role of genomic copy number variation in alzheimer's disease and mild cognitive impairment

158 Pages·2012·1.7 MB·English

ROLE OF GENOMIC COPY NUMBER VARIATION IN
ALZHEIMER'S DISEASE AND MILD COGNITIVE
IMPAIRMENT

Shanker Swaminathan

Submitted to the faculty of the University Graduate School
in partial fulfillment of the requirements
for the degree
Doctor of Philosophy
in the Department of Medical and Molecular Genetics,
Indiana University

August 2012
Accepted by the Faculty of Indiana University, in partial
fulfillment of the requirements for the Degree of Doctor of Philosophy.

____________________________________
Andrew J. Saykin, PsyD, Chair

____________________________________
Tatiana Foroud, PhD
Doctoral Committee

____________________________________
John I. Nurnberger, Jr, MD, PhD
May 23, 2012

____________________________________
Li Shen, PhD

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To my parents and sister

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ACKNOWLEDGEMENTS

This work would not have been possible without the help and support of a lot of people. I
would like to thank Dr. Andrew Saykin, my thesis advisor, for providing me the
opportunity to be a part of his lab and be able to pursue research in the field of imaging
genetics. Dr. Saykin has always encouraged me to be pursue new information and be up
to date with the current developments in the field. He has been a constant source of
support and guidance and was a person whom I could always turn to when I have had
problems. His feedback and suggestions have been very helpful. I would also like to
thank the members of my research committee: Drs. Tatiana Foroud, John Nurnberger
and Li Shen for their help in this work. They encouraged me to pursue this work and
offered feedback and suggestions which were very helpful. They also made sure that I
was on track with the program requirements and was making smooth progress towards
the PhD degree.

I would like to thank other members of the lab including Dr. Li Shen, Dr. Sungeun Kim,
Dr. Kwangsik Nho, Dr. Shannon Risacher, Susan Conroy, John West, Jing Wan, Kelley
Holohan and Vijay Ramanan for their help with this work. I was fortunate to work with
them on a number of projects, which enabled me to learn some of the methods used in
imaging analyses and genetic analyses. I am also grateful to Dr. Mark Inlow for his help
and guidance on the statistical analyses. I would also like to thank the faculty and staff at
the Center for Neuroimaging.

I express my gratitude to Dr. Kenneth Cornetta, Dr. Brittney-Shea Herbert, Dr. Terry
Reed and Peggy Knople for their guidance on the program requirements and for making
sure I was completing the requirements in a timely manner. I also thank the faculty and
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staff at the Department of Medical and Molecular Genetics as well as the staff of the
IUPUI Graduate Office and the Graduate Division of the Indiana University School of
Medicine for their help during the course of my study.

Finally, I would like to offer my heartfelt thanks to my family. They encouraged me to
pursue my interests in performing research and were there with me at every step. They
follow my progress keenly and are very interested in learning about the various projects I
am involved in as well the Genetics field in general. Their motivation and support has
helped me progress along smoothly and I would like to express my sincere gratitude to
them.

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ABSTRACT
Shanker Swaminathan

ROLE OF GENOMIC COPY NUMBER VARIATION IN ALZHEIMER'S DISEASE AND
MILD COGNITIVE IMPAIRMENT

Alzheimer's disease (AD) is the most common form of dementia defined by loss in
memory and cognitive abilities severe enough to interfere significantly with daily life
activities. Amnestic mild cognitive impairment (MCI) is a clinical condition in which an
individual has memory deficits not normal for the individual's age, but not severe enough
to interfere significantly with daily functioning. Every year, approximately 10-15% of
individuals with MCI will progress to dementia. Currently, there is no treatment to slow or
halt AD progression, but research studies are being conducted to identify causes that
can lead to its earlier diagnosis and treatment.

Genetic variation plays a key role in the development of AD, but not all genetic factors
associated with the disease have been identified. Copy number variants (CNVs), a form
of genetic variation, are DNA regions that have added genetic material (duplications) or
loss of genetic material (deletions). The regions may overlap one or more genes
possibly affecting their function. CNVs have been shown to play a role in certain
diseases.

