Novel human genetic variants associated with extrapulmonary tuberculosis: a pilot genome wide association studyReport as inadecuate




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BMC Research Notes

, 4:28

First Online: 31 January 2011Received: 02 August 2010Accepted: 31 January 2011DOI: 10.1186-1756-0500-4-28

Cite this article as: Oki, N.O., Motsinger-Reif, A.A., Antas, P.R. et al. BMC Res Notes 2011 4: 28. doi:10.1186-1756-0500-4-28

Abstract

BackgroundApproximately 5-10% of persons infected with M. tuberculosis develop tuberculosis, but the factors associated with disease progression are incompletely understood. Both linkage and association studies have identified human genetic variants associated with susceptibility to pulmonary tuberculosis, but few genetic studies have evaluated extrapulmonary disease. Because extrapulmonary and pulmonary tuberculosis likely have different underlying pathophysiology, identification of genetic mutations associated with extrapulmonary disease is important.

FindingsWe performed a pilot genome-wide association study among 24 persons with previous extrapulmonary tuberculosis and well-characterized immune defects; 24 pulmonary tuberculosis patients and 57 patients with M. tuberculosis infection served as controls. The Affymetrix GeneChip Human Mapping Xba Array was used for genotyping; after careful quality control, genotypes at 44,175 single nucleotide polymorphisms SNPs were available for analysis. Eigenstrat quantified population stratification within our sample; logistic regression, using results of the Eigenstrat analysis as a covariate, identified significant associations between groups. Permutation testing controlled the family-wise error rate for each comparison between groups. Four SNPs were significantly associated with extrapulmonary tuberculosis compared to controls with M. tuberculosis infection; one rs4893980 in the gene PDE11A, one rs10488286 in KCND2, and one rs2026414 in PCDH15; one was in chromosome 7 but not associated with a known gene. Two additional variants were significantly associated with extrapulmonary tuberculosis compared with pulmonary tuberculosis; one rs340708 in the gene FAM135B and one in chromosome 13 but not associated with a known gene. The function of all four genes affects cell signaling and activity, including in the brain.

ConclusionsIn this pilot study, we identified 6 novel variants not previously known to be associated with extrapulmonary tuberculosis, including two SNPs more common in persons with extrapulmonary than pulmonary tuberculosis. This provides some support for the hypothesis that the pathogenesis and genetic predisposition to extrapulmonary tuberculosis differs from pulmonary tuberculosis. Further study of these novel SNPs, and more well-powered genome-wide studies of extrapulmonary tuberculosis, is warranted.

AbbreviationsETBextrapulmonary tuberculosis

PTBpulmonary tuberculosis

PPDpurified protein derivative

SNPsingle nucleotide polymorphism

MAFminor allele frequency

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-4-28 contains supplementary material, which is available to authorized users.

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Author: Noffisat O Oki - Alison A Motsinger-Reif - Paulo RZ Antas - Shawn Levy - Steven M Holland - Timothy R Sterling

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