Division of Molecular B?iology and Human Genetics

Bioinformatics Research Group


PUBLICATIONS

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2023

  1. Joo, Y.Y., Pacheco, J.A., Thompson, W.K., Rasmussen-Torvik, L.J., Rasmussen, L.V., Lin, F.T.J., Andrade, M., Borthwick, K.M., Bottinger, E., Cagan, A., Carrell, D.S., Denny, J.C., Ellis, S.B., Gottesman, O., Linneman, J.G., Pathak, J., Peissig, P.L., Shang, N., Tromp, G., Veerappan, A., Smith, M.E., Chisholm, R.L., Gawron, A.J., Hayes, M.G., Kho, A.N. Multi-ancestry genome- and phenome-wide association studies of diverticular disease in electronic health records with natural language processing enriched phenotyping algorithm. PLoS One 18:e0283553, 2023. PMID: 37196047, PMC10191288, 10.1371/journal.pone.0283553.
  2. Musvosvi, M., Huang, H., Wang, C., Xia, Q., Rozot, V., Krishnan, A., Acs, P., Cheruku, A., Obermoser, G., Leslie, A., Behar, S.M., Hanekom, W.A., Bilek, N., Fisher, M., Kaufmann, S.H.E., Walzl, G., Hatherill, M., Davis, M.M., Scriba, T.J. T cell receptor repertoires associated with control and disease progression following Mycobacterium tuberculosis infection. Nat Med 29:258-269, 2023. PMID: 36604540, PMC9873565, 10.1038/s41591-022-02110-9. (Bioinformatics Unit members part of consortium)
  3. Shaw, J.A., Meiring, M., Allies, D., Cruywagen, L., Fisher, T.L., Kasavan, K., Roos, K., Botha, S.M., MacDonald, C., Hiemstra, A.M., Simon, D., van Rensburg, I., Flinn, M., Shabangu, A., Kuivaniemi, H., Tromp, G., Malherbe, S.T., Walzl, G., du Plessis, N. Optimising the yield from bronchoalveolar lavage on human participants in infectious disease immunology research. Sci Rep 13:8859, 2023. PMID: 37258565, PMC10231287, 10.1038/s41598-023-35723-2.
  4. Simba, H., Kuivaniemi, H., Abnet, C., Tromp, G., Sewram, V. Environmental and life-style risk factors for esophageal squamous cell carcinoma in Africa: A systematic review and meta-analysis. BMC Public Health 23(1);1782, 2023. PMID: 37710248, PMCID: PMC10500769, doi: 10.1186/s12889-023-16629-0.
  5. Kroon, E.E., Correa-Macedo, W., Evans, R., Seeger, A., Engelbrecht, L., Kriel, J.A., Loos, B., Okugbeni, N., Orlova, M., Cassart, P., Kinnear, C.J., Tromp, G.C., M?ller, M., Wilkinson, R.J., Coussens, A.K., Schurr, E., Hoal, E.G. Neutrophil extracellular trap formation and gene programs distinguish TST/IGRA sensitization outcomes among Mycobacterium tuberculosis exposed persons living with HIV. PLoS Genet. 19:e1010888, 2023. PMID: 37616312, PMCID: PMC10470897, doi: 10.1371/journal.pgen.10108,88. 
  6. Shaw, J.A., Meiring, M., Snyders, C., Everson, F., Sigwadhi, L.N., Ngah, V., Tromp G., Allwood, B., Koegelenberg, C.F.N., Irusen, E.M., Lalla, U., Baines, N., Zemlin, A.E., Erasmus, R.T., Chapanduka, Z.C., Matsha, T.E., Walzl, G., Strijdom, H., du Plessis, N., Zumla, A., Chegou, N., Malherbe, S.T., Nyasulu, P.S. Immunologic and vascular biomarkers of mortality in critical COVID-19 in a South African cohort. Front Immunol. 14:1219097, 2023. PMID: 37465683, PMCID: PMC10351604, doi: 10.3389/fimmu.2023.1219097.?

