Die Suche nach potentiellen Kandidatengenen für die Schizophrenie und die Bipolare Störung ist ein stark umforschtes Feld der modernen Psychiatrie. Das Fzd3-Gen findet sich auf dem Chromosom 8p21 und liegt auf einem Hotspot für Schizophrenien und bipolare Psychosen. Nach positiven, aber auch negativen Assoziationsanalysen für Einzelmarker und deren Haplotyp in asiatischen Populationen, untersuchten wir in einer Fall-Kontroll-Studie drei SNPs und deren Haplotyp bei 192 Patienten mit einer chronischen Schizophrenie, sowie bei 56 Patienten die an einer Bipolaren Störung litten. Als Vergleichsgruppe dienten 284 gesunde Blutspender. In vorliegender Studie ließen sich die Befunde der asiatischen Untersuchungen weder auf der Ebene der Einzelmarker, noch auf der Ebene der Haplotypen replizieren. / Polymorphisms in the human Fzd3 gene have been associated with schizophrenia and bipolar disease in several investigations in asian population. These findings could not be confirmed in following studies. After negative associations shown in a caucasian sample in the UK, we performed a case-control-study in a sample of 192 chronically ill schizophrenic and 56 bipolar subjects and 284 healthy controls in a German population. We tested 3 SNPs and their calculated haplotypes - we couldn't find any associations between Fzd3 and schizophrenia and bipolar disorder in our sample.

In den vergangenen Jahren wurde vermehrt das Gen, welches für Catechol-O-Methyltransferase codiert, als starker Kandidat für ein erhöhtes Schizophrenierisiko diskutiert. Grund dafür ist die zentrale Rolle der Catechol-O-Methyltransferase beim Katecholaminabbau im menschlichen präfrontalen Cortex. Aufgrund der zunehmend akzeptierten Tatsache, daß die singuläre Betrachtung einzelner Marker bei der komplexen genetischen Textur von Kandidatengenen nur wenig zur Erhellung komplexer Erkrankungen beizutragen vermag (Licinio, 2003), untersuchten wir neben dem Val108/158Met-Polymorphismus (rs4680) vier weitere, die COMT-Gen-Region umspannende SNPs (rs2097603, rs740603, rs4818, rs165599) an einer Stichprobe von 459 Schizophrenen und 150 Kontrollpersonen. Zwar ergab sich für den Marker rs740603 auf Intron 1 eine signifikante Allel- (p = 0.0060) und Genotypassoziation (p = 0.019), der funktionelle Val108/158Met-Polymorphismus (rs4680) zeigte aber keinen signifikanten Zusammenhang mit der Erkrankung. Zudem fand sich in unserer Haplotypanalyse keine Markerkombination, die in überdurchschnittlichem Zusammenhang mit schizophrenen Psychosen stand. Für die Untergruppe der zykloiden Psychosen ließ sich bei einem p-Wert von 0.031 eine 4-Marker-Kombination ermitteln, die die SNPs rs740603, rs4818, rs4680 und rs165599 einschliesst und die Region von Intron 1 bis 3´-UTR umspannt. Zusätzlich ergab sich in der Subgruppe der zykloiden Psychosen ein geschlechtsspezifischer Effekt im Sinne eines signifikanten 3-Marker-Haplotypen (rs4818-rs4680-rs165599) (p = .0044) in der Gruppe der Frauen (n = 27) mit rs165599 als stärkstem Einzelmarker. Aufgrund des komplexen genetischen Zusammenhangs zwischen den untersuchten Markern und der Erkrankung sollte auch in der zukünftigen Forschung eine differenzierte Betrachtung der verschiedenen schizophrenen Zustandsbilder angestrebt werden, wie dies die Klassifikation nach Leonhard ermöglicht. Neben gewebsspezifischen Transkriptionsfaktoren könnten auch epigenetische Faktoren, wie die Cytosinmethylierung von CpG-Stellen in promotorregulierenden Regionen, einen Erklärungsansatz für die Entstehung schizophrener Störungsbilder darstellen. / Since several years, the gene encoding catechol-O-methyltransferase (COMT) at chromosome 22q11 is discussed as a strong candidate for schizophrenia susceptibility due to its key function in degredation of catecholamines in the prefrontal cortex, a critical region of the human brain, involved in cognitive control processes, monitoring of information in working memory and in active judgments on information (Petrides, 2005). To test the association of the COMT gene locus with schizophrenia, we analysed five SNPs (rs2097603, rs740603, rs4818, rs4680, rs165599) spanning from the P2 promotor region (MB-COMT) to the 3´-UTR in 459 index cases, which fulfilled diagnistic criteria of schizophrenia according to DSM IV as well as 150 blood donors as population controls. According to differentiated psychopathology (Leonhard, 1999) probands were categorized into cycloid psychosis, unsystematic schizophrenia and systematic schizophrenia prior to genotyping. In intron 1 the marker rs740603 showed significant allele (p = 0.0060) and genotype (p = 0.019) association, but the functional Val105/158Met variant (rs4680) failed significant association with disease. Considering COMT haplotypes none of the marker combinations showed evidence for an association with schizophrenia. In the subgroup of cycloid psychosis we found 4-locus marker combinations rs740603-rs4818-rs4680-rs165599 associated with disease at p-level 0.031, spanning a region from intron 1 to the 3´-UTR. In conclusion, the genetic interaction of COMT SNPs and haplotypes and schizophrenia susceptibility appears complex across different populations and psychopathological phenotypes. Particularly structures potentially involved in mRNA expression levels need further scrutiny.

