Spinocerebellar ataxia type 7 (SCA7) is a hereditary neurodegenerative disorder affecting the cerebellum, pons and retina. SCA7 patients present with gait ataxia and visual impairment as the main symptoms. Anticipation, commonly observed in SCA7 families, is a phenomenon where an earlier age at onset and a more severe progression of disease is seen in successive generations. In order to identify the gene responsible for SCA7, we performed linkage analysis on a Swedish SCA7 kindred. Evidence for linkage of the SCA7 disease locus to a 32 cM region on chromosome 3p12-21.1, between markers D3S1547 and D3S1274, was established. A number of neurodegenerative disorders associated with anticipation are caused by expanded (CAG)n repeats in their respective disease genes. In order to isolate the SCA7 disease gene we, therefore, screened a human infant brain stem cDNA library for CAG repeat containing clones, mapping to chromosome 3. Four candidate clones were isolated and analysed, but could all be excluded as the SCA7 disease gene. In 1997, the SCA7 disease gene was identified and, as expected, shown to harbour a CAG repeat, expanded in SCA7 patients. Analysis of the SCA7 CAG repeat region in Swedish SCA7 patients demonstrated that CAG repeat size was negatively correlated to age at onset of disease. Furthermore, patients with larger repeats presented with visual impairment, whereas patients with smaller repeats presented with ataxia as the initial symptom. SCA7 is the most common autosomal dominant cerebellar ataxia in Sweden and Finland, but rare in other populations. In order to investigate if the relatively high frequency of SCA7 in these countries is the result of a founder effect in the region, a haplotype analysis was performed on all SCA7 families available. All 7 families shared a common haplotype of at least 1.9 cM surrounding the SCA7 locus. In addition, strong linkage disequilibrium was demonstrated for marker D3S1287 closely linked to the SCA7 gene, suggesting a founder effect for the SCA7 mutation in Sweden and Finland. The function of the SCA7 protein, ataxin-7, is not known and it does not show significant homologies to any previously known proteins. In order to gain insight into the function of ataxin-7 we analysed the expression of ataxin-7 in brain and peripheral tissue from SCA7 patients and controls. In brain, expression was found to be mainly neuronal with a nuclear subcellular localisation. Ataxin-7 expression was found throughout the CNS, not restricted to sites of pathology. We also confirmed previously reported findings of neuronal intranuclear inclusions (NIls) in the brains of SCA7 patients. Based on our findings, we conclude that the cell type specific neurodegeneration in SCA7 is not due to differences in expression pattern in affected and non-affected tissue or the distribution pattern of aggregated protein.

Studies on genetic variation can reveal effects on traits and disease, both in humans and in model organisms. Good technology for the analysis of DNA sequence variations is critical. Currently the development towards assays for large-scale and parallel DNA sequencing and genotyping is progressing rapidly. Single base primer extension (SBE) is a robust reaction principle based on four-colour fluorescent terminating nucleotides to interrogate all four DNA nucleotides in a single reaction. In this thesis, SBE methods were applied to the analysis and discovery of single nucleotide polymorphism (SNP) in the model organism Drosophila melanogaster and in humans. The tag-array minisequencing system in a microarray format is convenient for intermediate sized genotyping projects. The system is scalable and flexible to adapt to specialized and novel applications. In Study I of the thesis a tool was established to automate quality control of clustered genotype data. By calculating “Silhouette scores”, the SNP genotype assignment can be evaluated by a single numeric measure. Silhouette scores were then applied in Study I to compare the performance of four DNA polymerases and in Study III to evaluate freeze-dried reagents in the tag-array minisequencing system. The characteristics of the tag-array minisequencing system makes it suitable for inexpensive genome-wide gene mapping in the fruit fly. In Study II a high-resolution SNP map, and 293 genotyping assays, were established across the X, 2nd and 3rd chromosomes to distinguish commonly used Drosophila strains. A database of the SNP markers and a program for automatic allele calling and identification of map positions of mutants was also developed. The utility of the system was demonstrated by rapid mapping of 14 genes that disrupt embryonic muscle patterning. In Study III the tag-array minisequencing system was adapted to a lab-on-a-chip format for diagnostic testing for mutations in the TP53 gene. Freeze-drying was evaluated for storing reagents, including thermo-sensitive enzymes, on the microchip to reduce the complexity of the integrated test. Correct genotyping results were obtained using freeze-dried reagents in each reaction step of the genotyping protocol, both in test tubes and in single polymer test chambers. The results showed the potential of the approach to be implemented in fully integrated systems. The four-colour chemistry of SBE has been developed further to allow massively parallel sequencing (MPS) of short DNA fragments as in the Genome Analyzer system (Solexa/Illumina). In Study IV MPS was used to compare Nimblegen arrays and the SureSelect solution-based system for targeted enrichment of 56 continuous human candidate-gene regions totalling 3.1 Mb in size. Both methods detected known SNPs and discovered novel SNPs in the target regions, demonstrating the feasibility for complexity reduction of sequencing libraries by hybridization methods.

