A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other.

By Dale R. Nyholt. American Journal of Human Genetics, 2004

1,758 citations recorded by the source corpus.

Subfields: Genetics, Statistics and Probability

View Paper: https://www.semanticscholar.org/paper/6756da5a0d5e037a0c143e6418b85633561c927c

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Citations in the corpus

MultiPhen: Joint Model of Multiple Phenotypes Can Increase Discovery in GWAS (2012, methodology): “Here and subsequently, the univariate P value is calculated as the minimum univariate P value across the tested phenotypes corrected for the effective number of tests by applying a ‘‘Nyholt-Šidák correction’’ [16] (see Methods).”
So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests. (2007, background): “and compute , with removed from consideration, con(3) P ! a P ACT (2)”
Genome-wide association analysis by lasso penalized logistic regression (2009, background): “For a more detailed discussion of the multiple testing issues in SNP studies, see Nyholt (2004).”
Avoiding the high Bonferroni penalty in genome-wide association studies (2009, methodology): “The M eff approach was first proposed in genetic studies by Cheverud [2001] and later refined by Nyholt [2004].”
Interleukin 7 receptor α chain ( IL7R ) shows allelic and functional association with multiple sclerosis (2007, methodology): “0006 for rs6897932 was significant after accounting for multiple comparisons using a Bonferroni correction for the effective number of independent SNPs evaluated across the three gene”
Efficiency and power in genetic association studies (2005, background): “and (iii) evaluating statistical significance of putative finding”
The genetic architecture of the human cerebral cortex (2020, methodology): “To estimate themultiple testing burden associated with analyzing 70 phenotypes, we usedmatrix spectral decomposition (12), which yielded 60 independent traits, and a multiple testing significance threshold of P ≤ 8.”
Depression and Anxiety (2008, positive): “Correction for multiple testing was based on Matrix Spectral Decomposition suggested by Nyholt (2004), which corrects the α level, taking into account the correlations among the predictors (HR‐PRS, RMSSD‐PRS, current depression/anxiety, TCA use, SNRI use, and SSRI use).”
Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix (2005, methodology): “In Nyholt (2004)’s evaluation, the Meff method approximated the permutation test accurately, and was more than 100 times faster.”
Atopic dermatitis (2018, background): “Keratinocytes constitutively produce high amounts of IL-1a.(62,63) In inflammatory states human keratinocytes also produce IL-1b.”
Measuring Morphological Integration Using Eigenvalue Variance (2009, background): “The latter purpose was originally developed to determine the number of independent tests to calculate the significance threshold in QTL mapping based on the Bonferroni adjustment (Cheverud 2001; Nyholt 2004).”
Seven New Loci Associated with Age-Related Macular Degeneration (2013, background): “Ronnie J George [58], Christian Gieger [59], Neel Gupta [40], Stephanie A Hagstrom [60], Simon P Harding [61], Christos Haritoglou [62], John R Heckenlively [39], Frank G Holz [63], Guy Hughes [56,64], John P A Ioannidis [65,66,67], Tatsuro Ishibashi [68], Peronne Joseph [17,18], Gyungah Jun [4,69,7”