Access the full text.
Sign up today, get DeepDyve free for 14 days.
Kui Zhang, Zhaohui Qin, Jun Liu, Ting Chen, M. Waterman, Fengzhu Sun (2004)
Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies.Genome research, 14 5
Momiao Xiong, Li Jin (1999)
Comparison of the power and accuracy of biallelic and microsatellite markers in population-based gene-mapping methods.American journal of human genetics, 64 2
J. Neter, William Wasserman, M. Kutner (1974)
Applied linear statistical models : regression, analysis of variance, and experimental designs
Ping Zhang, Hiroki Ishiguro, T. Ohtsuki, Judith Hess, F. Carillo, Donna Walther, E. Onaivi, E. Onaivi, T. Arinami, George Uhl (2004)
Human cannabinoid receptor 1: 5′ exons, candidate regulatory regions, polymorphisms, haplotypes and association with polysubstance abuseMolecular Psychiatry, 9
Bjarni Halldó, Francisco De, La Vega, A. Clark, S. Istrail
Optimal Haplotype Block-free Selection of Tagging Snps for Genome-wide Association Studies
Qiqing Huang, Yun-Xin Fu, E. Boerwinkle (2003)
Comparison of strategies for selecting single nucleotide polymorphisms for case/control association studiesHuman Genetics, 113
A. Long, C. Langley (1999)
The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits.Genome research, 9 8
Kui Zhang, P. Calabrese, M. Nordborg, Fengzhu Sun (2002)
Haplotype block structure and its applications to association studies: power and study designs.American journal of human genetics, 71 6
E. Martin, E. Lai, J. Gilbert, A. Rogala, A. Afshari, J. Riley, K. Finch, Jeffery Stevens, K. Livak, B. Slotterbeck, S. Slifer, L. Warren, P. Conneally, D. Schmechel, D. Schmechel, I. Purvis, M. Pericak-Vance, A. Roses, J. Vance (2000)
SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease.American journal of human genetics, 67 2
J. Long, R. Williams, M. Urbanek (1995)
An E-M algorithm and testing strategy for multiple-locus haplotypes.American journal of human genetics, 56 3
S. Hamon, S. Kardia, E. Boerwinkle, Kiang Liu, Kathy Klos, A. Clark, C. Sing (2006)
Evidence for Consistent Intragenic and Intergenic Interactions between SNP Effects in the APOA1/C3/A4/A5 Gene ClusterHuman Heredity, 61
M. Byng, John Whittaker, Andrew Cuthbert, Christopher Mathew, Cathryn Lewis (2003)
SNP Subset Selection for Genetic Association StudiesAnnals of Human Genetics, 67
J. Bader (2001)
The relative power of SNPs and haplotype as genetic markers for association tests.Pharmacogenomics, 2 1
A. Rienzo, Alan Peterson, J. Garza, A. Valdes, M. Slatkin, N. Freimer (1994)
Mutational processes of simple-sequence repeat loci in human populations.Proceedings of the National Academy of Sciences of the United States of America, 91
H. Tabor, N. Risch, R. Myers (2002)
Candidate-gene approaches for studying complex genetic traits: practical considerationsNature Reviews Genetics, 3
D. Stram, C. Haiman, J. Hirschhorn, D. Altshuler, L. Kolonel, B. Henderson, M. Pike (2003)
Choosing Haplotype-Tagging SNPS Based on Unphased Genotype Data Using a Preliminary Sample of Unrelated Subjects with an Example from the Multiethnic Cohort StudyHuman Heredity, 55
P. Sullivan, M. Neale, M. Silverman, C. Harris-Kerr, M. Myakishev, B. Wormley, B. Webb, Y. Ma, K. Kendler, R. Straub (2001)
An association study of DRD5 with smoking initiation and progression to nicotine dependence.American journal of medical genetics, 105 3
(1993)
The how and why of generating gene genealogies
A. Valdes, M. Slatkin, N. Freimer (1993)
Allele frequencies at microsatellite loci: the stepwise mutation model revisited.Genetics, 133 3
L. Excoffier, M. Slatkin (1995)
Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.Molecular biology and evolution, 12 5
M. Hawley, Kenneth Kidd (1995)
HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes.The Journal of heredity, 86 5
T. Rebbeck, M. Spitz, Xifeng Wu (2004)
Assessing the function of genetic variants in candidate gene association studiesNature Reviews Genetics, 5
S. Hamon, J. Stengård, A. Clark, V. Salomaa, E. Boerwinkle, C. Sing (2004)
Evidence for Non‐additive Influence of Single Nucleotide Polymorphisms within the Apolipoprotein E GeneAnnals of Human Genetics, 68
