The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor in Philosophy by Marianne Lucy Johnstone April 2015 The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis 2015 Abstract Background Chronic pancreatitis (CP) is a disease of fibrosis of the pancreas for which alcohol is the main causative agent. However, only a small proportion of alcoholics develop chronic pancreatitis. Genetic polymorphism may affect pancreatitis risk. Aim To determine the factors required to classify a chronic pancreatic population and identify genetic variations that may explain why only some alcoholics develop chronic pancreatitis. Methods The most appropriate method of diagnosing CP was assessed using a systematic review. Genetics of different populations of alcohol-related chronic pancreatitics (ACP) were explored using four different techniques: genome-wide association study (GWAS); custom arrays; PCR of variable nucleotide tandem repeats (VNTR) and next generation sequencing (NGS) of selected genes. Results EUS and sMR were identified as giving the overall best sensitivity and specificity for diagnosing CP. GWAS revealed two associations with CP (identified and replicated) at PRSS1-PRSS2_rs10273639 (OR 0.73, 95% CI 0.68-0.79) and X-linked CLDN2_rs12688220 (OR 1.39, 1.28-1.49) and the association was more pronounced in the ACP group (OR 0.56, 0.48-0.64)and OR 2.11, 1.84-2.42). The previously identified VNTR in CEL was shown to have a lower frequency of the normal repeat in ACP than alcoholic liver disease (ALD; OR 0.61, 0.41-0.93). Homozygosity of the normal variant was more common in ALD than ACP (OR 0.53, 0.3-0.96) or Healthy Controls (OR 0.55, 0.3-1.00)). The NGS discovery phase lead on to validation of the 21 most significant SNPs with Sequenom array. This showed significance difference between ACP and ALD in allele frequency of the synonymous SNP, PRSS1_rs6666, (OR 1.99, 1.46-2.72) Conclusion A range of potential exonic and intronic sites have been identified that have association with a predisposition to developing chronic pancreatitis. These findings show that further work is justified to fully assess the interaction of the different polymorphisms and their phenotypic significance in development of the disease. Abstract 2 The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis 2015 Declaration I declare that this thesis and the research upon which is based is the result of my own work. Whereever I have incorporated the work of others it has been clearly stated. This work has not previously been submitted in any substance for any degree, not is it concurrenly being submitted in candidiature for this or at any other university. Part of this work has been published in: David C Whitcomb, Jessica LaRusch, Alyssa M Krasinskas, Lambertus Klei, Jill P Smith, Randall E Brand, John P Neoptolemos, Markus M Lerch, Matt Tector, Bimaljit S Sandhu, Nalini M Guda, Lidiya Orlichenko, Alzheimer’s Disease Genetics Consortium, Samer Alkaade, Stephen T Amann, Michelle A Anderson, John Baillie, Peter A Banks, Darwin Conwell, Gregory A Coté, Peter B Cotton, James DiSario, Lindsay A Farrer, Chris E Forsmark, Marianne Johnstone, Timothy B Gardner, Andres Gelrud, William Greenhalf, Jonathan L Haines, Douglas J Hartman, Robert A Hawes, Christopher Lawrence, Michele Lewis, Julia Mayerle, Richard Mayeux, Nadine M Melhem, Mary E Money, Thiruvengadam Muniraj, Georgios I Papachristou, Margaret A Pericak-Vance, Joseph Romagnuolo, Gerard D Schellenberg, Stuart Sherman, Peter Simon, Vijay P Singh, Adam Slivka, Donna Stolz, Robert Sutton, Frank Ulrich Weiss, C Mel Wilcox, Narcis Octavian Zarnescu, Stephen R Wisniewski, Michael R O’Connell, Michelle L Kienholz, Kathryn Roeder, M Michael Barmada, Dhiraj Yadav & Bernie Devlin Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis Nature Genetics 2012 Dec;44(12):1349-54 Declaration 3 The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis 2015 James A Nicholson, William Greenhalf, Richard Jackson, Trevor F Cox, Jane V Butler, Thomas Hanna, Sara Harrison, Christopher J Grocock, Christopher Halloran, Nathan R Howes, Michael G Raraty, Paula Ghaneh, Marianne Johnstone, Sanchoy Sarkar, Howard L Smart, Johnathon C Evans, Robert Sutton, John P Neoptolemos, Martin G Lombard Incidence of Post-ERCP Pancreatitis from Direct Pancreatic Juice Collection in Hereditary Pancreatitis and Familial Pancreatic Cancer before and after the Introduction of Prophylactic Pancreatic Stents and Rectal Diclofenac Pancreas. 2014 Nov 26 James A Nicholson, Marianne Johnstone, William Greenhalf Divisum May be Preserving Pancreatic Function in CFTR Patients-But at a Cost American Journal of Gastroenterology. 