At the start of this work, only one published study had examined CNVs in late-onset AD
and none had examined MCI. In order to determine the possible involvement of CNVs in
AD and MCI susceptibility, genome-wide CNV analyses were performed in participants
from three cohorts: the ADNI cohort, the NIA-LOAD/NCRAD Family Study cohort, and a
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unique cohort of clinically characterized and neuropathologically verified individuals.
Only participants with DNA samples extracted from blood/brain tissue were included in
the analyses. CNV calls were generated using genome-wide array data available on
these samples. After detailed quality review, case (AD and/or MCI)/control association
analyses including candidate gene and genome-wide approaches were performed.

Although no excess CNV burden was observed in cases compared to controls in the
three cohorts, gene-based association analyses identified a number of genes including
the AD candidate genes CHRFAM7A, RELN and DOPEY2. Thus, the present work
highlights the possible role of CNVs in AD and MCI susceptibility warranting further
investigation. Future work will include replication of the findings in independent samples
and confirmation by molecular validation experiments.

Andrew J. Saykin, PsyD, Chair

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TABLE OF CONTENTS

List of Tables ................................................................................................................... x
List of Figures ................................................................................................................ xii
List of Abbreviations ..................................................................................................... xiv
I. Introduction
A. Alzheimer's disease ......................................................................................... 1
B. Role of genetic variation in Alzheimer's disease .............................................. 4
C. Copy number variation .................................................................................. 11
D. Mechanisms for formation of copy number variations .................................... 12
E. Methods for copy number variation detection ................................................ 16
F. Copy number variation detection algorithms .................................................. 20
G. Copy number variation in selected neuropsychiatric disorders ...................... 23
H. Copy number variation in Alzheimer's disease .............................................. 33
I. Statement of purpose ...................................................................................... 35
II. Genomic Copy Number Analysis in Alzheimer's Disease and Mild Cognitive
Impairment: An ADNI Study
A. Introduction .................................................................................................... 37
B. Methods......................................................................................................... 40
C. Results .......................................................................................................... 47
D. Discussion ..................................................................................................... 59
III. Analysis of Copy Number Variation in Alzheimer's Disease:
the NIA-LOAD/NCRAD Family Study
A. Introduction .................................................................................................... 65
B. Methods......................................................................................................... 68
C. Results .......................................................................................................... 75
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D. Discussion ..................................................................................................... 88
IV. Analysis of Copy Number Variation in Alzheimer's Disease in a Cohort of
Clinically Characterized and Neuropathologically Verified Individuals
A. Introduction .................................................................................................... 97
B. Methods......................................................................................................... 99
C. Results ........................................................................................................ 104
D. Discussion ................................................................................................... 116
V. Summary and Future Directions .............................................................................. 120
References .................................................................................................................. 127
Curriculum Vitae

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LIST OF TABLES

1. Genes associated with early-onset familial Alzheimer's disease .................................. 6
2. Summary of published genome-wide association studies in Alzheimer's
disease ............................................................................................................................ 7
3. Examples of copy number variations and selected neuropsychiatric
disorders ....................................................................................................................... 24
4. Sample demographics of participants in the ADNI cohort .......................................... 48
5. Characteristics of copy number variation calls in the three diagnostic
groups from participants in the ADNI cohort .................................................................. 49
6. Participants in the ADNI cohort grouped by copy number variation
call size ......................................................................................................................... 50
7. Genes that had copy number variation calls from at least one
Alzheimer's disease and/or one mild cognitive impairment participant
and no healthy controls in the ADNI cohort using the candidate
gene approach .............................................................................................................. 54
8. Significant (uncorrected p<0.05, relative to healthy controls) genes
present in either Alzheimer's disease and/or mild cognitive impairment
participants, but not healthy controls in the ADNI cohort using the whole
genome approach ......................................................................................................... 56
9. Sample demographics of participants in the NIA-LOAD/NCRAD Family
Study cohort .................................................................................................................. 76
10. Characteristics of copy number variation calls from participants in the
NIA-LOAD/NCRAD Family Study cohort ........................................................................ 77
11. Participants in the NIA-LOAD/NCRAD Family Study cohort grouped by
copy number variation call size ...................................................................................... 78
x