P=0.0085); genotypes AT + TT from rs3820589 conferred protection against incipient DN in the overall population (OR 0.36; CI95% 0.16-0.78; P=0.0132) and in the female population (OR 0.14; CI95% 0.02-0.52; P=0.0122). (2) SLC2A2: genotypes GA+GG from rs5396 conferred protection against overt DN in the male patients (OR 0.29; CI95% 0.12-0.69; P=0.0052); genotypes AG+GG from rs6800180 conferred protection against overt DN in the male patients (OR 0.16; CI95% 0.14-0.90; P=0.0324). (3) HNF1A: genotypes AC + CC from rs1169288 conferred risk to overt DN in the overall population (OR 2.23; CI95% 1.16-4.38; P=0.0175); genotypes CG+GG from rs1169289 conferred risk to overt DN in the overall population (OR 3.43; CI95% 1.61-7.73; P=0.002); (4) TGFB1: genotypes CT + TT from 1800468 conferred risk to incipient DN in the overall population (OR 2.99; CI95% 1.26-7.02; P=0.0116) and the polymorphic allele T from SNP rs1800469 conferred risk to a lower eGFR (p=0.0271). (5) DCP1A: the polymorphic allele A from SNP rs11925433 was also associated with a lower eGFR (p=0.0075). In conclusion, SNPs in the genes encoding proteins GLUT-1, GLUT-2, HNF-1, TGF- e SMIF, all involved in the pathogenesis of DN, conferred susceptibility to this chronic complication in the T1DM patients evaluated in the present study

No description available.

Depuis l'émergence du concept de cellules souches cancéreuses (CSC), de telles cellules ont été isolées à partir de diverses tumeurs solides, dont les glioblastomes. Les CSC et les propriétés qui les caractérisent permettent de mieux comprendre l'hétérogénéité tumorale, ainsi que l'agressivité de certaines tumeurs et les récidives après traitement. Avec la mise en évidence des CSC, un nouveau paradigme est apparu dans le domaine de la thérapie anticancéreuse visant à cibler non seulement les cellules de la masse tumorale, mais également les CSC, plus résistantes aux chimio- et radiothérapies, mais aussi capables d'entrer en quiescence et de reformer la tumeur d'origine. L'isolement de CSC à partir des tumeurs, leur physiopathologie et la recherche de molécules capables de les détruire ou de les différencier afin de les rendre plus sensibles aux traitements mobilisent un nombre croissant d'équipes de recherche et certaines industries pharmaceutiques. Cette thèse présente un travail sur des CSC isolées de glioblastomes humains et s'inscrit dans la démarche énoncée ci-dessus.

Reduction in dopamine receptor D2, has been associated with insufficient brain reward, food addiction, obesity, and type 2 diabetes (T2D). Our aim was to assess whether the genetic variability responsible for this reduction is associated with poor dietary compliance and life style habits in T2D patients. Genetic-analysis was done for 109 T2D individuals who completed a 24-week randomized clinical trial and were assigned to follow either a low-GI or a high-fibre diet. Polymorphisms of TaqIA and C957T were compared with physical and biochemical measures. Regardless of dietary treatments, individuals with the C957T-T allele and the TaqIA-A2 allele were significantly associated with blood pressure reduction. Carriers of the T allele significantly lowered their body mass index (BMI) over the 24-week trial. Our findings suggest that the presence of the TaqIA-A2 allele is associated with a decrease in blood pressure. The C957T-T allele was associated with decrease in pressure and body weight.

Reduction in dopamine receptor D2, has been associated with insufficient brain reward, food addiction, obesity, and type 2 diabetes (T2D). Our aim was to assess whether the genetic variability responsible for this reduction is associated with poor dietary compliance and life style habits in T2D patients. Genetic-analysis was done for 109 T2D individuals who completed a 24-week randomized clinical trial and were assigned to follow either a low-GI or a high-fibre diet. Polymorphisms of TaqIA and C957T were compared with physical and biochemical measures. Regardless of dietary treatments, individuals with the C957T-T allele and the TaqIA-A2 allele were significantly associated with blood pressure reduction. Carriers of the T allele significantly lowered their body mass index (BMI) over the 24-week trial. Our findings suggest that the presence of the TaqIA-A2 allele is associated with a decrease in blood pressure. The C957T-T allele was associated with decrease in pressure and body weight.

