Introduction: In Africa, it is estimated that cardiovascular disease (CVD) will affect approximately 1.3 million people per annum over the following 20 years. C-reactive protein (CRP) is a predictor of CVD risk and certain CRP gene polymorphisms can result in altered CRP concentrations. The distribution of CRP gene polymorphisms is ethnic-specific and extrapolating information from other populations to the black South African population, reported to harbour considerable genetic variation, should be avoided. This highlights the fact that genetic research among black South Africans is necessary. Objectives: The main aim of this dissertation was to determine the association between various polymorphisms (reported and novel [single nucleotide polymorphisms (SNPs)] within the CRP gene with CRP concentrations [measured as high sensitivity (hs)-CRP concentrations] in a black South African population undergoing an epidemiological transition. Interactions between specific CRP polymorphisms and certain environmental factors on hs-CRP concentrations were also investigated. Methods: This cross-sectional study (n=1,588) was nested within the Prospective Urban and Rural Epidemiological (PURE) study. Genotyping was performed using Illumina VeraCode technology on the BeadXpress® platform. Hs-CRP concentrations were measured by the use of a sequential multiple analyser computer (SMAC) through a particle-enhanced immunoturbidometric assay. Results: All the SNPs adhered to the assumptions of Hardy-Weinberg equilibrium, although the distribution of several SNPs differed from that reported in other population groups. Three SNPs (rs3093058, rs3093062 and rs3093068) were associated with a significant (p ≤ 0.05) increase in CRP concentrations. Five SNPs (rs1205, rs1341665, rs2794520, rs7553007 and rs2027471) were associated with a significant (p ≤ 0.05) decrease in CRP concentrations. This difference in effect was most probably due to changes in gene function brought about by the localisation of these SNPs in the CRP gene. Men and urban individuals were more likely to present with significant associations between the SNPs investigated and CRP concentrations. The difference in the prevalence of the alleles associated with higher CRP concentrations in this population compared to non-African populations could possibly explain the increased CRP concentrations that are observed in the black South African population. Gene-gender (rs1205, rs1341665 and rs2027474) as well as gene-environmental (rs3093068) interactions were also observed. Conclusions: CRP concentrations are in themselves a complex trait and there are many factors at play that influence their expression. Numerous factors (both genetic and environmental) are involved and no single factor acting alone is likely to have enough of an influence to be used as a clinical diagnostic test of CRP concentrations. These results provide valuable information on the regulation of CRP in a black South African population as well as contribute to the literature of CRP on a global level. / Thesis (MSc (Nutrition))--North-West University, Potchefstroom Campus, 2013.

Introduction: In Africa, it is estimated that cardiovascular disease (CVD) will affect approximately 1.3 million people per annum over the following 20 years. C-reactive protein (CRP) is a predictor of CVD risk and certain CRP gene polymorphisms can result in altered CRP concentrations. The distribution of CRP gene polymorphisms is ethnic-specific and extrapolating information from other populations to the black South African population, reported to harbour considerable genetic variation, should be avoided. This highlights the fact that genetic research among black South Africans is necessary. Objectives: The main aim of this dissertation was to determine the association between various polymorphisms (reported and novel [single nucleotide polymorphisms (SNPs)] within the CRP gene with CRP concentrations [measured as high sensitivity (hs)-CRP concentrations] in a black South African population undergoing an epidemiological transition. Interactions between specific CRP polymorphisms and certain