2001.tex

\documentclass[11pt,a4paper]{iopthsis}
\usepackage{alltt,chicago,float}
% \usepackage{chapterbib}
\usepackage{epsfig,graphicx}

\input{macros}

\begin{document}
%\maketitle
%add customized cover page on 31-1-2001
\thispagestyle{empty}
\vskip 8cm
\begin{center}
{
\Large\bf
Statistical Power Analysis and Related Issues
in Human Genetic Linkage and Association
}

\vskip 2cm

{\large by}

\vskip 1cm

{
\Large
Jing Hua Zhao
}
\large\vskip 0.5cm
Bachelor of Medicine, Shandong Medical University (1985)\\
Master of Medicine, Shanghai Medical University (1988)\\

\vskip 1cm

{\large
A thesis submitted for the degree of Doctor of Philosphy of the University of
London}

\vskip 4.5cm

{
\Large
Division of Psychological Medicine\\
Institute of Psychiatry\\
King's College London\\ \vskip 0.3cm
The United Kingdom
\vskip 1cm
{\large May 2004}
}
\end{center}

% page showing dedication
% 3-6-2002
\newpage
\topmargin=2in
\thispagestyle{empty}
\begin{center}
{\bf\Large TO MY FAMILY}
\end{center}

\newpage
\topmargin=0in
\include{cover}
\pagenumbering{roman}
\renewcommand\contentsname{Table of Contents}
\setcounter{page}{0}
\tableofcontents
\listoftables
\listoffigures
\newpage
\pagestyle{plain}
{\bf\huge Abbreviations}

\begin{tabular}{ll}
\\
AFBAC & Affected family based-controls \\
ASP/APM & Affected sib pair/affected pedigree member \\
% BST & Binary search tree \\
% CLT & Central limit theorem \\
cM & CentiMorgan \\
% CPG & Condition on parental genotype \\
% DA & Data augmentation \\
DNA & deoxyribonucleic acid \\
ELOD & Expected lod score \\
EM/ECM & Expectation/Conditional-maximisation \\
FFT & Fast Fourier Transform \\
GAW & Genetic analysis workshop \\
GEE & Generalised estimating equations \\
HWE & Hardy-Weinberg equilibrium \\
IBD/IBS & Identity by descent/state \\
IML & Interactive matrix language (SAS) \\
LD & Linkage disequilibrium \\
MCMC & Markov chain Monte Carlo \\
MLE & Maximum likelihood estimate \\
MLS & Maximum lod score \\
MRCA & Most recent common ancestor \\
NCP & Noncentrality parameter \\
NPL & Nonparametric linkage statistic \\
QTL & Quantitative trait locus \\
RFLP & Restricted-fragment length polymorphism\\
SNP & Single nucleotide polymorphism \\
TDT & Transmission/disequilibrium test \\
\\
\\
\end{tabular}

\newpage
{\bf\huge References to computer programs}

\begin{tabular}{ll}
\\
APM & Weeks \& Lange (1988)\\
ASPEX & Hinds \& Risch (1996)\\
CHRSIM & Speer et al. (1992), Terwilliger et al. (1993)\\
EH/EHPLUS & Xie \& Ott (1993), Zhao J et al. (2000)\\
ESPA & Sandkuijl (1989)\\
FASTLINK & Cottingham et al. (1993)\\
GASP & Wilson et al. (1996)\\
GENEHUNTER & Kruglyak et al. (1996)\\
GENEHUNTER PLUS & Kong \& Cox (1997)\\
HAPLO & Hawley \& Kidd (1995)\\
LIPED & Ott (1974)\\
LINKAGE & Lathrop et al. (1994)\\
MENDEL & Lange et al. (1988) \\
MFLINK & Curtis \& Sham (1995)\\
MORGAN & Thompson (2001) \\
MULTTDT & Zhao et al. (2000)\\
PAP & Hasstedt \& Cartwright (1981), Hasstedt (1982, 1994)\\
PDT & Martin et al. (2000) \\
POINTER & Lalouel \& Morton (1981), Morton et al. (1983)\\
SIMLINK & Ploughman \& Boehnke (1989)\\
SLINK & Ott (1989), Weeks et al. (1990)\\
SOLAR & Almasy \& Blangero (1998)\\
SPLINK & Holmans (1993)\\
TRANSMIT & Clayton (1999)\\
VITESSE & O'Connell \& Weeks (1995), O'Connell (2001)\\
\\
\end{tabular}
%{\bf\Huge Mathematical symbols}
%\begin{tabular}{ll}
%\\
%$\alpha$& Type I error rate \\
%$\beta$ & Type II error rate \\
%$\gamma$& Genotypic relative risk \\
%$\delta$& Noncentrality paramter of $\chi^2$ distribution/disequilibrium parameter \\
%$\lambda_R$ &Ratio of reccurrence risk of type R relative of an affected individual \\
%& and the population prevalence \\
%$\theta$& Recombination rate between loci during meiosis \\
%$\rho$  & Proportion of linked families \\
%$K$     & Population disease prevalence \\
%\\
%\end{tabular}
\newpage
\setcounter{page}{0}
\pagenumbering{arabic}

\include{ch01}
\include{ch02}
\include{ch03}
\include{ch04}
\include{ch05}
\include{ch06}
\include{ch07}
\include{ch08}
\appendix
\include{eh}
\include{chap}

\nocite{*}
\bibliographystyle{chicago}
\bibliography{2001}

\newpage
\begin{tabular}{ll}
Common journal abbreviations \\
\hline
Abbreviation & Full name \\
\hline
Am J Hum Genet & American Journal of Human Genetics \\
Am J Med Genet & American Journal of Medical Genetics \\
Ann Hum Genet & Annals of Human Genetics \\
Ann Math Stat & Annals of Mathematical Statistics \\
Ann Rev Genet & Annual Review of Genetics \\
Ann Statist & Annals of Statistics \\
Behav Genet & Behavior Genetics \\
Epidemiol Rev & Epidemiological Reviews \\
Genet Epidemiol & Genetic Epidemiology \\
Genet Res & Genetic Research \\
Genome Res & Genome Research \\
Hum Biol & Human Biology \\
Hum Hered & Human Heredity \\
Hum Mol Genet & Human Molecular Genetics \\
Int Stat Rev & International Statistical Review \\
J Amer Stat Assoc & Journal of American Statistical Association \\
J Comp Biol & Journal of Computational Biology \\
J Hered & Journal of Heredity \\
J Roy Stat Soc & Journal of Royal Statistical Society \\
J Stat Plan Infer & Journal of Statistical Planning and Inference \\
Nat Genet & Nature Genetics \\
Proc Natl Acad Sci & Proceedings of National Academy of Science \\
Stat Med & Statistics in Medicine \\
Stat Meth Med Res & Statistical Methods in Medical Research \\
Theor Popul Biol & Theoretical Population Biology \\
\hline
\end{tabular}
\end{document}

\title
{
\Large % PhD Thesis
Statistical Power Analysis and Related Issues\\
in Human Genetic Linkage and Association
% Human Genetic Linkage, Association, and Power
}
\author{
Jing Hua Zhao\\ \\
Division of Psychological Medicine\\
Institute of Psychiatry\\
King's College London
}
\date{\today}