Arisen from the Pure Parsimony Haplotyping problem in the bioinformatics, we developed the Minimum Rainbow Subgraph problem (MRS problem): Given a graph $G$, whose edges are coloured with $p$ colours. Find a subgraph $F\\\\subseteq G$ of $G$ of minimum order and with $p$ edges such that each colour occurs exactly once. We proved that this problem is NP-hard, and even APX-hard. Furthermore, we stated upper and lower bounds on the order of such minimum rainbow subgraphs. Several polynomial-time approximation algorithms concerning their approximation ratio and complexity were discussed. Therefore, we used Greedy approaches, or introduced the local colour density $\\\\lcd(T,S)$, giving a ratio on the number of colours and the number of vertices between two subgraphs $S,T\\\\subseteq G$ of $G$. Also, we took a closer look at graphs corresponding to the original haplotyping problem and discussed their special structure.

Goal of this Thesis is the comparison of the Grayling˘s genetic diversity. The complete mitochondrial DNA (mtDNA) control region (1083 base pairs) and gene for cytochrom B (1076 base pairs) were sequenced in 147 European grayling (Thymallus thymallus), from 21 populations in Czech Republic, Slovakia and Bosnia. In samples, 17 haplotypes were detected with average haplotype diversity Hd = 0,5480 and genic differentiation (FST) from 0,001 to the 0.9341. The most common haplotype TH1 was detected in 92 samples. An inferred intraspecific phylogenetic tree revealed three well-separated clades. One clade was represented by Danubian haplotypes from Slovakia. Second highly divergent clade contained individuals from river Vrbas in Bosnia, and the last biggest clade included haplotypes of all three sea basins from Czech Republic. We suppose that the gained results will be later utilized to the choice of suitable conservation measures that will lead to stabilization of the state of ancestral population of this ever more rare species in our region.

Genetic causes of medullary thyroid carcinoma and Hirschsprung's disease Abstract Medullary thyroid carcinoma (MTC) and Hirschsprung's disease (HSCR) are classified as simple neurocristopathies, i.e. diseases linked to neural crest-derived cells. MTC is derived from parafollicular cells of the thyroid and HSCR is characterized by absence of enteric ganglia in the gastrointestinal tract. The RET proto-oncogene is only expressed in neural crest-derived cells, including parafollicular cells and enteric neurons. The RET encodes a transmembrane tyrosinekinase receptor that plays an important role during proliferation, differentiation and cell survival, and activates many signaling pathways. If the strictly regulated activation fails, e.g. due to mutations in the specific gene locations, the RET becomes a highly effective oncogene. Activating germline mutations in the RET proto- oncogene lead to hereditary forms of MTC, whereas sporadic forms of MTC are caused by somatic mutations in the tumor tissue. On the contrary, inactivating mutations induce migration failure of ganglion cell precursors during the development of enteric nervous system and result in the development of HSCR. In rare cases, the coexistence of both diseases is caused by mutations with a dual gain-of-function and loss-of-function character....