environmental factors on hs-CRP concentrations were also investigated. Methods: This cross-sectional study (n=1,588) was nested within the Prospective Urban and Rural Epidemiological (PURE) study. Genotyping was performed using Illumina VeraCode technology on the BeadXpress® platform. Hs-CRP concentrations were measured by the use of a sequential multiple analyser computer (SMAC) through a particle-enhanced immunoturbidometric assay. Results: All the SNPs adhered to the assumptions of Hardy-Weinberg equilibrium, although the distribution of several SNPs differed from that reported in other population groups. Three SNPs (rs3093058, rs3093062 and rs3093068) were associated with a significant (p ≤ 0.05) increase in CRP concentrations. Five SNPs (rs1205, rs1341665, rs2794520, rs7553007 and rs2027471) were associated with a significant (p ≤ 0.05) decrease in CRP concentrations. This difference in effect was most probably due to changes in gene function brought about by the localisation of these SNPs in the CRP gene. Men and urban individuals were more likely to present with significant associations between the SNPs investigated and CRP concentrations. The difference in the prevalence of the alleles associated with higher CRP concentrations in this population compared to non-African populations could possibly explain the increased CRP concentrations that are observed in the black South African population. Gene-gender (rs1205, rs1341665 and rs2027474) as well as gene-environmental (rs3093068) interactions were also observed. Conclusions: CRP concentrations are in themselves a complex trait and there are many factors at play that influence their expression. Numerous factors (both genetic and environmental) are involved and no single factor acting alone is likely to have enough of an influence to be used as a clinical diagnostic test of CRP concentrations. These results provide valuable information on the regulation of CRP in a black South African population as well as contribute to the literature of CRP on a global level. / Thesis (MSc (Nutrition))--North-West University, Potchefstroom Campus, 2013.

En la present tesi doctoral es va establir i calcular els factors genètics de risc per a la forma tardana de la malaltia d'Alzheimer (MA). Foren analitzats un total de 15 variants gèniques (polimorfismes) ubicats en alguns dels gens candidats que codifiquen per a proteïnes involucrades en la fisiopatologia de la MA. Les freqüències gèniques i genotípiques de tots els polimorfismes, així com les freqüències haplotípiques d'aquelles variants que estaven en desequilibri de lligament, foren comparades entre una població de 136 individus amb diagnòstic clínic de MA i una població de 91 individus sense deteriorament cognitiu (tots amb edats superiors als 65 anys i sense cap relació de parentesc).Es va trobar una associació estadísticament significativa entre l'al·lel e4 del gen APOE i la MA (OR ajustada per sexe i edat de 7.8), així com una altre associació positiva entre el polimofisme *159C/T del gen Neprilysin i la MA (OR del subgrup menor de 75 anys i homozigots CC = 2.87). Finalment, es va trobar una sobre representació significativa del genotip GG, situat en l'exó 5 del gen BACE1, en els pacients d'Alzheimer (OR = 2.14 ). També es va obtenir una associació significativa entre el polimorfisme analitzat en el gen HSP70-2 i la presència de simptomatologia no cognitiva en els pacients que havien estat avaluats amb test neuropsiquiàtric (NPI).Tots aquests estudis confirmen la base genètica de la forma tardana de la MA i demostren la importància de l'epidemiologia genètica i dels estudis de tipus cas-control en aquelles malalties complexes com la MA. / En la presente tesis doctoral se establecieron y calcularon los factores genéticos de riesgo para la forma tardía de la enfermedad de Alzheimer (EA). Para ello se analizaron un total de 15 variantes génicas (polimorfismos) que se encuentran en algunos de los genes candidatos que codifican proteínas involucradas en la fisiopatología de la EA. Las frecuencias génicas y genotípicas de todos los polimorfismos, así como las frecuencias haplotípicas de