The key to the complexity of higher organisms lies not in the number of protein coding genes they carry, but rather in the intrinsic complexity of the gene regulatory networks. The major effectors of transcriptional regulation are proteins called transcription factors, and in this thesis four papers describing genome-wide studies of seven such factors are presented, together with studies on components of the chromatin and transcriptome. In Paper I, we optimized a large-scale in vivo method, ChIP-chip, to study protein – DNA interactions using microarrays. The metabolic-disease related transcription factors USF1, HNF4a and FOXA2 were studied in 1 % of the genome, and a surprising number of binding sites were found, mostly far from annotated genes. In Paper II, a novel sequencing based method, ChIP-seq, was applied to FOXA2, HNF4a and GABPa, allowing a true genome-wide view of binding sites. A large overlap between the datasets were seen, and molecular interactions were verified in vivo. Using a ChIP-seq specific motif discovery method, we identified both the expected motifs and several for co-localized transcription factors. In Paper III, we identified and studied a novel transcription factor, ZBED6, using the ChIP-seq method. Here, we went from one known binding site to several hundred sites throughout the mouse genome. Finally, in Paper IV, we studied the chromatin landscape by deep sequencing of nucleosomal DNA, and further used RNA-sequencing to quantify expression levels, and extended the knowledge about the binding profiles for the transcription factors NFY and TCF7L2.

In the past century, the scope of patentable objects has greatly expanded. Patents are now being granted on living organisms, human biological material and genes. What are the consequences of such practices for scientific research and health care? One of the fundamental philosophical questions behind this issue is the following: are we justified in patenting human genetic material? An examination of the traditional philosophical justification of intellectual property will allow us to critically explore whether or not this practice is ethically justifiable. It will be argued that the consequentialist justification of intellectual property requires, in this present case, that we modify the patent regimes in order to maximise social benefits and minimize public burdens.

Genome-wide association studies (GWAS)s provide an unbiased means of exploring the landscape of complex genetic disease. As such, these studies have identified genetic variants that are robustly associated with a multitude of conditions. I hypothesize that these genetic variants serve as excellent tools for evaluation of the genetic interface between epidemiologically related conditions. Herein, I test the association between SNPs associated with either (i) plasma lipids, (ii) rheumatoid arthritis (RA) or (iii) diabetes mellitus (DM) and late-onset Alzheimer’s disease (AD) to identify shared genetic variants. Regarding the most significantly AD-associated variants, I have also attempted to elucidate their molecular function. Only cholesterol-associated SNPs, as a group, are significantly associated with AD. This association remains after excluding APOE SNPs and suggests that peripheral and or central cholesterol metabolism contribute to AD risk. The general lack of association between RA-associated SNPs and AD is also significant in that these data challenge the hypothesis that genetic variants that increase risk of RA confer protection against AD. Functional studies of variants exhibiting novel associations with AD reveal that the lipid-associated SNP rs3846662 modulates HMGCR exon 13 splicing differentially in different cell types. Although less clear, trends were also observed between the RA-associated rs2837960 and the expression of several BACE2 isoforms, and between the DM-associated rs7804356 and expression of a rare SKAP2 isoform, respectively. In conclusion, the overlap of lipid-, RA- or DM-associated SNPs with AD is modest but in several instances significant. Continued analysis of the interface between GWAS of separate conditions will likely facilitate novel associations missed by conventional GWAS. Furthermore, the identification of functional variants associated with multiple conditions should provide insight into novel mechanisms of disease and may lead to the identification of new therapeutic targets in an era of personalized genomic medicine.

