A Simulation Study of Permutation, Bootstrap, and Gene Dropping for Assessing Statistical Significance in the Case of Unequal Relatedness

被引：36

作者：

Cheng, Riyan ^{[1
]}

Palmer, Abraham A. ^{[1
,2
]}

机构：

[1] Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA

[2] Univ Chicago, Dept Psychiat & Behav Neurosci, Chicago, IL 60637 USA

来源：

GENETICS | 2013年 / 193卷 / 03期

基金：

美国国家卫生研究院;

关键词：

QUANTITATIVE TRAIT LOCI; ADVANCED INTERCROSS LINES; GENOME-WIDE ASSOCIATION; APPROXIMATE THRESHOLDS; TESTS; POPULATION; VARIANCE;

D O I：

10.1534/genetics.112.146332

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

We used simulations to evaluate methods for assessing statistical significance in association studies. When the statistical model appropriately accounted for relatedness among individuals, unrestricted permutation tests and a few other simulation-based methods effectively controlled type I error rates; otherwise, only gene dropping controlled type I error but at the expense of statistical power.

引用

页码：1015 / +

页数：16

共 39 条

[1] Estimation of variance components of quantitative traits in inbred populations [J].

Abney, M ;

McPeek, MS ;

Ober, C .

AMERICAN JOURNAL OF HUMAN GENETICS, 2000, 66 (02) :629-650

[2] Quantitative-trait homozygosity and association mapping and empirical genomewide significance in large, complex pedigrees: Fasting serum-insulin level in the hutterites [J].

Abney, M ;

Ober, C ;

McPeek, MS .

AMERICAN JOURNAL OF HUMAN GENETICS, 2002, 70 (04) :920-934

[3] Permutation tests for univariate or multivariate analysis of variance and regression [J].

Anderson, MJ .

CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES, 2001, 58 (03) :626-639

[4] Permutation tests for multi-factorial analysis of variance [J].

Anderson, MJ ;

Ter Braak, CJF .

JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION, 2003, 73 (02) :85-113

[5]

[Anonymous], 1993, An introduction to the bootstrap

[6]

Bates D., 2009, Mixed-Effects Models in S and S-PLUS

[7] Genome-Wide Association Studies and the Problem of Relatedness Among Advanced Intercross Lines and Other Highly Recombinant Populations [J].

Cheng, Riyan ;

Lim, Jackie E. ;

Samocha, Kaitlin E. ;

Sokoloff, Greta ;

Abney, Mark ;

Skol, Andrew D. ;

Palmer, Abraham A. .

GENETICS, 2010, 185 (03) :1033-1044

[8] A simple correction for multiple comparisons in interval mapping genome scans [J].

Cheverud, JM .

HEREDITY, 2001, 87 (1) :52-58

[9] Naive application of permutation testing leads to inflated type I error rates [J].

Churchill, G. A. ;

Doerge, R. W. .

GENETICS, 2008, 178 (01) :609-610

[10]

CHURCHILL GA, 1994, GENETICS, V138, P963

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