aquellos polimorfismos que se encontraron en desequilibrio de ligamiento, fueron comparadas entre una población de 136 individuos con diagnóstico clínico de EA y una población de 91 individuos sin deterioro cognitivo (todos con edades superiores a los 65 años y sin relación de parentesco).Se halló una asociación estadísticamente significativa entre el alelo e4 del gen APOE y la EA (OR ajustada por sexo y edad de 7.8), así como otra asociación positiva entre el polimofismo *159C/T del gen Neprilysin y la EA (OR del subgrupo menor de 75 años y homocigotos CC = 2.87). Finalmente, se encontró una sobre representación significativa del genotipo GG, situado en el exón 5 del gen BACE1, en los pacientes de Alzheimer (OR = 2.14 ). También se obtuvo una asociación significativa entre el polimorfismo analizado en el gen HSP70-2 y la presencia de sintomatología no cognitiva en los pacientes que habían sido evaluados con test neuropsiquiátrico (NPI).Todos estos estudios confirman la base genética de la forma tardía de la EA y demuestran la importancia de la epidemiología genética y de los estudios de tipo caso-control en aquellas enfermedades complejas como la EA. / In the present thesis, genetic risk factors for late onset Alzheimer's disease (AD) have been evaluated. A total of 15 polymorphisms located in several candidate genes involved in AD pathophysiology were analysed in a sample set comprising 136 AD patients and 91 non-demented elderly control individuals. A statistically significant association was found between the e4 allele of the APOE gene and AD (age- and sex-adjusted OR = 7.8). An association was also found between the *159C/T polymorphism located at the Nerprilysin gene (the OR for those individuals younger than 75 years old and homozygous for the C allele was 2.87). Finally, an over representation of the GG genotype of the BACE1 exon 5 was found in AD patients compared to controls (OR = 2.14). An elevated propensity to develop non-cognitive alterations in AD patients was found to be associated with the A2 allele of the HSP70-2 gene.All of these results confirm the genetic susceptibility to AD and clearly demonstrate the usefulness of genetic epidemiology tools as well as the case-control approaches in identifying genes related to complex disorders such as AD.

Aquest treball és una contribució als estudis de diversitat del genoma humà i pretén estudiar la variació genètica existent a nivell mundial en dos gens, causants de malaltia, el gen CFTR i el gen GBA, en cromosomes d'individus sans. Mutacions en aquests gens produeixen la fibrosi quística i la malaltia de Gaucher respectivament. La fibrosi quística és la malaltia autosòmica recessiva més comuna en poblacions europees. La malaltia de Gaucher és la malaltia lisosòmica d'acumulació lipídica més freqüent. L'estudi analitza la variació genètica en diferents polimorfismes d'ambdós gens; reconstrueix els haplotips i analitza la seva distribució geogràfica; i analitza l'extensió i distribució geogràfica del desequilibri de lligament entre loci. Pel gen GBA, hem ampliat la regió, abastant fins al gen PKLR (que codifica per a la piruvat quinasa). A més a més, pel cas de CFTR, pot ajudar a entendre l'origen de les mutacions més freqüents causants de fibrosi quística. / This work is a contribution to human genome diversity studies and it aims to study the world-wide genetic variation that exists in two disease genes, CFTR and GBA gene, in healthy chromosomes. Mutations in these genes are known to cause cystic fibrosis and Gaucher disease respectively. Cystic fibrosis is the most common severe autosomal recessive disease in patients of European descent. Gaucher disease is the most frequent lysosomal storage disorder. The study analyzes the genetic variation in CFTR and GBA polymorphisms; estimates haplotype frequencies and describes their geographic distribution; and measures linkage disequilibrium between loci. For GBA gene, we have extended the analysis covering PKLR gene (that encodes for a pyruvate kinase). Moreover, for CFTR gene, we have tried to understand the origin of the most common cystic fibrosis causing mutations.

