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Blissett Bookbindt 020 8992 3965 Linkage Analysis of Mendelian Forms of Complex Disorders in a South American Population By Nicolas Guillermo Pineda-Trujillo Submitted for the degree of Doctor of Philosophy University College London, UCL September 2005 The Galton Laboratory Wolfson House 4 Stephenson Way London NW1 2HE UMI Number: U593114 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. Dissertation Publishing UMI U593114 Published by ProQuest LLC 2013. Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 To my Mother and to the memory o f my Father, who passed away during the time I was in London doing my PhD. ACKNOWLEDGMENTS I am very grateful to my supervisors, Andres and Dallas, for all the help, patience and support they gave to me during these three years. I, sometimes, did not have anyone else to tell about my worry than themselves, and always found support and relief in their words. Special thanks to Andres, for keeping on supporting me since we met in Colombia (1996), whilst I was still an undergraduate. My career owes much to you. Special thanks to Dallas for her patience with this “naughty boy”. I have learned loads from you. I also would like to thank my collaborators and friends in Colombia, specially Doctors Comejo, Lopera, Carrizosa and Sonia Moreno. I enjoy working with you all and appreciate your friendship. Thanks also to my colleagues in the Galton lab. Special thanks to Danny, for the moments of laughter and those “quick drinks”. Thanks to Ibi for helping me with my English, to Sijia for your friendship and interesting conversations; to Barbara, Coni, Ning Ning, Winston, James (Ibi’s husband), Luis and Lupe. Thanks guys for everything. Special thanks also to Fabrice, Ian Evans and Jacques Gianino. I can not finish without mentioning the immense support given to me by Kevin Fowler, the postgraduate coordinator in Biology. Thanks very much. Special thanks to Katherine Montague for proof reading some chapters of this thesis. You offered me your help and it will never be forgotten. God bless you. Thanks to COLCIENCIAS for funding me during this journey. Linkage Analysis of Mendelian forms of Complex Disorders in a South American Population Abstract Genetic analysis in Mendelian forms of complex disorders may help increase our understanding of the biology of these disorders. Genes identified in Mendelian forms could also be relevant for disease susceptibility of the more common forms of the disease. I have studied a collection of patient samples from Antioquia, Colombia, including Mendelian and sporadic forms of four well characterized diseases: Parkinson’s [PD], Generalized epilepsy with Febrile Seizures Plus [GEFS+], Batten’s disease and Type 1 Diabetes [T1D]. In addition, I studied two extended families with unusual disorders. Affected individuals in one family presented with episodic crisis of abdominal pain, possibly corresponding to Abdominal Epilepsy [AE]. Patients from the other family presented with a multiform movement disorder [MMD], at times diagnosed as Parkinson’s or Huntington’s disease. Brain pathology from an affected individual showed the presence of iron deposits as a key finding. I subsequently performed linkage analysis of these families. Initial analysis focused on testing linkage to known candidate genes or regions. If these proved negative or if no candidate gene/region was available, a genome scan was then conducted. I have excluded all previously known genes/loci in two out of six families with GEFS+. The remaining four families were found linked to either SCN1A or GABRG2 genes. In a family with Parkinson disease, a novel mutation was identified in exon 3 of the PARK2 gene. It was not possible to establish whether a common chromosome was involved in the same mutation reported separately by both a Spanish group and we since those mutant chromosomes are presenting a very different haplotype in both populations. In Batten disease, the first mutation in CLN5 gene outside Europe was found, which leads to a variant of the juvenile form rather than to a late infantile presentation of Neuronal Ceroid Lipofuscinosis. For TID, a haplotype on chromosome 2 was found to be segregating with the disease in a large family with autoimmune T1D. Regarding the two genome wide scans, in MMD, suggestion of linkage to two functionally candidate genes was found. These are the Neurogolobin (NGB) and the Ferritin heavy polypeptide (FTH1) genes. In Abdominal epilepsy, a locus was identified on chromosome 8 and fine mapping led to the identification of a critical region extending 1.3 Mb at 8ql3. LINKAGE ANALYSIS OF MENDELIAN FORMS OF COMPLEX DISORDERS IN A SOUTH AMERICAN POPULATION TABLE OF CONTENTS Dedication Acknowledgements ABSTRACT List of Tables ............................................................................................................. XII List of Figures ............................................................................................................ XIV CHAPTER ONE INTRODUCTION................................................................................................................ 1 1. Gene mapping of complex traits ..................................................................................... 3 2. Linkage analysis in Mendelian traits ..............................................................................4 2.1 The beginning of a positional cloning study ........................................................... 4 2.2 The first successes of positional cloning ..................................................................5 2.3 Simple inheritance .....................................................................................................6 2.4 Homozygosity mapping ............................................................................................6 3. Genetic Markers................................................................................................................7 4. Databases for genes identified ..................................................................................................8 4.1 Disease associated genes ........................................................................................... 8 4.2 Type and frequency of mutations , ............................................................... 8 5. Isolate populations ............................................................................................................9 6. Antioquia (Colombia) .....................................................................................................10 7. Aims................................................................................................................................. 13 Specific aim s ...............................................................................................................13 V CHAPTER TWO METHODS......................................................................................................................... 14 1. Methods of analysis, Basic Principles and implementation ..........................................15 1.1 Linkage Analysis ......................................................................................................15 1.2 Power simulations ...................................................................................................