In Silico Haplotyping, Genotyping and Analysis of Resequencing Data Using Markov Models
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IN SILICO HAPLOTYPING, GENOTYPING AND ANALYSIS OF RESEQUENCING DATA USING MARKOV MODELS by Yun Li A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biostatistics) in The University of Michigan 2009 Doctoral Committee: Professor Gonçalo R. Abecasis, Co-Chair Professor Michael Lee Boehnke, Co-Chair Professor Margit Burmeister Professor Roderick J.A. Little Assistant Professor Noah A. Rosenberg © Yun Li 2009 To Mom, Dad, Iory and Duan. ii Acknowledgements I am grateful to the myriad of people who have made this work possible. First of all, I would like to thank Gonçalo and Mike for teaching me about science, for letting me discover how much I can enjoy research, for being encouraging and enthusiastic both because of and despite what we found, for guiding me to grow up as an independent researcher, for being exceptional role models both career-wise and family-wise, and for being approachable anytime I need help. I owe gratitude to my committee: Rod, Margit and Noah for their help and guidance beyond their duties as committee members. I sincerely appreciate their time, advice, and encouragement. Special thanks to Rod for brining in the missing data perspectives; to Margit for always asking questions that I have an answer in the next few slides; and to Noah for access to the HGDP data. I would like also to thank the CSG members: they make everyday research joyful and keep my spirits up even during my down times. I am also fortunate to be around a group of good friends including Qixuan, Jin, Rui, Jun, and Liming, who have made my 5-year graduate studies more colorful. iii I thank my parents for their support and encouragement throughout the years, Iory for putting up with sometimes a different me at home, and Duan for brining me endless of joys. iv TABLE OF CONTENTS Dedication. .......................................................................................................................................ii Acknowledgements .........................................................................................................................iii List of Figures .................................................................................................................................vi List of Tables..................................................................................................................................vii Abstract .........................................................................................................................................viii Chapter 1. Introduction ......................................................................................................... 1 1.1 Complex diseases ............................................................................................................... 1 1.2 Genome-wide association studies (GWAS)........................................................................ 3 1.3 The next-generation: Resequencing-based approaches...................................................... 5 1.4 The scope of this dissertation ............................................................................................. 6 2. Haplotype Reconstruction .................................................................................. 9 2.1 Introduction........................................................................................................................ 9 2.2 Methods............................................................................................................................ 10 2.3 Data .................................................................................................................................. 20 2.4 Results.............................................................................................................................. 21 2.5 Discussion ........................................................................................................................ 25 3. Genotype Imputation (In Silico Genotyping) in Candidate Gene and Genome-Wide Association Studies .......................... 32 3.1 Introduction...................................................................................................................... 32 3.2 Methods............................................................................................................................ 34 3.3 Data .................................................................................................................................. 40 3.4 Results.............................................................................................................................. 44 3.5 Discussion ........................................................................................................................ 54 4. Analysis of Resequencing Data......................................................................... 75 4.1 Introduction...................................................................................................................... 75 4.2 Methods............................................................................................................................ 76 4.3 Results and implications................................................................................................... 78 4.4 Discussion ........................................................................................................................ 91 5. Conclusions and Discussions .......................................................................... 104 5.1 Review of Previous Chapters ......................................................................................... 104 5.2 Remarks on Subsequent Analysis................................................................................... 107 5.3 Limitations and Future Directions.................................................................................. 109 5.4 Conclusion...................................................................................................................... 110 References ................................................................................................................................... 113 v List of Figures Figure 2.1 Cartoon Illustrations of Haplotype Reconstruction and Genotype Inference. .................................................................................. 26 Figure 2.2 Quality Measures for Accuracy of Reconstructed Haplotypes.................. 27 Figure 3.1 Disease-SNP Association Chi-Square Test: Imputed versus Experimental in the AMD Candidate Gene Study. .............................................................. 59 Figure 3.2 Improvement in r2 for the Fine-mapping Panel of 521 SNPs in FUSION.60 Figure 3.3 Assessment of Quality Measures for Individual Imputed Genotypes. ...... 61 Figure 3.4 ROC Curve Comparing Two Measures of Data Quality. .......................... 62 Figure 3.5 FUSION T2D Association P-values: Imputed vs Genotyped. .................. 65 Figure 3.6 Imputation Improves Quality of LD Estimates: r2. ................................... 66 Figure 3.7 Imputation Improves Quality of LD Estimates: D’................................... 67 Figure 3.8 Evaluation of Imputation Accuracy across HGDP Panels: Percentage of Alleles Imputed Incorrectly....................................................................... 70 Figure 3.9 Evaluation of Imputation Accuracy across HGDP Panels: Coverage at r2 Threshold 0.8............................................................................................. 71 Figure 4.1 Low-pass vs. Deep Sequencing: Polymorphism Discovery...................... 99 Figure 4.2 Low-pass vs. Deep Sequencing: Information/Effective Sample Size..... 101 vi List of Tables Table 2.1 Quality of Haplotype and Missing Genotype Estimates in Simulated Datasets...................................................................................... 28 Table 2.2 Quality of Reconstructed Haplotypes in FUSION Trio Dataset................. 29 Table 2.3 Benefits of Incorporating External Information for Haplotyping............... 30 Table 3.1 Quality of Imputed Genotypes in the AMD Candidate Gene Study. .......... 58 Table 3.2 Comparison of Imputed and Experimental Genotypes for a Subset of SNPs Showing Strong Association in FUSION.................................................... 63 Table 3.3 Coverage of the Phase II HapMap with Commercial Genotyping Panels, before and after Imputation......................................................................... 68 Table 3.4 Imputed Genotypes Result in Increased Power........................................... 72 Table 3.5 Effect of Increasing Reference Panel Size on Imputation Accuracy........... 73 Table 4.1 Accuracy of Imputed Genotypes Using Shotgun Re-sequence Data as Input............................................................ 94 Table 4.2 Proportion of Variants Discovered, by Re-sequencing Investment. ........... 95 Table 4.3 Proportion of Variants Discovered, by Re-sequencing Error Rate. ............ 96 Table 4.4 Accuracy of Genotype Predictions, by Re-sequencing Investment. ........... 97 Table 4.5 Accuracy of Genotype Predictions, by Re-sequencing Error Rate. ............ 98 Table 4.6 Low-pass vs. Deep Sequencing: Imputation Accuracy at Discovered Loci. ....................................................................................... 100 Table 4.7 Imputation Quality using a Smaller or Larger “Re-sequencing HapMap”: Accuracy...................................................................................................