A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa

Rafal S. Sobota, Catherine M. Stein, Nuri Kodaman, Isaac Maro, Wendy Wieland-Alter, Robert P. Igo, Albert Magohe, La Shaunda L. Malone, Keith Chervenak, Noemi B. Hall, Mecky Matee, Harriet Mayanja-Kizza, Moses Joloba, Jason H. Moore, William K. Scott, Timothy Lahey, W. Henry Boom, C. Fordham von Reyn, Scott M. Williams, Giorgio Sirugo

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6 Scopus citations


One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an “experiment of nature” design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts of tuberculosis from Tanzania and Uganda to identify genetic loci associated with MTB infection in the context of HIV-infection. Among these individuals, 244 tested were tuberculin skin test (TST) positive either at enrollment or during the >8 year follow up, while 225 were not. We identified a genome-wide significant association between a dominant model of rs877356 and binary TST status in the combined cohort (Odds ratio = 0.2671, p = 1.22x10-8). Association was replicated with similar significance when examining TST induration as a continuous trait. The variant lies in the 5q31.1 region, 57kb downstream from IL9. Two-locus analyses of association of variants near rs877356 showed a haplotype comprised of rs877356 and an IL9 missense variant, rs2069885, had the most significant association (p = 1.59x10-12). We also replicated previously linked loci on chromosomes 2, 5, and 11. IL9 is a cytokine produced by mast cells and TH2 cells during inflammatory responses, providing a possible link between airway inflammation and protection from MTB infection. Our results indicate that studying uninfected, HIV-positive participants with extensive exposure increases the power to detect associations in complex infectious disease.

Original languageEnglish (US)
Article numbere1006710
JournalPLoS genetics
Issue number6
StatePublished - Jan 1 2017


ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

Cite this

Sobota, R. S., Stein, C. M., Kodaman, N., Maro, I., Wieland-Alter, W., Igo, R. P., Magohe, A., Malone, L. S. L., Chervenak, K., Hall, N. B., Matee, M., Mayanja-Kizza, H., Joloba, M., Moore, J. H., Scott, W. K., Lahey, T., Boom, W. H., von Reyn, C. F., Williams, S. M., & Sirugo, G. (2017). A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa. PLoS genetics, 13(6), [e1006710]. https://doi.org/10.1371/journal.pgen.1006710