Recent Genome Wide Association Studies (GWAS) have identified a series of single nucleotide polymorphism (SNP)s that are associated with Alzheimer’s disease (AD). One of the SNPs, rs3851179 (G/A), is near the gene phosphatidylinositol-binding clathrin assembly protein (PICALM). To evaluate whether this SNP is associated with PICALM expression, we quantified PICALM mRNA in 56 brain cDNA samples. Using linear regression analysis, we analyzed PICALM expression relative to rs3851179, AD status, and cell type specific markers. An association was detected between rs3851179 and PICALM, microvessel mRNA, glial fibrillary acidic protein (GFAP) mRNA, and synaptophysin (SYN) mRNA. To gain clarity into other possible SNP mechanisms, we searched brain cDNA for PICALM splice variants. We identified several PICALM splice variants involving exons 13-19. To identify and gain an estimation of relative abundance of splice variants, we PCR-amplified across exons 13-20 in cDNA from six individuals, three rs3851179 GG individuals and three rs3851179 AA individuals. Sequencing the cloned isoforms we found that PICALM lacking exon 13 (delta 13) is the most abundant isoform. Other isoforms detected included deletion of exon 18-19. We targeted the latter part of the gene, exon 17-20, to investigate unequal allelic expression using next generation sequencing. Individuals heterozygous for rs76719109 (n= 35), located in exon 17, were used to study the abundance of G/T allele in cDNA and genomic DNA. When we analyzed the T:G allelic ratio, the variant lacking exons 18 and 19 showed unequal allelic expression (p-value < 0.001) in a subset of individuals. One individual was an outlier, showing overall unequal allelic expression, which maybe be harboring a rare mutation capable of modifying PICALM expression. The PICALM intronic SNP rs588076 was associated with delta 18-19 isoform splicing (p-value < 0.001). In conclusion, this study gained a greater insight into the role of AD genetics in PICALM expression and splicing.

Thesis (doctoral)--Göteborg University, 2005. / Includes bibliographical references (p. 438-449) and index.

Thesis (doctoral)--Göteborg University, 2005. / Includes bibliographical references (p. 438-449) and index.

Advances in high-throughput genomic technologies have facilitated the collection of DNA information for thousands of individuals, providing unprecedented opportunities to explore the genetic architecture of complex disease. One important finding has been that the majority of variants in the human genome are low in frequency or rare. It has been hypothesised that recent explosive growth of the human population afforded unexpectedly large amounts of rare variants with potentially deleterious effects, suggesting that rare variants may play a role in disease predisposition. But, importantly, rare variants embody a source of information through which we may learn more about our recent evolutionary history. In this thesis, I developed several statistical and computational methods to address problems associated with the analysis of rare variants and, foremost, to leverage the genealogical information they encode. First, one constraint in genome-wide association studies is that lower-frequency variants are not well captured by genotyping methods, but instead are predicted through imputation from a reference dataset. I developed the meta-imputation method to improve imputation accuracy by integrating genotype data from multiple, independent reference panels, which outperformed imputations from separate references in almost all comparisons (mean correlation with masked genotypes r²&GT;0.9). I further demonstrated in simulated case-control studies that meta-imputation increased the statistical power to identify low-frequency variants of intermediate or high penetrance by 2.2-3.6%. Second, rare variants are likely to have originated recently through mutation and thereby sit on relatively long haplotype regions identical by descent (IBD). I developed a method that exploits rare variants as identifiers for shared haplotype segments around which the breakpoints of recombination are detected using non-probabilistic approaches. In coalescent simulations, I show that such breakpoints can be inferred with high accuracy (r²&GT;0.99) around rare variants at frequencies &LT;0.05%, using either haplotype or genotype data. Third, I show that technical error poses a major problem for the analysis of whole-genome sequencing or genotyping data, particularly for alleles below 0.05% frequency (false positive rate, FPR=0.1). I therefore propose a novel approach to infer IBD segments using a Hidden Markov Model (HMM) which operates on genotype data alone. I incorporated an empirical error model constructed from error rates I estimated in publicly available sequencing and genotyping datasets. The HMM was robust in presence of error in simulated data (r²&GT;0.98) while nonprobabilistic methods failed (r²&LT;0.02). Lastly, the age of an allele (the time since its creation through mutation) may provide clues about demographic processes that resulted in its observed frequency. I present a novel method to estimate (rare) allele age based on the inferred shared haplotype structure of the sample. The method operates in a Bayesian framework to infer pairwise coalescent times from which the age is estimated using a composite posterior approach. I show in simulated data that coalescent time can be inferred with high accuracy (rank correlation &GT;0.91) which resulted in a likewise high accuracy for estimated age (&GT;0.94). When applied to data from the 1000 Genomes Project, I show that estimated age distributions were overall conform with frequency-dependent expectations under neutrality, but where patterns of low frequency and old age may hint at signatures of selection at certain sites. Thus, this method may prove useful in the analysis of large cohorts when linked to biomedical phenotype data.