2022

  1. Curry, B.D., van, T.W.E., Maasdorp, E., Nortje, A., Irusen, E.M., Maree, D., Koegelenberg, C.F.N., Allwood, B.W. Correlation between lung function tests and peak oxygen consumption in post-TB lung disease. Int J Tuberc Lung Dis 26:259-267, 2022. PMID: 35197166, 10.5588/ijtld.21.0504.
  2. Hiemstra, A.M., MacDonald, C.E., van Rensburg, I.C., Stanley, K., Maasdorp, E., Mc Anda, S., T?nsing, S., Shaw, J.A., Tromp, G., van der Spuy, G.D., Urdahl, K.B., Lewinsohn, D.M., Kuivaniemi, H., Du Plessis, N., Malherbe, S.T., Walzl, G. Cascade Immune Mechanisms of Protection against Mycobacterium tuberculosis (IMPAc-TB): study protocol for the Household Contact Study in the Western Cape, South Africa. BMC Infect Dis 22:381, 2022. PMID: 35428268, PMC9012070, 10.1186/s12879-022-07349-8.
  3. Jacobs, R., Awoniyi, D.O., Baumann, R., Stanley, K., McAnda, S., Kaempfer, S., Malherbe, S.T., Singh, M., Walzl, G., Chegou, N.N. Concurrent evaluation of cytokines improves the accuracy of antibodies against Mycobacterium tuberculosis antigens in the diagnosis of active tuberculosis. Tuberculosis (Edinb) 133:102169, 2022. PMID: 35121532, 10.1016/j.tube.2022.102169. (Bioinformatics Unit members part of consortium)
  4. Kotze, L.A., van der Spuy, G., Leonard, B., Penn-Nicholson, A., Musvosvi, M., McAnda, S., Malherbe, S.T., Erasmus, M., Scriba, T., Koegelenberg, C.F.N., Allwood, B.W., Walzl, G., du Plessis, N. Targeted Gene Expression Profiling of Human Myeloid Cells From Blood and Lung Compartments of Patients With Tuberculosis and Other Lung Diseases. Front Immunol 13:839747, 2022. PMID: 35356003, PMC8959218, 10.3389/fimmu.2022.839747. 
  5. Madhvi, A., Mishra, H., Chegou, N.N., Mkhonza, M.N., Ndou, S., Tromp, G., Baker, B. Comparison of Cytokines Expression from Human Monocyte-Derived Macrophages Infected with Different Species of Mycobacteria. J Interferon Cytokine Res 42:141-152, 2022. PMID: 35167347, 10.1089/jir.2021.0216.
  6. Meier, S., Seddon, J.A., Maasdorp, E., Kleynhans, L., du Plessis, N., Loxton, A.G., Malherbe, S.T., Zak, D.E., Thompson, E., Duffy, F.J., Kaufmann, S.H.E., Ottenhoff, T.H.M., Scriba, T.J., Suliman, S., Sutherland, J.S., Winter, J., Kuivaniemi, H., Walzl, G., Tromp, G. Neutrophil degranulation, NETosis and platelet degranulation pathway genes are co-induced in whole blood up to six months before tuberculosis diagnosis. PLoS One17:e0278295, 2022. PMID: 36454773, PMC9714760, 10.1371/journal.pone.0278295.
  7. Meiring, C., Schurz, H., van Helden, P., Hoal, E., Tromp, G., Kinnear, C., Kleynhans, L., Glanzmann, B., van Schalkwyk, L., Miller, M., M?ller, M. African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity. Sci Rep 12:14979, 2022. PMID: 36056068, PMC9440078, 10.1038/s41598-022-19025-7.
  8. Simba, H., Tromp, G., Sewram, V., Mathew, C.G., Chen, W.C., Kuivaniemi, H. Esophageal Cancer Genomics in Africa: Recommendations for Future Research. Front Genet 13:864575, 2022. PMID: 35401654, PMC8990314, 10.3389/fgene.2022.864575.
  9. Sutherland, J.S., van der Spuy, G., Gindeh, A., Thuong, N.T.T., Namuganga, A., Owolabi, O., Mayanja-Kizza, H., Nsereko, M., Thwaites, G., Winter, J., Dockrell, H.M., Scriba, T.J., Geluk, A., Corstjens, P., Stanley, K., Richardson, T., Shaw, J.A., Smith, B., Malherbe, S.T., Walzl, G. Diagnostic Accuracy of the Cepheid 3-gene Host Response Fingerstick Blood Test in a Prospective, Multi-site Study: Interim Results. Clin Infect Dis74:2136-2141, 2022. PMID: 34550342, PMC9258935, 10.1093/cid/ciab839.
  10. Swart, Y., van Eeden, G., Uren, C., van der Spuy, G., Tromp, G., M?ller, M. GWAS in the southern African context. PLoS One 17:e0264657, 2022. PMID: 36170230, PMC9518849, 10.1371/journal.pone.0264657.
  11. van Eeden, G., Uren, C., Pless, E., Mastoras, M., van der Spuy, G.D., Tromp, G., Henn, B.M., M?ller, M. The recombination landscape of the Khoe-San likely represents the upper limits of recombination divergence in humans. Genome Biol 23:172, 2022. PMID: 35945619, PMC9361568, 10.1186/s13059-022-02744-5.

 