The Russian wheat aphid (RWA) (Diuraphis noxia Kurdjumov) is one of the important insect pests of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.) and other grasses. To date, there are four RWA biotypes identified in South Africa. The virulent biotypes emerged, partly due to climate change and new genetic variations within populations of RWA; hence there is a need to improve host-plant resistance, as an effective control measure. Bread wheat (Triticum aestivum L.) accession Cereal Introduction (CItr) 2401 is known to be resistant to all RWA biotypes worldwide. The goal of this study was to use a backcrossed near-isogenic line (NIL) BC5F5 mapping population, developed from a cross between CItr 2401 and susceptible Kavkaz, to identify and validate single nucleotide polymorphism (SNP) markers linked to the resistance phenotype in CItr 2401. This was achieved by (i) conducting a preliminary study that evaluated the suitability of simple sequence repeat (SSR) markers previously reported in literature for discriminating stacked RWA resistance genes and, (ii) employing SNP markers for the first time in a RWA resistance study as a future alternative to the widely used SSR markers. None of the tested SSR markers showed potential use in marker-assisted selection (MAS). The mapping population was phenotypically evaluated for RWA resistance using the four South African biotypes, viz. RWASA1, RWASA2, RWASA3 and RWASA4. Analysis of variance (ANOVA) showed significant (P<0.001) differences of genotypes after confirming the normality of residuals and homogeneity of variance. The Illumina iSelect 9,000 wheat SNP platform was used to genotype the two crossing parents and a selection of 24 NIL genotypes from the mapping population. Eight SNP markers found to be linked to the phenotype were converted to breeder-friendly and high-throughput Kompetitive allele-specific polymerase chain reaction (KASP) markers. The designed KASP markers were validated on the two crossing parents, the 24 NIL sent for SNP genotyping, on the mapping population and on the preliminary study genotypes for their effectiveness. The KASP assays developed in this study will be useful for stacking the RWA resistance from CItr 2401 with other Dn genes effective against the RWA. / Life and Consumer Sciences / M. Sc. (Life Sciences)

La génomique d'association cherche à déterminer des liens entre le génome et des traits ou phénotypes, notamment dans le contexte de maladies. Aujourd'hui, les études les plus fréquentes en génomique d’association sont les études génome entier, qui analysent autant de variants du génomes (SNPs) que possible, sans avoir de préjugé a priori sur leur fonction biologique. Cependant, les méthodes de génotypage utilisées pour ces études ne permettent pas toujours d'obtenir des informations précises dans une région hypervariable comme la région HLA, qui joue un rôle crucial dans l'immunité, et les variants génétiques de ces régions sont souvent prédits par des approches bioinformatiques. J'ai durant ma thèse créé un nouvel outil, HLA-Check, permettant d'évaluer, à partir des génotypes obtenus par puce de génotypage, la plausibilité de données d'allèles HLA d'un même individu, et démontré que cette technique permettait d'identifier plus précisément les individus dont les allèles HLA avaient été mal caractérisés afin de les retyper ou de les écarter de l'étude. Un article documentant cet outil a été publié dans BMC Bioinformatics. J'ai également effectué une étude d'association génome entier sur le déclenchement de la cirrhose chez les patients co-infectés par le VIH (virus de l'immunodéficience humaine) et le VHC (virus de l'hépatite C). La coinfection par ces deux maladies est fréquente en raison de modes d’infection similaires, et l'infection par le VIH stimule l'activité du VHC et accélère la fibrose du foie puis sa cirrhose, causant la mort des patients co-infectés. Mon étude porte sur 306 patients co-infectés issus de la cohorte ANRS CO-13 HEPAVIH. J'ai ainsi pu mettre en évidence trois signaux associés avec le déclenchement de la cirrhose, dont deux ont un lien pertinent avec les maladies hépatiques (gene CTNND2 et gene MIR7-3HG). L'identification de ces nouveaux variants devrait permettre une meilleure compréhension des mécanismes moléculaires de la cirrhose, et contribuer au développement de nouvelles stratégies diagnostiques ou thérapeutiques. L’article documentant cette étude est en cours de publication. / Association genomics aims at finding links between the genome and some traits or illnesses. Today, the most frequent studies in this field are genome wide association studies (GWAS), which analyze as many genome variants (mainly Single Nucleotide Polymorphisms) as possible, without any a priori on their biological function. However, genotyping methods used in these studies may be insufficient to get reliable information in higly variable regions such as the HLA which plays a crucial role in immunity, and the genetic variants of such regions are often predicted using bioinformatics approaches. During my PhD, I have created a new tool, HLA-Check, that allows to rate the plausibility of HLA alleles from the genotypes obtained from genotyping chips. I also assesses its performances and showed that it was able to point out individuals with a wrong HLA typing, in order to retype them or remove them from the study. An article documenting this tool was published in BMC Bioinformatics. I have also performed a genome-wide association study on cirrhosis outbreak in individuals coinfected with HIV (human immunodeficiency virus) and HCV (hepatitis C virus). Because of similar infection routes (blood-related), co-infection with those two viruses are frequent, and the infection by HIV enhances HCV activity and increases liver fibrosis leading to cirrhosis and death of co-infected patients. Our study has dealt with 306 co-infected patients from the ANRS CO-13 HEPAVIH cohort. I could point out three statistically significant signals, two of them being highly relevant for their involvement in liver diseases (gene CTNND2 and gene MIR7-3HG). The identification of these new variants should lead to a better understanding of the molecular mechanisms involved in cirrhosis, and should contribute to the rational developement of new diagnostic or therapeutic strategies. A publication is under way.