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Next Generation Sequencing in Human Diseases Unicentre CH-1015 Lausanne http://serval.unil.ch RYear : 2016 NEXT GENERATION SEQUENCING IN HUMAN DISEASES Royer-Bertrand Béryl Royer-Bertrand Béryl, 2016, NEXT GENERATION SEQUENCING IN HUMAN DISEASES Originally published at : Thesis, University of Lausanne Posted at the University of Lausanne Open Archive http://serval.unil.ch Document URN : urn:nbn:ch:serval-BIB_4CE29719D9DB2 Droits d’auteur L'Université de Lausanne attire expressément l'attention des utilisateurs sur le fait que tous les documents publiés dans l'Archive SERVAL sont protégés par le droit d'auteur, conformément à la loi fédérale sur le droit d'auteur et les droits voisins (LDA). A ce titre, il est indispensable d'obtenir le consentement préalable de l'auteur et/ou de l’éditeur avant toute utilisation d'une oeuvre ou d'une partie d'une oeuvre ne relevant pas d'une utilisation à des fins personnelles au sens de la LDA (art. 19, al. 1 lettre a). A défaut, tout contrevenant s'expose aux sanctions prévues par cette loi. Nous déclinons toute responsabilité en la matière. Copyright The University of Lausanne expressly draws the attention of users to the fact that all documents published in the SERVAL Archive are protected by copyright in accordance with federal law on copyright and similar rights (LDA). Accordingly it is indispensable to obtain prior consent from the author and/or publisher before any use of a work or part of a work for purposes other than personal use within the meaning of LDA (art. 19, para. 1 letter a). Failure to do so will expose offenders to the sanctions laid down by this law. We accept no liability in this respect. Département de Biologie Computationnelle NEXT GENERATION SEQUENCING IN HUMAN DISEASES Thèse de doctorat ès sciences de la vie (PhD) présentée à la Faculté de biologie et de médecine de l’Université de Lausanne par Béryl ROYER-BERTRAND Ingénieur en Biosciences de l’INSA, Lyon, France Jury Prof. Barbara Wildhaber, Président Dr. Carlo Rivolta, Directeur de thèse Dr. Patrick Descombe, Expert Dr. Pascal Escher, Expert Lausanne 2016 2 Table of Content Table of Content .................................................................................................................................................. 3 Acknowledgements ............................................................................................................................................ 4 Summary ................................................................................................................................................................ 5 Résumé .................................................................................................................................................................... 6 1 General introduction ................................................................................................................................. 7 1.1 Human diseases with a genetic origin ....................................................................................... 8 1.1.1 Introduction to ocular melanomas .................................................................................. 12 1.1.2 Introduction to Mendelian diseases ............................................................................... 14 1.2 Next-generation sequencing ....................................................................................................... 16 1.2.1 Current usage of NGS ............................................................................................................. 16 1.2.2 NGS technology used during the thesis ......................................................................... 18 1.3 Development of bioinformatics pipelines for genetic diseases ................................... 21 1.3.1 Bioinformatics for Cancer analysis ................................................................................. 23 1.3.2 Bioinformatics in Mendelian diseases ........................................................................... 23 1.4 Aim of this thesis ............................................................................................................................. 29 2 Results ........................................................................................................................................................... 31 2.1 Overview of NGS analysis of human diseases ..................................................................... 32 2.2 Ocular Melanomas ........................................................................................................................... 32 2.3 Rare inherited Mendelian disorders ....................................................................................... 33 3 Discussion ................................................................................................................................................... 37 4 Bibliography ............................................................................................................................................... 45 5 Articles (main contributor) ................................................................................................................. 51 5.1 Overview of NGS analysis of human diseases ..................................................................... 52 5.2 Ocular Melanomas ........................................................................................................................... 62 5.2.1 Conjunctival Melanoma ........................................................................................................ 62 5.2.2 Uveal Melanoma ...................................................................................................................... 65 5.3 Rare inherited Mendelian disorders ....................................................................................... 75 5.3.1 HSPA9 .......................................................................................................................................... 75 6 Appendix ...................................................................................................................................................... 85 6.1 NANS ..................................................................................................................................................... 86 6.2 ASAH1 ................................................................................................................................................... 98 6.3 NBAS ................................................................................................................................................... 104 6.4 CEP78 ................................................................................................................................................. 116 6.5 TTLL5 ................................................................................................................................................. 124 3 Acknowledgements Foremost, I would like to thank my thesis supervisor, Dr. Carlo Rivolta, for giving me the possibility to join his group, for his useful comments and suggestions throughout the Ph.D. I also would like to acknowledge Dr. Alexandre Moulin and Prof. Andrea Superti- Furga for their guidance. I would like to thank all the DGM/DBC members for their advice during the whole doctorate and the creation of this thesis. A special thank goes to Nicola Bedoni, who has always been present since the beginning of the thesis, as well as Katarina Cisarova and Mathieu Quinodoz for their patience, their fun and support. I am grateful to all my friends, colleagues and members of ADAS but especially to Nada and Anaïs for always being close no matter how far we were. Finally, the biggest and warmest thank you goes to my parents and my family, who always believed in me and supported me throughout my entire studies and all my decisions. In particular, I want to thank Aurélien, who always helped me through every crisis and has been the most patient listener, great adviser and best friend (and much more). 4 Summary Over the past years, Next-Generation Sequencing (NGS) has become an effective and accurate tool for the detection of potential causes and for the better understanding of human genetic diseases. Here, I applied bioinformatics analysis of NGS data to shed new light on the biology of two very different types of diseases, ocular melanomas and Mendelian diseases. For each patient, we sequenced either the coding regions of the genes, by means of Whole-Exome Sequencing (WES), or the full genome, by means of Whole-Genome Sequencing (WGS), this latter giving more complete and more diverse genetics alterations, compared to WES. In the first part, I exploit the WGS data to understand the genetic causes of two subtypes of ocular melanomas, Uveal Melanoma (UM) and Conjunctival Melanoma (CM), both characterized by an overall high rate of metastatic transformation and mortality. Via the full genome sequencing of 2 patients with CM, we highlighted the presence of a high number of somatic mutations with a majority of cytosine to tyrosine (C>T) substitutions, specifically found at the 3’ end of pyrimidine dinucleotide. They are classical features of UV light mutational signature. From a cohort of 34 patients with UM, we determined the genomic landscape of UM, which is very distinct from CM. More specifically, we detailed four classes of UM, depending on specific genetic alterations, corresponding to large copy number variants and mutations in
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