lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection

Ahmad Vaez; Peter J van der Most; Bram P Prins; Harold Snieder; Edwin van den Heuvel; Behrooz Z Alizadeh; Ilja M Nolte

doi:10.1093/bioinformatics/btw021

lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection

Ahmad Vaez, Peter J van der Most, Bram P Prins, Harold Snieder, Edwin van den Heuvel, Behrooz Z Alizadeh, Ilja M Nolte

Research output: Contribution to journal › Article › Academic › peer-review

5 Citations (Scopus)

Abstract

Genome-wide association study (GWAS) of a biomarker is complicated when the assay procedure of the biomarker is restricted by a Limit of Detection (LOD). Those observations falling outside the LOD cannot be simply discarded, but should be included into the analysis by applying an appropriate statistical method. However, the problem of LOD in GWAS analysis of such biomarkers is usually overlooked. 'lodGWAS' is a flexible, easy-to-use R package that provides a simple and elegant way for GWAS analysis of such biomarkers while simultaneously accommodating the problem of LOD by applying a parametric survival analysis method.

Original language	English
Pages (from-to)	1552-1554
Number of pages	3
Journal	Bioinformatics (Oxford, England)
Volume	32
Issue number	10
Early online date	22-Jan-2016
DOIs	https://doi.org/10.1093/bioinformatics/btw021
Publication status	Published - 15-May-2016

Keywords

REGRESSION

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btw021
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5 Citations
1 Software

lodGWAS: Genome-Wide Association Analysis of a Biomarker Accounting for Limit of Detection: Genome-wide association (GWAS) analyses of a biomarker that account for the limit of detection.
Vaez, A. (Developer), Nolte, I. M. (Developer) & van der Most, P. J. (Developer), 2015
Research output: Non-textual form › Software › Academic

Lifelines Biobank
Bakker, S. (Creator), Dotinga, A. (Creator), Vonk, J. M. (Creator), Smidt, N. (Creator), Scholtens, S. (Creator), Swertz, M. (Creator), Wijmenga, C. (Creator), Wolffenbutel, B. H. (Creator), Stolk, R. (Creator), van Zon, S. (Creator), Rosmalen, J. (Creator), Postma, D. S. (Creator), de Boer, R. (Creator), Navis, G. (Creator), Slaets, J. (Creator), Ormel, J. (Creator), van Dijk, F. (Creator) & Bolmer, B. (Data Manager), Lifelines, 2006
https://www.lifelines.nl/ and one more link, https://catalogue.lifelines.nl/ (show fewer)
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Cite this

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AU - van der Most, Peter J

AU - Prins, Bram P

AU - Snieder, Harold

AU - van den Heuvel, Edwin

AU - Alizadeh, Behrooz Z

AU - Nolte, Ilja M

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JF - Bioinformatics (Oxford, England)

IS - 10

ER -

lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection

Abstract

Keywords

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Research output

lodGWAS: Genome-Wide Association Analysis of a Biomarker Accounting for Limit of Detection: Genome-wide association (GWAS) analyses of a biomarker that account for the limit of detection.

Datasets

Lifelines Biobank

Cite this