Algorithms for analyzing complex structural variations in cancer genomes

Analysis of somatic alterations in cancer genomes has been accelerated through the rapid growth of the quantity, quality and depth of data generated by next-generation sequencing (NGS). Previously most of cancer genome studies were focusing on single nucleotide variations (SNVs), small insertions and deletions (INDELs), or somatic copy number alterations (SCNAs). Recently, there is a paradigm shift in the cancer genome study that more efforts have been devoted to characterizing large scale structural variations (SVs) in various cancer genomes. However, there are still pressing needs for designing specific computational algorithms to tackle the challenges caused by the complexity of cancer genomes. The first part of my thesis is developing a novel computational method called Weaver, which takes whole genome sequencing (WGS) alignment as core input and generates a precise rearrangement map for cancer genomes. Weaver identifies SVs with base-pair resolution and applies a probabilistic graphical model to simultaneously quantify allele specific copy number of SVs (ASCNS) and genomic regions (ASCNG). Through evaluation on simulated datasets with different parameter settings, Weaver was demonstrated to be highly accurate and be able to significantly refine the analysis of complex cancer genomes. The second part of this study is applying Weaver on two widely used cancer cell lines: MCF-7 and HeLa. For both cell lines, we generated base-pair resolution ASCNS and ASCNG for the first time. The detailed characterization of genomes for MCF-7 and HeLa may serve as valuable resource for future studies based on these two cell lines, by replacing reference genome with cancer specific genomes. We have found that allele specific expression can be explained by the profiled ASCNG for both cell lines. We have also discovered that a large portion of promoter-promoter interactions, detected by ChIA-PET, are found to be formed by distal genomic regions linked to be adjacent by somatic translocations in MCF-7 genome, showing that phased SVs analysis by Weaver has enabled the analysis of interaction between genomic rearrangements and long-range gene regulation at much broader scale. The last part of this thesis is applying Weaver on large-scale primary tumor data, com- posed by 600 TGCA WGS samples. To our knowledge, this is the largest whole genome SV and base-pair resolution ASCNG analysis for primary cancer genomes to date. We analyzed two mechanisms, breakage-fusion-bridge (BFB) and tandem duplication (TD), for recurrent focal amplifications and found different frequently focal amplified regions have different enrichment of specific tumor types. We proposed a new pan-cancer classification method, for the first time utilizing SV pattern, that categorizes 600 TCGA samples across 17 tumor types into five subtypes with potential clinical relevance. Our pan-cancer classification has the potential of prognostic assessment for future patients regardless of their tumor types. In order to gain knowledge on the landscape of cancer genome structural alterations, in this thesis, we developed an algorithm which handles WGS data and specifically tackles the complexity in aneuploid cancer genomes. The integrative method combining the analysis of SVs and SCNAs enabled novel findings when applied on cancer cell lines and primary tumors

Genome structure and pathogenicity of the fungal wheat pathogen Mycosphaerella graminicola

