Abstract
The statistical testing of multiple genetic markers in genetic linkage and association studies is discussed and shown to lead to a multiple-testing problem. Various solutions are discussed and demonstrated on published data. The false discovery rate (FDR) and several approaches of estimating it, are mentioned. Randomization (permutation) testing is highly recommended.
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References
Clerget-Darpoux F, Babron MC, Bonaiti-Pellie C (1987) Power and robustness of the linkage homogeneity test in genetic analysis of common disorders. J Psychiatr Res 21:625–630
Sherrington R, Brynjolfsson J, Petursson H, Potter M, Dudleston K, Barraclough B, Wasmuth J, Dobbs M, Gurling H (1988) Localization of a susceptibility locus for schizophrenia on chromosome 5. Nature 336:164–167
Bonferroni CE (1936) Teoria statistica delle classi e calcolo delle probabilità . Pubblicazioni del Istituto Superiore di Scienze Economiche e Commerciali di Firenze 8:3–62
Cheverud JM (2001) A simple correction for multiple comparisons in interval mapping genome scans. Heredity 87:52–58
Devlin B, Roeder K, Wasserman L (2003) Analysis of multilocus models of association. Genet Epidemiol 25:36–47
Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100:9440–9445
Efron B (2004) Large-Scale Simultaneous Hypothesis Testing: The Choice of a Null Hypothesis. Journal of the American Statistical Association 99:96–104
Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125:279–284
Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308:385–389. Epub 2005 Mar 2010
Fisher RA (1935) The design of experiments. Oliver & Boyd, Edinburgh
Manly BFJ (2007) Randomization, bootstrap, and Monte Carlo methods in biology. Chapman & Hall/CRC, Boca Raton, FL
Nijenhuis A, Wilf HS (1978) Combinatorial algorithms for computers and calculators. Academic, New York
Sham PC, Curtis D (1995) Monte Carlo tests for associations between disease and alleles at highly polymorphic loci. Ann Hum Genet 59:97–105
Kimmel G, Shamir R (2006) A fast method for computing high-significance disease association in large population-based studies. Am J Hum Genet 79:481–492
Skol AD, Scott LJ, Abecasis GR, Boehnke M (2006) Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 38:209–213. Epub 2006 Jan 2015
Lazzeroni LC, Lange K (1998) A conditional inference framework for extending the transmission/disequilibrium test. Hum Hered 48:67–81
Hoh J, Wille A, Ott J (2001) Trimming, weighting, and grouping SNPs in human case-control association studies. Genome Res 11:2115–2119
McIntyre LM, Martin ER, Simonsen KL, Kaplan NL (2000) Circumventing multiple testing: a multilocus Monte Carlo approach to testing for association. Genet Epidemiol 19:18–29
Becker T, Cichon S, Jonson E, Knapp M (2005) Multiple testing in the context of haplotype analysis revisited: application to case-control data. Ann Hum Genet 69:747–756
Hoh J, Ott J (2000) Scan statistics to scan markers for susceptibility genes. Proc Natl Acad Sci U S A 97:9615–9617
Zheng G, Freidlin B, Gastwirth JL (2006) Comparison of robust tests for genetic association using case-control studies. IMS Lecture Notes-Monograph Series 49:253–265
Matthews AG, Haynes C, Liu C, Ott J (2008) Collapsing SNP genotypes in case-control genome-wide association studies increases the type I error rate and power. Statistical Applications in Genetics and Molecular Biology 7:Art. 23
Zhang Q, Wang S, Ott J (2008) Combining identity by descent and association in genetic case-control studies. BMC Genet 9:42
Fung HC, Scholz S, Matarin M, Simon-Sanchez J, Hernandez D, Britton A, Gibbs JR, Langefeld C, Stiegert ML, Schymick J, Okun MS, Mandel RJ, Fernandez HH, Foote KD, Rodriguez RL, Peckham E, De Vrieze FW, Gwinn-Hardy K, Hardy JA, Singleton A (2006) Genome-wide genotyping in Parkinson’s disease and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 5:911–916
Balding DJ (2006) A tutorial on statistical methods for population association studies. Nat Rev Genet 7:781–791
Lander E, Kruglyak L (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 11:241–247
Pe’er I, Yelensky R, Altshuler D, Daly MJ (2008) Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet Epidemiol 32:381–385
Ott J (2004) Association of genetic loci: Replication or not, that is the question. Neurology 63:955–958
Gotzsche PC (2006) Believability of relative risks and odds ratios in abstracts: cross sectional study. Bmj 333:231–234
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Zhang, Q., Ott, J. (2009). Multiple Comparisons/Testing Issues. In: Handbook on Analyzing Human Genetic Data. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69264-5_9
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DOI: https://doi.org/10.1007/978-3-540-69264-5_9
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