Cohen’s h for detection of disease association with rare genetic variants

BMC Genomics

Jih-I Yeh¹  Shu-Hui Wen² 

[1] Department of Family Medicine, Buddhist Tzu-Chi General Hospital, 707, Sec 3, Chung-Yang Rd, Hualien 97002, Taiwan;Department of Public Health, College of Medicine, Tzu-Chi University, 701, Sec 3, Chung-Yang Rd, Hualien 97004, Taiwan

关键词: Rare variant;    Power;    Odds ratio;    Cohen’s h;    Effect size;   

Others  :  1128500
DOI  :  10.1186/1471-2164-15-875

 received in 2014-06-20, accepted in 2014-10-03,  发布年份 2014

【 摘 要 】

Background

The power of the genome wide association studies starts to go down when the minor allele frequency (MAF) is below 0.05. Here, we proposed the use of Cohen’s h in detecting disease associated rare variants. The variance stabilizing effect based on the arcsine square root transformation of MAFs to generate Cohen’s h contributed to the statistical power for rare variants analysis. We re-analyzed published datasets, one microarray and one sequencing based, and used simulation to compare the performance of Cohen’s h with the risk difference (RD) and odds ratio (OR).

Results

The analysis showed that the type 1 error rate of Cohen’s h was as expected and Cohen’s h and RD were both less biased and had higher power than OR. The advantage of Cohen’s h was more obvious when MAF was less than 0.01.

Conclusions

Cohen’s h can increase the power to find genetic association of rare variants and diseases, especially when MAF is less than 0.01.

【 授权许可】

   
2014 Wen and Yeh; licensee BioMed Central Ltd.

【 图 表 】

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