Introdução: Com o melhor controle das causas ambientais, as doenças genéticas e as malformações congênitas cada vez mais ganham destaque como fatores morbidade e mortalidade, assim como cada vez mais se reconhece a importância da base genética para as doenças comuns. Desta forma, é necessário desenvolver estratégias de prevenção e controle destas condições, assim como acesso aos cuidados de saúde para pessoas com ou em risco de desenvolver uma doença genética. A integração da genética na Atenção Primária à Saúde (APS) parece ser uma alternativa para se desenvolver ações de prevenção e controle, assim como facilitar o acesso da comunidade aos cuidados de saúde com base no conhecimento sobre a genética. Para tanto, é necessário que os profissionais da APS tenham um conhecimento básico sobre genética, as principais condições, as formas de manejo e prevenção. Objetivo: Avaliar se a aplicação de um programa educativo de genética médica direcionado às equipes de APS pode contribuir para integrar conceitos e atitudes relacionados à identificação, ao manejo e à prevenção de malformações congênitas e doenças genéticas. Métodos: O programa foi planejado por profissionais do Serviço de Genética Médica do Hospital de Clínicas de Porto Alegre e aplicado em três Unidades Básicas de Saúde (UBS) do Serviço de Saúde Comunitária do Grupo Hospitalar Conceição. O programa foi constituído por encontros realizados nas próprias UBS com ênfase nos seguintes temas: conceitos básicos em genética, avaliação genética de famílias, teratógenos e prevenção de defeitos congênitos, genética da deficiência intelectual, erros inatos do metabolismo e triagem neonatal, oncogenética, genética das doenças crônicas comuns e aconselhamento genético e préconcepcional. Foi desenvolvido material de apoio para os participantes e material educativo para a comunidade. O programa foi avaliado através de pré e pós-teste, bem como um questionário de auto-avaliação aplicado aos profissionais da APS sobre o conhecimento e confiança em prover cuidados com bases genéticas aos pacientes e famílias. Além disso, foi aplicado um questionário sobre a relevância do programa para a prática clínica e a utilização dos recursos apresentados ou disponibilizados durante o programa. Resultados: Quarenta e três profissionais participaram do programa. Em duas das três UBS encontramos um aumento estatisticamente significativo no número de acertos do pós-teste quando comparado ao préteste. Durante o programa foram desenvolvidos materiais educativos para a comunidade (folders) e para os profissionais (Manual de Genética Médica para a Atenção Primária à Saúde). A maioria dos profissionais relatou um maior conhecimento e confiança após o programa, referiu que o programa influenciou a sua prática clínica e informou utilizar os recursos de informação apresentados e o material educativo elaborado durante o programa. Conclusão: O programa proporcionou uma aproximação da genética médica com a APS, fazendo com que os profissionais atentem para a genética como determinante de doenças na comunidade. Entretanto percebeu-se a necessidade de estratégias de educação continuada e suporte contínuo à APS, com o intuito de fortalecer a integração das duas especialidades, colocando-se em prática a genética comunitária. / Introduction: Genetic disease and birth defects are increasingly gaining prominence as factors morbidity and mortality, as well as it is increasingly recognized the importance of the genetic basis for common diseases. So, it is necessary to develop strategies for the prevention and control of these conditions, as well for the access to health care for people with or at risk of developing a genetic disease. On this way, it is necessary to develop strategies for prevention and control of these conditions, as well as to provide access to health care for people with or at risk of developing a genetic disease. The integration of Medical Genetics and Primary Health Care (PHC) seems to be an alternative to develop actions of prevention and control, and to facilitate community access to health care based on knowledge about genetics. Therefore, it is necessary that primary care professionals have a basic knowledge about genetics, the main conditions, management measures and prevention of genetics conditions. Aim: To evaluate if the application of an educational program in Medical Genetics directed to PHC teams can help to integrate concepts and attitudes related to the identification, management and prevention of congenital malformations and genetic diseases. Method: The program was designed by health professional of the Medical Genetics Service/Hospital de Clínicas de Porto Alegre and applied to three Basic Health Unitis (BHU) of Community Health Service/Grupo Hospitalar Conceição. The program consisted of meetings that took place at the BHU, which emphasis on the following topics: basic concepts in genetics; genetic evaluation of families; teratogenic agents and prevention of birth defects; genetics of mental retardation; inborn errors of metabolism and neonatal screening; cancer genetics; genetics of common chronic diseases; and genetic and preconception counseling. It was developed support materials for participants and educational material for the community. The program was evaluated through pre and post-test, as well through self-assessment questionnaire applied to the PHC professionals based on the knowledge and confidence in providing care with genetic basis to patients and families. In addition, a questionnaire was applied about the relevance of the program for clinical practice and use of the resources presented or made available during the program. Results: Forty three professionals participated in the program. In two of the three BHU it was found a statistically significant increase in the number of hits from the post-test compared to pre-test. Most professionals reported increased knowledge and confidence after the program, said that the program influenced their clinical practice and informed that the information resources and educational material presented during the program were useful. Conclusions: The program provided an approximation between Genetic Medicine and PHC, so that professionals pay attention to the genetic determinants of disease in the community. However it was realized the need for strategies for continuing education and ongoing support to the APS, with the aim of strengthening the integration of the two specialties, bringing to practice the community genetics.