Melampyrum nemorosum agg. is very complicated group of hemiparasitic plants. According to the traditional concept, 15 species is distinguished. Recent molecular analyses show a need of critical taxonomic revision of group and a potential importance of ancient hybridization. Analysis of 3 regions of cpDNA (trnTUGU-trnLUAA, psbA-trnHGUG, rpl32-trnLUAG) and 2 regions of nuclear DNA (Agt1 and At103) reveals well supported lineage with limited geographical distribution. Morphology and genome size of genetically supported lineages were compared.

Melampyrum nemorosum agg. is very complicated group of hemiparasitic plants. According to the traditional concept, 15 species is distinguished. Recent molecular analyses show a need of critical taxonomic revision of group and a potential importance of ancient hybridization. Analysis of 3 regions of cpDNA (trnTUGU-trnLUAA, psbA-trnHGUG, rpl32-trnLUAG) and 2 regions of nuclear DNA (Agt1 and At103) reveals well supported lineage with limited geographical distribution. Morphology and genome size of genetically supported lineages were compared.

Arisen from the Pure Parsimony Haplotyping problem in the bioinformatics, we developed the Minimum Rainbow Subgraph problem (MRS problem): Given a graph $G$, whose edges are coloured with $p$ colours. Find a subgraph $F\\\\subseteq G$ of $G$ of minimum order and with $p$ edges such that each colour occurs exactly once. We proved that this problem is NP-hard, and even APX-hard. Furthermore, we stated upper and lower bounds on the order of such minimum rainbow subgraphs. Several polynomial-time approximation algorithms concerning their approximation ratio and complexity were discussed. Therefore, we used Greedy approaches, or introduced the local colour density $\\\\lcd(T,S)$, giving a ratio on the number of colours and the number of vertices between two subgraphs $S,T\\\\subseteq G$ of $G$. Also, we took a closer look at graphs corresponding to the original haplotyping problem and discussed their special structure.:Mathematics and biology - having nothing in common? I. Going for a start 1. Introducing haplotyping 2. Becoming mathematical II. The MRS problem 3. The graph theoretical point of view 3.1. The MRS problem 3.2. The MRS problem on special graph classes 4. Trying to be not that bad 4.1. Greedy approaches 4.2. The local colour density 4.3. MaxNewColour 5. What is real data telling us? And the work goes on and on Bibliography

