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Cohen’s h for detection of disease association with rare genetic variants
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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198687/ https://www.ncbi.nlm.nih.gov/pubmed/25294186 http://dx.doi.org/10.1186/1471-2164-15-875 |
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author | Wen, Shu-Hui Yeh, Jih-I |
author_facet | Wen, Shu-Hui Yeh, Jih-I |
author_sort | Wen, Shu-Hui |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-875) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4198687 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41986872014-10-17 Cohen’s h for detection of disease association with rare genetic variants Wen, Shu-Hui Yeh, Jih-I BMC Genomics Methodology Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-875) contains supplementary material, which is available to authorized users. BioMed Central 2014-10-08 /pmc/articles/PMC4198687/ /pubmed/25294186 http://dx.doi.org/10.1186/1471-2164-15-875 Text en © Wen and Yeh; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Methodology Article Wen, Shu-Hui Yeh, Jih-I Cohen’s h for detection of disease association with rare genetic variants |
title | Cohen’s h for detection of disease association with rare genetic variants |
title_full | Cohen’s h for detection of disease association with rare genetic variants |
title_fullStr | Cohen’s h for detection of disease association with rare genetic variants |
title_full_unstemmed | Cohen’s h for detection of disease association with rare genetic variants |
title_short | Cohen’s h for detection of disease association with rare genetic variants |
title_sort | cohen’s h for detection of disease association with rare genetic variants |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198687/ https://www.ncbi.nlm.nih.gov/pubmed/25294186 http://dx.doi.org/10.1186/1471-2164-15-875 |
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