Investigating the Genetic Influences of the Germline and Somatic Genomes in Three Subtypes of Lung Cancer By Timothy Daniel O’Brien Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Human Genetics May 31, 2017 Nashville, Tennessee Approved: Zhongming Zhao, Ph.D. Melinda Aldrich, Ph.D. Tony Capra, Ph.D. Jirong Long, Ph.D. Nancy Cox, Ph.D. David Samuels, Ph.D. Copyright © 2017 by Timothy Daniel O’Brien All Rights Reserved ii To my parents, Dan and Bernie, for their unending support and who have always encouraged me to follow my dreams and To my wife, Barbara, who has always supported me in everything I do. iii ACKNOWLEDGMENTS The work in this dissertation would not have been possible without the support from the Human Genetics Training Grant provided by the National Institute of General Medical Sciences Training Grant (T32GM080178) and the National Institutes of Health grant (R01LM011177). Additionally, support was provided by the LUNGevity Foundation and Upstate Lung Cancer for the work done in Chapter IV. I would also like to acknowledge my outside collaborators for their contributions to this dissertation. William Pao and Hailing Jin from Vanderbilt and Uma Saxena, Martin J. Aryee, Mari Mino-Kenudson, Jeffrey A. Engelman, Long P. Le, A. John Iafrate, and Rebecca S. Heist from Massachusetts General Hospital for their work on Chapter IV. Also, my collaborator Maria T. Landi from the National Cancer Institute for her support on Chapter II. Finally, Pierre Massion from Vanderbilt for his support on Chapter III. Also, many members of the Zhao lab for all of their contributions to this dissertation. I would also like to thank members of my dissertation committee: David Samuels (chair), Melinda Aldrich, Tony Capra, Jirong Long, Nancy Cox, and Zhongming Zhao. I have really been inspired by this group of great scientists. My thesis project, and my scientific thinking in general, have been greatly improved from each meeting. I thank David Samuels for being a great dissertation chair and always having an open door when I needed any help. Special thanks for Tony Capra and his lab for welcoming me over the last year. I really appreciate the friendship and support from the entire lab. Also, Melinda Aldrich, her lab, and members of the TREAT group at Vanderbilt for their feedback on my work and giving me the opportunity to see lung cancer from a different perspective. iv Additional thanks to members of the Zhao lab past and present. Their help in technical skills and scientific thinking have helped me in my entire graduate career. Especially lab members: Junfeng Xia, Huy Vuong, Pora Kim, Qingguo Wang, Feixiong Cheng, Junfei Zhao, Ramkrishna (Santu) Mitra, Quan Wang, Mingyu Shao, and Peilin Jia for all their help with analyses in the lab. I especially would like to thank Peilin Jia. From the first day of my rotation she has helped me in many ways. From teaching me how to be a computational scientist to thinking critically and scientifically, she has greatly helped me as a scientist and has been a great mentor. I would also like to especially thank my mentor Zhongming Zhao. He has really helped me grow as a scientist and has been a great mentor. He has taught me about scientific writing, critical thinking, and many other skills required of a scientist. He has always had the time to help with any problems and was always available for discussion. I would like to thank members of the CHGR/VGI and the students of the HGEN program. The student group has been a great resource of friendship and scientific support. Also, Roz Johnson and Dana Campbell for their help with everything related to the HGEN program. I also thank David Miller and members of the Miller lab past and present. Cody Smith for all of the help and support for my early years in the lab. The work I did and friendships I made really inspired me to attend graduate school. Also, David Miller for his guidance and mentoring. Additional thanks to my friends and family back in Washington and in Tennessee. I appreciate all the support and guidance over these past years. Finally, I would like to thank my wife and fellow grad student Barbara O’Brien. From the first day of graduate school, she has helped me in so many ways from qualifying exam prep to listening to way too many practice talks. At this point I think she knows as much about my project as I do. I really appreciate all of your support. v TABLE OF CONTENTS Page ACKNOWLEDGMENTS ............................................................................................................. iv LIST OF TABLES ......................................................................................................................... xi LIST OF FIGURES ..................................................................................................................... xiii Chapter I. Introduction ................................................................................................................................ 1 Overview and epidemiology of lung cancer ............................................................................... 3 Risk factors associated with lung cancer..................................................................................... 4 Histological classifications of lung cancer .................................................................................. 6 Germline influence on lung cancer ............................................................................................. 7 Familial lung cancer ................................................................................................................ 7 Candidate gene studies ............................................................................................................ 8 Genome-wide association studies ............................................................................................ 9 Functional elements................................................................................................................... 14 Lung cancer from a somatic perspective ................................................................................... 15 Candidate somatic studies ..................................................................................................... 15 LUAD ................................................................................................................................ 16 LUSC ................................................................................................................................. 16 SCLC.................................................................................................................................. 16 Genome-wide somatic studies ............................................................................................... 17 LUAD ................................................................................................................................ 17 LUSC ................................................................................................................................. 18 SCLC.................................................................................................................................. 19 Overlap of genetic features in lung cancer subtypes .................................................................... 20 Summary and overview of dissertation ......................................................................................... 22 vi II. Exploration of the Germline Genome Identifies Weak Sharing of Genetic Association Signals in Three Lung Cancer Subtypes: Evidence at the SNP, Gene, Regulation, and Pathway Levels ............................................................................................................................. 24 Introduction ............................................................................................................................... 24 Methods ..................................................................................................................................... 26 GWAS dataset ....................................................................................................................... 26 Genomic annotation of GWAS SNPs .................................................................................... 26 Converting hg18 SNPs to hg19 SNPs ................................................................................... 27 Identification of SNPs in LD with the genotyped SNPs ....................................................... 27 GTEx eQTLs ......................................................................................................................... 28 Lung tissue eQTLs from Hao et al. study ............................................................................. 29 FANTOM5 transcribed enhancers ......................................................................................... 29 IM-PET predicted enhancers ................................................................................................. 30 Locus level analysis ............................................................................................................... 30 Pathway enrichment analysis................................................................................................. 31 GWAS Catalog SNPs ...........................................................................................................