Die räumliche Organisation des Chromatins im Zellkern ist für die Regulierung der Genexpression von großer Bedeutung. Genomische Varianten können die räumliche Organisation jedoch stören und Fehlbildungen und Krankheiten verursachen. In diploiden Genomen sind die meisten genomischen Varianten heterozygot und beeinflussen hauptsächlich das homologe Chromosom, auf dem sie sich befinden. Daher ist eine allelspezifische Analyse wichtig, erweist sich aber mit aktuellen Methoden zur Erfassung der Chromatinkonformation als äußerst schwierig. Erstens ist der Haplotyp, der die Verteilung unterschiedlicher Allele über die homologen Chromosomen beschreibt, oft unbekannt. Zweitens ist, insbesondere in Genomen mit geringer Variantendichte, wie dem menschlichen Genom, eine eindeutige Zuordnung der sequenzierten Genomabschnitte (Reads) zu ihrem Ursprungschromosom häufig nicht möglich, was die Erstellung haplotypspezifischer Chromatinkontaktmatrizen von guter Qualität verhindert. Genome Architecture Mapping (GAM) ist eine vielversprechende neue Methode mit dem Potential zur haplotypspezifischen Analyse der Chromatinkonformation. In dieser Dissertation zeige ich zunächst, dass GAM-Daten wertvolle Haplotypinformationen enthalten. Dann stelle ich GAMIBHEAR vor, einen graphenbasierten Ansatz, der die von GAM-Daten abgeleiteten Phaseninformationen nutzt, um genaue und vollständige Haplotypen zu rekonstruieren. Schließlich stelle ich Co-Phasing vor, eine neue Read-Phasing-Strategie, die erstmalig die eindeutige Zuordnung von variantenfreien Reads zu ihrem homologen Ursprungschromosom ermöglicht und somit auch die Erstellung detaillierter haplotypspezifischer Chromatinkontaktmatrizen in Maus und Mensch. Im Gegensatz zu früheren Erkenntnissen belegen meine Ergebnisse große Unterschiede in der räumlichen Organisation homologer Chromosomenkopien und ermöglichen erstmals einen sehr detaillierten Einblick in die haplotypspezifische Chromatinkonformation des menschlichen Genoms. / The spatial organization of chromatin in the nucleus plays an essential role in precise gene expression. Genomic variants can disrupt this spatial organization, potentially causing malformations and diseases. In diploid genomes, most genomic variants are heterozygous and mainly influence the homologous chromosome they reside on. Studying the effects of these variants in an allele-specific manner is crucial but has proven challenging using current state-of-the-art techniques. First, the haplotype describing the distribution of variant alleles over the homologous chromosomes is often unknown. Second, especially in genomes with a low variant density, such as the human genome, most sequencing reads map to genomic regions that are identical between homologous chromosomes, making it difficult to determine their origin. Thus, the read-phasing efficiency is insufficient to generate haplotype-specific chromatin contact matrices of good quality. Genome Architecture Mapping (GAM) is a promising new method for haplotype-specific analysis of chromatin conformation. In this thesis, I first demonstrate the ability of GAM data to provide valuable haplotype information. Then, I introduce GAMIBHEAR, a graph-based approach that leverages the GAM-derived phase information to infer accurate and complete haplotypes. Finally, building on GAMIBHEAR, I present Co-Phasing, a novel read-phasing strategy that allows for the unique assignment of variant-free reads to their homologous chromosome of origin and thus enables the creation of detailed haplotype-specific chromatin contact matrices in mouse and human. In contrast to previous findings, my results show significant differences in the spatial organization of homologous chromosomes and provide the first detailed view of haplotype-specific chromatin conformation in the human genome.

Bisherige Methoden der Haplotyp-Block-Definition zielen entweder auf abwesende Rekombinationsereignisse oder eine effiziente Beschreibung genomischer Variation. Die vorliegende Arbeit definiert Blöcke von Single Nucleotide Polymorphisms (SNP) als Gebiete erhöhten Kopplungsungleichgewichtes (LD). Für dieses Ziel wird ein neues, entropie-basiertes Maß für LD zwischen multiplen Markern/Loci (Normalized Entropy Difference) entwickelt und als eine Multilocus-Erweiterung des paarweisen Maßes r2 charakterisiert. Ein zugehöriger Algorithmus für die Block-Definition wird vorgeschlagen. Seine Evaluierung an einem Datensatz des menschlichen Chromosoms 12 vom Internationalen Haplotype Map Projekt zeigt die Nützlichkeit der abgeleiteten Blöcke in Hinblick auf verschiedene Eigenschaften, einschließlich ihrer chromosomalen Coverage und der Anzahl sowie des Anteils der häufigen Block-Haplotypen. Der wesentliche Einfluß der SNP-Dichte auf die zu entdeckenden LD- und Blockstrukturen wird demonstriert. Der Erfolg von Assoziationsstudien in komplexen Erkrankungen mit Block-Haplotypen als multiallelischen Markern wird davon abhängen, ob die Common Variants/Common Diseases (CV/CD) Hypothese für solche Erkrankungen erfüllt ist. / Current approaches to haplotype block definition target either absent recombination events or the efficient description of genomic variation. This thesis aims to define blocks of single nucleotide polymorphisms (SNP) as areas of elevated linkage disequilibrium (LD). To this end, a new entropy-based measure for LD between multiple markers/loci, the Normalized Entropy Difference, is developed and is characterized as a multilocus extension of the pairwise measure r2. A corresponding algorithm for the block definition is proposed. Its evaluation on a data set of human chromosome 12 from the International Haplotype Map project proves the usefulness of the derived blocks with respect to several features, including their chromosomal coverage and the number and portion of common block haplotypes. The critical role of the SNP density for detectable LD and block structure is demonstrated. The success of association studies in common diseases with block haplotypes serving as multi-allelic markers will depend on whether the Common Variants/Common Diseases (CV/CD) hypothesis holds true for those diseases.