EXPLORING THE GENETIC ARCHITECTURE OF LATE-ONSET ALZHEIMER DISEASE IN AN ...

118 Pages·2012·1.44 MB·English

EXPLORING THE GENETIC ARCHITECTURE OF LATE-ONSET ALZHEIMER
DISEASE IN AN AMISH POPULATION

By
Anna Christine Cummings

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
December, 2012
Nashville, Tennessee

Approved:
Professor Dana C. Crawford
Professor Jonathan L. Haines
Professor William K. Scott
Professor Michael G. Tramontana
Professor Bingshan Li

i
To my husband, Christopher, and son, Titus
And
To my parents, Bernard and Christine Davis
ii
ACKNOWLEDGEMENTS

The work presented in this dissertation was supported by NIH grants AG019085
to Jonathan L. Haines and AG019726 to William K. Scott, a Discovery Grant from
Vanderbilt University, and Michael J Fox Foundation grants. I would like to thank all
individuals and communities for so graciously participating in these studies. None of
this work would have been possible without them.
The work presented here was guided and greatly improved by the input from
my thesis committee: Dana Crawford (my committee chair), William Scott, Bingshan Li,
and Michael Tramontana. Special acknowledgements are due to my mentor, Jonathan
Haines. I am especially grateful for his expertise, guidance, time, and patience.
I am thankful for all the members of the Haines lab (Nathalie Schnetz-Boutaud,
Ping Mayo, Brent Anderson, Melissa Allen, Jacob McCauley, William Bush, Kylee
Spencer, Sharon Liang, Rebecca Zuvich, Olivia Veatch, Mary Davis, Joshua Hoffman,
and Laura D’Aoust) for being helpful in so many ways and for creating an enjoyable,
fun, and collaborative work environment.
I would also like to thank all members of the CHGR. So many people have
played a role in this work for which I am very grateful. A special thanks is due to Lan
Jiang who patiently provided much training for genetic analyses in the Amish. I would
also like to thank all of my fellow students who have been so kind and supportive along
the way.

iii
TABLE OF CONTENTS

Page
DEDICATION ............................................................................................................ ii
ACKNOWLEDGEMENTS ....................................................................................... iii
LIST OF TABLES ....................................................................................................... iv
LIST OF FIGURES ................................................................................................... viii
LIST OF APPENDICES ............................................................................................ ix
Chapter
I. INTRODUCTION.............................................................................................1

Pathophysiology and diagnosis of Alzheimer disease .................................. 2
Epidemiology of and risk factors for Alzheimer disease ............................. 5
The search for genetic risk factors for late-onset Alzheimer disease ........... 7
The utility of genetically isolated populations ............................................. 11
The Amish .......................................................................................................... 12
Previous work…………………………………………………………………14
Summary ............................................................................................................ 16

II. QUALITY CONTROL PROCEDURES FOR A GENOME-WIDE
STUDY IN AN AMISH POPULATION .....................................................17

Introduction ....................................................................................................... 17
Methods .............................................................................................................. 20
Results ................................................................................................................ 23
Discussion .......................................................................................................... 35

III. GENOME-WIDE LINKAGE AND ASSOCIATION STUDY FOR
ALZHEIMER DISEASE IN AN AMISH POPULATION .......................38

Introduction ....................................................................................................... 38
Methods .............................................................................................................. 40
Subjects .................................................................................................. 40
Clinical data .......................................................................................... 40
Genotyping ........................................................................................... 41
Statistical analysis ................................................................................ 43
Evaluation of the MMSE and Word List Learning .......................... 45
iv
Results ................................................................................................................ 48
APOE ..................................................................................................... 48
Genome-wide Association .................................................................. 49
Genome-wide Linkage ........................................................................ 52
Evaluation of the MMSE and Word List Learning .......................... 55
Discussion .......................................................................................................... 62
Acknowledgements .......................................................................................... 66

IV. SEQUENCE ANALYSIS OF A NOVEL ALZHEIMER DISEASE
CANDIDATE GENE: CTNNA2 ...................................................................67

Introduction ....................................................................................................... 67
Methods .............................................................................................................. 69
Study population ................................................................................. 69
Sequencing ............................................................................................ 69
Sequence processing ............................................................................ 72
Analysis ................................................................................................. 73
Genotyping ........................................................................................... 74
Results ................................................................................................................ 74
Variants in the exons ........................................................................... 74
Extra-exonic variants ........................................................................... 77
Discussion .......................................................................................................... 81
Acknowledgements .......................................................................................... 82

V. CONCLUSION ................................................................................................84

Summary ............................................................................................................ 84
Future Directions .............................................................................................. 87

