An adaptive permutation approach for genome-wide association study: Evaluation and recommendations for use

BioData Mining

Volumn 7, Issue 1, 2014, Pages

  Che, Ronglin ^a   Jack, John R ^a   Motsinger Reif, Alison A ^a   Brown, Chad C ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE PERMUTATION; ARTICLE; BINOMIAL DISTRIBUTION; FEASIBILITY STUDY; GENE MUTATION; GENETIC ASSOCIATION; GENETIC MODEL; GENOMICS; NONPARAMETRIC TEST; PHARMACOGENOMICS; PRIORITY JOURNAL; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84902053607     PISSN: None     EISSN: 17560381     Source Type: Journal    
DOI: 10.1186/1756-0381-7-9     Document Type: Article

References (12)

1. Sequential Monte-Carlo p-values. Besag J, Clifford P, Biometrika 1991 78 2 301 304 10.1093/biomet/78.2.301
2. Monte Carlo evaluation of resampling-based hypothesis tests. Boos DD, Zhang J, J Am Stat Assoc 2000 95 450 486 492 10.1080/01621459.2000.10474226
3. Permutation p-values should never be zero: calculating exact p-values when permutations are randomly drawn. Phipson B, Smyth GK, Stat Appl Genet Mol Biol 2010 9 rticle39 21044043
4. Empirical threshold values for quantitative trait mapping. Churchill GA, Doerge RW, Genetics 1994 138 3 963 971 7851788 (Pubitemid 24337818)
5. Prioritizing GWAS results: a review of statistical methods and recommendations for their application. Cantor RM, Lange K, Sinsheimer JS, Am J Hum Genet 2010 86 1 6 22 10.1016/j.ajhg.2009.11.017 20074509
6. A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. Gao X, Starmer J, Martin ER, Genet Epidemiol 2008 32 4 361 369 10.1002/gepi.20310 18271029 (Pubitemid 351656307)
7. Accounting for multiple comparisons in a genome-wide association study (GWAS). Johnson RC, Nelson GW, Troyer JL, Lautenberger JA, Kessing BD, Winkler CA, O'Brien SJ, BMC Genomics 2010 11 724 10.1186/1471-2164-11-724 21176216
8. PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies. Browning BL, BMC Bioinformatics 2008 9 309 10.1186/1471-2105-9-309 18620604
9. A fast method for computing high-significance disease association in large population-based studies. Kimmel G, Shamir R, Am J Hum Genet 2006 79 3 481 492 10.1086/507317 16909386 (Pubitemid 44384257)
10. PERMORY: an LD-exploiting permutation test algorithm for powerful genome-wide association testing. Pahl R, Schafer H, Bioinformatics 2010 26 17 2093 2100 10.1093/bioinformatics/btq399 20605926
11. Genetic association studies. Lunetta KL, Circulation 2008 118 1 96 101 10.1161/CIRCULATIONAHA.107.700401 18591452
12. Genome-wide association and pharmacological profiling of 29 anticancer agents using lymphoblastoid cell lines. Brown CC, Havener TM, Medina MW, Jack JR, Krauss RM, McLeod HL, Motsinger-Reif AA, Pharmacogenomics 2014 15 2 137 146 10.2217/pgs.13.213 24444404