New approaches are needed to manage and analyze the enormous quantity of biological data generated by modern technologies. Existing solutions are often fragmented and uncoordinated and, thus, they require considerable bioinformatics skills from users. Three applications have been developed illustrating different strategies to help users without extensive IT knowledge to take maximum profit from their data. SNPator is an easy-to-use suite that integrates all the usual tools for genetic association studies: from initial quality control procedures to final statistical analysis. CHAVA is an interactive visual application for CNV calling from aCGH data. It presents data in a visual way that helps assessing the quality of the calling and assists in the process of optimization. Haplotype Association Pattern Analysis visually presents data from exhaustive genomic haplotype associations, so that users can recognize patterns of possible associations that cannot be detected by single-SNP tests. / Calen noves aproximacions per la gestió i anàlisi de les enormes quantitats de dades biològiques generades per les tecnologies modernes. Les solucions existents, sovint fragmentaries i descoordinades, requereixen elevats nivells de formació bioinformàtica. Hem desenvolupat tres aplicacions que il•lustren diferents estratègies per ajudar als usuaris no experts en informàtica a aprofitar al màxim les seves dades. SNPator és un paquet de fàcil us que integra les eines usades habitualment en estudis de associació genètica: des del control de qualitat fins les anàlisi estadístiques. CHAVA és una aplicació visual interactiva per a la determinació de CNVs a partir de dades aCGH. Presenta les dades visualment per ajudar a valorar la qualitat de les CNV predites i ajudar a optimitzar-la. Haplotype Pattern Analysis presenta dades d’anàlisi d’associació haplotípica de forma visual per tal que els usuaris puguin reconèixer patrons de associacions que no es possible detectar amb tests de SNPs individuals.

Les duplicacions segmentàries (DSs), o també anomenades duplicons o Low copy Repeats (LCRs), són regions de coma mínim 1 kb amb un alt nivell d'identitat (>90%), que estan presents almenys dues vegades en el genoma. La regió 8p23.1 consta de 6.5 Mb a la part distal del braç curt del cromosoma 8 i està flanquejada per duplicacions segmentàries. Degut a la seva arquitectura genòmica aquesta regió és susceptible a patir reordenaments mediats per recombinació homòloga no al·lèlica entre les DSs, com per exemple la inversió polimòrfica de 8p23.1 [inv(8)(p23)], present en un de cada quatre individus de la població general europea i japonesa, així com d'altres reorganitzacions menys corrents.El treball realitzat en aquesta tesi doctoral pretén aprofundir en la caracterització de la complexa arquitectura genòmica d'aquesta regió. En la nostra primera aproximació a l'estudi de les DSs que flanquegen la regió cromosòmica 8p23.1, es va identificar una nova família gènica específica de primats, la família gènica FAM90A.Així, bona part d'aquesta tesi doctoral està centrada en l'anàlisi de l'origen, formació, evolució i expansió de FAM90A en els homínids. Per altra banda també s'ha analitzant en detall la variabilitat de FAM90A com a variant en número de còpia (CNV) en diferents poblacions humanes.Finalment, s'ha establert la freqüència de la inversió que afecta a 8p23.1 en població espanyola. També s'ha procedit a genotipar diversos individus homozigots per la inversió i s'ha predit l' estatus de la inversió en 150 individus del projecte HapMap i s'ha analitzat l'efecte que té aquesta reorganització sobre els nivells d'expressió dels gens de la regió. / Segmental duplications (SDs), also known as duplicons or Low Copy Repeats (LCRs), are regions of a minimum of 1 kb with a high sequence identity level (>90%), which are present at least two times in the genome. The 8p23.1 region extends 6.5 Mb at the distal part of the short arm of chromosome 8 and it is flanked by segmental duplications. Due to its genomic architecture the region is prone to suffer rearrangements mediated by non-allelic homologous recombination between these SDs, such as the polymorphic inversion of 8p23.1 [inv(8)(p23)], which is present in one out of every four of European and Japanese general population individuals, as well as other less frequent rearrangements.The aim of the work presented in this doctoral thesis is to get insights in the characterization of the genomic architecture of this complex region. Our first approach to study the SDs flanking 8p23.1 region resulted in the identification of a novel gene family which is primate specific, the FAM90A gene family. Thus, this doctoral thesis is mainly focused on the analysis of the origins, formation, evolution and expansion of FAM90A in hominoids. It has also been analyzed in detail the variability of FAM90A as a copy number variant (CNV) in different human populations.Finally, it has been established the frequency of the inversion affecting 8p23.1 region in the Spanish population. Several homozygous inverted individuals have been genotyped and the status for the inversion has been predicted for 150 HapMap individuals, as well as the effect of this rearrangement on the gene expression levels of the genes contained in the region.