REFERENCES ...........................................................................................................99

v
LIST OF TABLES

Table Page
1.1 Late-onset Alzheimer disease genes…………………………………………………10
1.2 Expected kinship coefficients for some familial relationships ............................... 14
1.3 Regions with LOD score >3 in previously published linkage scans in subsets of
the current Amish dataset ............................................................................................. 16
2.1 Average percentage of heterozygosity for SNPs on the X chromosome for
individuals whose reported and genetic sex are potentially discrepant .............. 26
2.2 Lowest mean IBS for sibling pairs ............................................................................... 32
2.3 Highest mean IBS for other relatives pairs ................................................................. 33
3.1 Genome-wide dataset .................................................................................................... 43
3.2 MQLS-corrected APOE allele frequencies .................................................................. 48
3.3 Age of onset and number of affected versus unaffected individuals by APOE
genotype .......................................................................................................................... 49
3.4 Most significant genome-wide association results .................................................... 51
3.5 Most significant multipoint linkage results ............................................................... 54
3.6 MMSE and Word list learning Z scores per LOAD risk group defined by APOE ...
…………………………………………………………………………………………...58
3.7 Kruskal Wallis test results with follow-up two-sample Wilcoxon rank sum test
results ............................................................................................................................... 59
3.8 Analysis of covariance test results with follow-up pairwise test results ............... 60
3.9 Spearman’s correlation between 2p12 lod scores and Z scores of MMSE and
Word List learning ......................................................................................................... 61
vi
4.1 Sequencing dataset characteristics including total number of individuals, APOE
genotype, and mean and range of ages of exam and onset ..................................... 70
4.2 Whole exome sequence quality of dataset used for analysis ................................... 71
4.3 Summary of all detected SNVs in the exons of CTNNA2 and LRRTM1 ................ 76
4.4 Summary of selected non-exonic SNVs with at least a 30% difference in allele
frequency between LOAD and cognitively normal individuals in the
subpedigrees showing the most evidence for linkage at 2p12 ............................... 79
4.5 Sequenom-generated genotype results of rs72822556 ............................................. 80
vii
LIST OF FIGURES

Figure Page
2.1 Quantile-quantile plots of MQLS p-values before (a) and after (b) removing
additional SNPs with MQLS-adjusted minor allele frequencies <0.05 .................. 23
2.2 Manhattan plots of the MQLS resultsbefore and after removing additional SNPs
with MQLS-adjusted minor allele frequencies <5% ................................................. 24
2.3 Population structure of the Amish .............................................................................. 28
2.4 Output from Graphical Representation of Relationships using raw data ............. 30
2.5 Output from Graphical Representation of Relationships ........................................ 31
2.6 Flowchart of SNP and sample quality control procedures ...................................... 34
3.1 MQLS Manhattan plot ................................................................................................... 52
3.2 Strongest multipoint linkage peaks ............................................................................. 55

viii
LIST OF APPENDICES

Appendix Page
A. Most significant genome-wide association results, stratified .................................. 90
B. Regions with at least one SNP with a two-point HLOD ≥ 3……………………….91
C. Distributions of Z scores from the Mini-Mental State Exam (MMSE_Z), Word List
Memory trials 1-3, delayed recall, delayed recall, savings, recognition-yes, and
recognition-no ................................................................................................................ 96
D. Scatter plots of recessive (left) and dominant (right) per-family lod scores versus
Z scores from the Mini-Mental State Exam (MMSE_Z), Word List Memory trials
1-3, delayed recall, savings, recognition-yes, and recognition-no .......................... 97
E. Spearman’s correlation between 2p12 lod scores and Z scores of Word List
learning with MMSE Z as a covariate ......................................................................... 98

ix
CHAPTER I

INTRODUCTION

Alzheimer Disease (AD) is the most common cause of dementia, affects over 5
million individuals over the age of 65 in the United States (1), is the fifth-leading cause
of death in the United States for individuals over the age of 65 (2), and is an increasingly
serious public health issue. AD is a progressive neurodegenerative disorder of the brain
characterized by loss of memory and cognitive abilities, development of
neuropsychiatric symptoms and behavioral changes, and loss of daily independent
function. With inadequate treatments and no cure, the nature of this disease puts a
heavy burden on individuals, their families, caregivers, and society as a whole. With
our aging population, this burden will only increase as the number of affected
individuals is expected to triple by 2050 (1).
AD can be divided into two categories: early-onset and late-onset. Individuals
younger than 65 have the early-onset form but account for less than 5% of all AD cases
(3). Dominant mutations in three genes cause susceptibility to the majority of early-
onset familial AD: amyloid precursor protein [APP] (4) and presenilin 1 and 2 [PS1, PS2]
genes (5-7). However, these three genes combined only contribute to less than 2% of all
cases of AD. The much more common form, late-onset Alzheimer disease (LOAD),
describes AD when it occurs in individuals older than or equal to 65 (8). Unlike early-
onset where most of the genetic risk is identified and follows a simple Mendelian
pattern, the majority of the genetic risk of LOAD is unexplained and has a much more
1