Toshihiro Tanaka (2003)
The International HapMap ProjectNature, 426
高畑 尚之, A. Clark (1993)
Mechanisms of molecular evolution : introduction to molecular paleopopulation biology
R. Hudson (1990)
Gene genealogies and the coalescent process., 7
R. Anney, C. Olsson, Mehrnoush Lotfi-Miri, G. Patton, R. Williamson (2004)
Nicotine dependence in a prospective population-based study of adolescents: the protective role of a functional tyrosine hydroxylase polymorphism.Pharmacogenetics, 14 2
M. Slatkin (1995)
A measure of population subdivision based on microsatellite allele frequencies.Genetics, 139 1
D. Goldman, M. Urbanek, D. Guenther, R. Robin, J. Long (1997)
Linkage and association of a functional DRD2 variant [Ser311Cys] and DRD2 markers to alcoholism, substance abuse and schizophrenia in Southwestern American Indians.American journal of medical genetics, 74 4
N. Chapman, E. Wijsman (1998)
Genome screens using linkage disequilibrium tests: optimal marker characteristics and feasibility.American journal of human genetics, 63 6
M. Weale, C. Depondt, S. Macdonald, Alice Smith, P. Lai, S. Shorvon, N. Wood, D. Goldstein (2003)
Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: implications for linkage-disequilibrium gene mapping.American journal of human genetics, 73 3
S. Zöllner, A. Haeseler (2000)
A coalescent approach to study linkage disequilibrium between single-nucleotide polymorphisms.American journal of human genetics, 66 2
D. Goldstein, K. Ahmadi, M. Weale, N. Wood (2003)
Genome scans and candidate gene approaches in the study of common diseases and variable drug responses.Trends in genetics : TIG, 19 11
V. Contini, F. Marques, C. Garcia, M. Hutz, Claiton Bau (2006)
MAOA‐uVNTR polymorphism in a Brazilian sample: Further support for the association with impulsive behaviors and alcohol dependenceAmerican Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 141B
J. Weber, Carmen Wong (1993)
Mutation of human short tandem repeats.Human molecular genetics, 2 8
Tao Li, Chi-Ken Chen, Xun Hu, D. Ball, Shih-ku Lin, Wai Chen, P. Sham, E. Loh, Robin Murray, D. Collier (2004)
Association analysis of the DRD4 and COMT genes in methamphetamine abuseAmerican Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 129B
Recent efforts have focused on the challenges of finding alleles that contribute to health‐related phenotypes in genome‐wide association studies. However, in candidate gene studies, where the genomic region of interest is small and recombination is limited, factors that affect the ability to detect disease‐susceptibility alleles remain poorly understood. In particular, it is unclear how varying the number of markers on a haplotype, the type of marker (e.g., single nucleotide polymorphism (SNP), short tandem repeat (STR)), including the causative site (cs) as a genetic marker, or population demographics influences the power to detect a candidate gene. We evaluated the power of association tests using coalescent‐modeled computer simulations. Results show that an effective number of markers on a haplotype is dependent on whether the cs is included as a marker. When the analyses include the cs, highest power is achieved with a single‐marker association test. However, when the cs is excluded from analyses, the addition of more nonfunctional SNPs on the haplotype increases power to a certain point under most scenarios. We find a rapidly expanding population always has lower power compared to a population of constant size; although utilizing markers with a frequency of at least 5% improves the chance of detecting an association. Comparing the mutational properties of a nonfunctional SNP versus an STR, multi‐allelic STRs provide more or comparable power than a bi‐allelic SNP unless SNP frequencies are constrained to 10% or more. Similarly, including an STR with SNPs on a haplotype improves power unless SNP frequencies are 5% or more. © 2007 Wiley‐Liss, Inc.
American Journal of Medical Genetics part B – Wiley
Published: Jan 5, 2008
Keywords: haplotype; power; short tandem repeat; SNP; demographics
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.