2012 Nov;107(11):1758-9 (letter) Marianne Johnstone, Richard Jackson, Thomas Hanna, James A Nicholson, William Greenhalf, Robert Sutton Accuracy of diagnostic tests for chronic pancreatitis: systematic review and meta-analyses GUT submitted 2015 Declaration 4 The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis 2015 ABSTRACT 2 Decloration 3 Contents 5 Figures 10 Tables 13 Abbreviations 16 Acknowledgements 20 1 CHAPTER 1: INTRODUCTION 22 1.1 Chronic Pancreatitis 22 1.1.1 Epidemiology 23 1.1.2 Pathogenesis of Chronic Pancreatitis 25 1.1.3 Aetiology 31 1.1.4 Risk Factors for Chronic Pancreatitis 34 1.1.5 Diagnosis of Chronic Pancreatitis 35 1.1.6 Consequences of the Development of Chronic Pancreatitis 40 1.1.7 Summary 42 1.2 Alcohol Metabolism 43 1.2.1 Ethanol Metabolism 43 1.2.2 Metabolism of Triglycerides 45 1.2.3 Effects of Ethanol Metabolism 46 1.2.4 Ethanol Metabolism and Alcoholism 48 1.2.5 Summary 49 1.3 Alcoholic Liver Disease 50 1.3.1 Definition of Alcoholic Liver Disease 50 1.3.2 Pathophysiology of Alcoholic Liver Disease 51 1.3.3 Natural History of Alcoholic Liver Disease 51 1.3.4 Diagnosis of Alcoholic Liver Disease 52 Contents 5 The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis 2015 1.3.5 Chronic Pancreatitis and Alcoholic Liver Disease 52 1.3.6 Summary 55 1.4 Genetics 56 1.4.1 Characterising Genetic Differences 56 1.4.2 Genetics of Chronic Pancreatitis 57 1.4.3 The Genetics of Alcohol Metabolism 64 1.4.4 Genetics of Alcohol Liver Disease 70 1.4.5 Methods for Assessing Genetic Variation 71 1.4.6 Summary 76 2 CHAPTER 2: AIM AND OBJECTIVES 77 2.1 Aim 77 2.2 Objectives 77 3 CHAPTER 3: SYSTEMATIC REVIEW OF THE DIAGNOSIS OF CHRONIC PANCREATITIS 78 3.1 Materials and Methods 78 3.1.1 Data Sources and Search Strategy 78 3.1.2 Study Selection 79 3.1.3 Data Extraction 79 3.1.4 Data Synthesis and Analysis 79 3.1.5 Quality Assessment 80 3.1.6 Statistical Analysis 80 3.2 Results 84 3.2.1 Population 84 3.2.2 Gold Standards 84 3.2.3 Index Tests 85 3.2.4 Variation Over Time 85 Contents 6 The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis 2015 3.2.5 Comparison of Specific Test 85 3.2.6 Publication bias 86 3.3 Discussion 100 4 CHAPTER 4: GENOME-WIDE ASSOCIATION STUDY 104 4.1 Discussion 104 5 CHAPTER 5: NEXT GENERATION SEQUENCING 106 5.1 Materials and Methods 106 5.1.1 Patients and samples 106 5.1.2 DNA Preparation 112 5.1.3 DNA Quality Control 113 5.1.4 Selection of Genes of Interest 114 5.1.5 Sequence Capture (Haloplex) 115 5.1.6 Ion Torrent™ 117 5.1.7 Data Output from Ion Torrent™ 117 5.1.8 Data Analysis from Ion Torrent™ 118 5.1.9 Linkage Disequilibrium 120 5.1.10 Concordance of Results between Modalities 121 5.1.11 Sequenom Validation 121 5.1.12 Haplotype Analysis 122 5.2 Results 123 5.2.1 Patients 123 5.2.2 Next Generation Sequencing Analysis 124 5.2.3 Known Chronic Pancreatitis Associated Variant Analysis 126 5.2.4 Known Variants in Genes of Alcohol Metabolism 131 5.2.5 Next Generation Sequencing SNPs of Interest 135 5.2.6 Biological Effects of SNPs of Interest 138 Contents 7 The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis 2015 5.2.7 Linkage Disequilibrium 139 5.2.8 Tagging SNPs 139 5.2.9 Sensitivity Sub-analysis of Next Generation Sequencing Samples 142 5.2.10 Internal Validation - Next Generation Sequencing compared with Genome-wide Association Study 145 5.2.11 Next Generation Sequencing Validation with Sequenom (Stage 1) 146 5.2.12 Next Generation Sequencing Validation with Sequenom (Stage 2) 147 5.2.13 Next Generation Sequencing Haplotype Analysis 152 5.3 Discussion 154 5.3.1 Previous Identified Variants 154 5.3.2 Significant SNPs identified in the NGS analysis 156 5.3.3 Quality of Next Generation Sequencing Results 165 5.3.4 Statistical Analysis 167 6 CHAPTER 6: VARIABLE NUCULEOTIDE TANDAM REPEAT IN CARBOXYL-ESTER LIPASE 168 6.1 Materials and Methods 168 6.1.1 Patients 168 6.1.2 Association of Carboxyl-Ester Lipase Variable Nucleotide Tandem Repeat 170 6.2 Results 171 6.3 Discussion 176 7 CHAPTER 7: OVERALL DISCUSSION 178 7.1 Patients 178 7.1.1 Definition of Alcohol Excess 178 7.1.2 Defining the Presence or Absence of Pancreatitis 178 7.1.3 Control Groups 179 7.1.4 Heterogeneity between Groups 180 Contents 8 The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis 2015 7.1.5 Bias in Sample Source 180 7.2 Synonymous SNPs 181 8 CHAPTER 8: CONCLUSION 182 9 CHAPTER 9: REFERENCES 184 10 CHAPTER 10: APPENDICES 210 10.1 Common Alleles of Genes of Alcohol Metabolism 210 10.1.1 Alcohol