The phytopathogenic fungus Mycosphaerella graminicola (Fuckel) J. Schröt. in Cohn (asexual stage: Zymoseptoria tritici (Desm.) Quaedvlieg & Crous) causes septoria tritici leaf blotch (STB) in wheat and is one of the most important diseases of this crop worldwide. However, STB control, mainly based on the use of resistant cultivars and fungicides, is significantly hampered by the limited understanding of the genetic and biochemical bases of pathogenicity, and mechanisms of infection and resistance in the host. M. graminicola has a very active sexual cycle under field conditions, which is an important driver of STB epidemics. Moreover, it results in high genetic diversity of field populations that causes a major challenge for the development and sustainable management of resistant cultivars and the discovery of new antifungal compounds. Understanding the role of the sexual and asexual life cycles on genome composition of this versatile pathogen and its infection strategy is crucial in order to develop novel control methods. Chapter 1 is an introduction to the biology and pathogenicity of M. graminicola. In addition, it shortly describes the impact of improved and novel technologies on the speed, scope and scale of comparative genomics research. Chapter 2 provides detailed genetic analyses of two M. graminicola mapping populations, using mainly DArT markers, and the analysis of the meiotic transmission of unequal chromosome numbers. Polymorphisms in chromosome length and number were frequently observed in progeny isolates, of which 15–20% lacked one or more chromosomes despite their presence in one or both parents, but these had no apparent effect on sexual and pathogenic fitness. M. graminicola has up to eight so called dispensable chromosomes that can be easily lost - collectively called the dispensome - which is, so far, the highest number of dispensable chromosomes reported in filamentous fungi. They represent small-sized chromosomes and make up 38% of the chromosome complement of this pathogen. Much of the observed genome plasticity is generated during meiosis and could explain the high adaptability of M. graminicola in the field. The generated linkage map was crucial for finishing the M. graminicola genome sequence. Chapter 3 describes the M. graminicola genome sequence with highlights on genome structure and organization including the eight dispensable chromosomes. The genome comprises a core set of 13 chromosomes and a dispensome, consisting of eight chromosomes that are distinct from the core chromosomes in structure, gene and repeat content. The dispensome contains a higher frequency of transposons and the genes have a different codon use. Most of the genes present one the dispensome are also present on the core chromosomes but little synteny is observed neither between the M. graminicola dispensome and the core chromosomes nor with the chromosomes of other related Dothideomycetes. The dispensome likely originates from ancient horizontal transfer(s) from (an) unknown donor(s). Chapter 4 shows a global analysis of proteins secreted by M. graminicola in apoplastic fluids during infection. It focuses mainly on fungal proteins secreted in a compatible interaction. The study showed that many of the annotated secreted proteins have putative functions in fungal pathogenicity, such as cell wall degrading enzymes and proteases, but the function of a substantial number of the identified proteins is unknown. During compatible interactions proteins are primarily secreted during the later stages. However, many pathogenesis-related host proteins, such as PR-2, PR-3 and PR-9, accumulated earlier and at higher concentrations during incompatible interactions, indicating that fungal effectors are recognized by resistant plants and trigger resistant gene-mediated defence responses, though without a visible hypersensitive response. Chapter 5 further details the initial identification and characterization of necrosis-inducing proteins that are produced in culture filtrates (CFs) of M. graminicola. The necrosis-inducing activity of CFs is light dependent and inactivated by proteinase K and heat treatment (100C). This is reminiscent of the necrosis-inducing properties of host selective toxins of other Dothideomycete pathogens such as Stagonospora nodorum and Pyrenophora tritici-repentis. Subsequent purifications of CFs and mass spectrometry identified several candidate proteins with necrosis-inducing activity. Heterologous expression of the two most prominent proteins in Pichia pastoris produced sufficient quantities for infiltration assays in a panel of wheat cultivars that showed differential responses, suggesting specific recognition. Chapter 6 provides a general discussion of the thesis and puts the results obtained in a broader perspective with a focus on the genome structure of M. graminicola and its function. In addition, aspects of the hemi-biotrophic lifestyle, the relevance of secreted proteins for the wheat-M. graminicola pathosystem in relation to gene-for-gene models and the potential implications for resistance breeding strategies are discussed. </p

The Genetic and Epigenetic Basis Involved in the Pathophysiology of ASD: Therapeutic Implications

The prevalence of autism has increased in an exponential way in the past few years. Many monogenetic mutations as well as copy number variants and single nucleotide polymorphisms have been associated with autism spectrum disorders (ASD), a large proportion of which occur in genes associated with synaptogenesis and synaptic function. However, the increase in appearance of genetic alterations does not explain the etiology of an elevated number of ASD cases. Recent research is now focusing on the role of environmental/epigenetic factors, which by themselves and/or in combination with classical genetic factors, may be the root cause of a large number of ASDs. In this chapter we review the current literature regarding the epigenetic changes involved in ASD, including their possible mechanisms of action such as oxidative stress, altered fatty acid metabolism, mitochondrial dysfunction, DNA methylation and histone methylation (via the one‐carbon metabolism cycle), histone variants, and ATP‐dependent chromatin remodeling. We discuss possible new biochemical markers related to autism as well as new lines of research for therapeutic targets

Abstracts from the 50th European Society of Human Genetics Conference: Posters

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A New Multiple-Distribution GAN Model to Solve Complexity in End-to-End Chromosome Karyotyping

With significant development of Internet of medical things (IoMT) and cloud-fog-edge computing, medical industry is now involving medical big data to improve quality of service in patient care. Karyotyping refers classifying human chromosomes. However, performing karyotyping task generally requires domain expertise in cytogenetics, long-period experience for high accuracy, and considerable manual efforts. An end-to-end chromosome karyotype analysis system is proposed over medical big data to automatically and accurately perform chromosome related tasks of detection, segmentation, and classification. Facing image data generated and collected by means of edge computing, we firstly utilize visual feature to generate chromosome candidates with Extremal Regions (ER) technology. Due to severe occlusion and cross overlapping, we utilize ring radius transform to cluster pixels with same property to approximate chromosome shapes. To solve the problem of unbalanced and small dataset by covering diverse data patterns, we proposed multidistributed generated advertising network (MD-GAN) to perform data enhancement by generating additional training samples. Afterwards, we fine-tune CNN for chromosome classification task by involving generated and sufficient training images. Through experiments in self-collected datasets, the proposed method achieves high accuracy in tasks of chromosome detection, segmentation, and classification. Moreover, experimental results prove that MD-GAN-based data enhancement contributes to classification results of CNN to a certain extent