2021

  1. Baguma, R., Mbandi, S.K., Rodo, M.J., Erasmus, M., Day, J., Makhethe, L., de Kock, M., van Rooyen, M., Stone, L., Bilek, N., Steyn, M., Africa, H., Darboe, F., Chegou, N.N., Tromp, G., Walzl, G., Hatherill, M., Penn-Nicholson, A., Scriba, T.J. Inflammatory Determinants of Differential Tuberculosis Risk in Pre-Adolescent Children and Young Adults. Front Immunol 12:639965, 2021. PMID: 33717192, PMC7947716, 10.3389/fimmu.2021.639965.
  2. Bezuidenhout, M.C., Wiese, O.J., Moodley, D., Maasdorp, E., Davids, M.R., Koegelenberg, C.F., Lalla, U., Khine-Wamono, A.A., Zemlin, A.E., Allwood, B.W. Correlating arterial blood gas, acid-base and blood pressure abnormalities with outcomes in COVID-19 intensive care patients. Ann Clin Biochem 58:95-101, 2021. PMID: 33103442, 10.1177/0004563220972539.
  3. Eckold, C., Kumar, V., Weiner, J., Alisjahbana, B., Riza, A.L., Ronacher, K., Coronel, J., Kerry-Barnard, S., Malherbe, S.T., Kleynhans, L., Stanley, K., Ruslami, R., Ioana, M., Ugarte-Gil, C., Walzl, G., van Crevel, R., Wijmenga, C., Critchley, J.A., Dockrell, H.M., Cliff, J.M. Impact of Intermediate Hyperglycemia and Diabetes on Immune Dysfunction in Tuberculosis. Clin Infect Dis 72:69-78, 2021. PMID: 32533832, PMC7823074, 10.1093/cid/ciaa751. (Bioinformatics Unit members part of consortium)
  4. Leukes, V.N., Dorhoi, A., Malherbe, S.T., Maasdorp, E., Khoury, J., McAnda, S., Walzl, G., du Plessis, N. Targeting of myeloid-derived suppressor cells by all-trans retinoic acid as host-directed therapy for human tuberculosis. Cell Immunol 364:104359, 2021. PMID: 33865151, PMC8493473, 10.1016/j.cellimm.2021.104359.
  5. Moodley, K., Maasdorp, E., Rennie, S. Could human challenge studies for COVID-19 vaccines be justified in South Africa? S Afr Med J 111:559-562, 2021. PMID: 34382566.
  6. Müller, S.J., Schurz, H., Tromp, G., van der Spuy, G.D., Hoal, E.G., van Helden, P.D., Owusu-Dabo, E., Meyer, C.G., Muntau, B., Thye, T., Niemann, S., Warren, R.M., Streicher, E., M?ller, M., Kinnear, C. A multi-phenotype genome-wide association study of clades causing tuberculosis in a Ghanaian- and South African cohort. Genomics 113:1802-1815, 2021. PMID: 33862184, 10.1016/j.ygeno.2021.04.024.
  7. Mutavhatsindi, H., van der Spuy, G.D., Malherbe, S.T., Sutherland, J.S., Geluk, A., Mayanja-Kizza, H., Crampin, A.C., Kassa, D., Howe, R., Mihret, A., Sheehama, J.A., Nepolo, E., Günther, G., Dockrell, H.M., Corstjens, P., Stanley, K., Walzl, G., Chegou, N.N. Validation and Optimization of Host Immunological Bio-Signatures for a Point-of-Care Test for TB Disease. Front Immunol 12:607827, 2021. PMID: 33717089, PMC7952865, 10.3389/fimmu.2021.607827.
  8. Scriba, T.J., Fiore-Gartland, A., Penn-Nicholson, A., Mulenga, H., Kimbung Mbandi, S., Borate, B., Mendelsohn, S.C., Hadley, K., Hikuam, C., Kaskar, M., Musvosvi, M., Bilek, N., Self, S., Sumner, T., White, R.G., Erasmus, M., Jaxa, L., Raphela, R., Innes, C., Brumskine, W., Hiemstra, A., Malherbe, S.T., Hassan-Moosa, R., Tameris, M., Walzl, G., Naidoo, K., Churchyard, G., Hatherill, M. Biomarker-guided tuberculosis preventive therapy (CORTIS): a randomised controlled trial. Lancet Infect Dis 21:354-365, 2021. PMID: 33508224, PMC7907670, 10.1016/s1473-3099(20)30914-2. (Bioinformatics Unit members part of consortium)
  9. Shaw, J.A., Meiring, M., Cummins, T., Chegou, N.N., Claassen, C., Du Plessis, N., Flinn, M., Hiemstra, A., Kleynhans, L., Leukes, V., Loxton, A.G., MacDonald, C., Mtala, N., Reuter, H., Simon, D., Stanley, K., Tromp, G., Preiser, W., Malherbe, S.T., Walzl, G. Higher SARS-CoV-2 seroprevalence in workers with lower socioeconomic status in Cape Town, South Africa. PLoS One 16:e0247852, 2021. PMID: 33630977, PMC7906413, 10.1371/journal.pone.0247852.
  10. van Eeden, G., Uren, C., van der Spuy, G., Tromp, G., M?ller, M. Local ancestry inference in heterogeneous populations-Are recent recombination events more relevant? Brief Bioinform 222021. PMID: 34343255, 10.1093/bib/bbab300.
  11. Womersley, J.S., Spies, G., Tromp, G., Seedat, S., Hemmings, S.M.J. Longitudinal telomere length profile does not reflect HIV and childhood trauma impacts on cognitive function in South African women. J Neurovirol27:735-749, 2021. PMID: 34448146, PMC8602727, 10.1007/s13365-021-01009-4.
  12. Yoon, S., Wang, X., Vongpunsawad, S., Tromp, G., Kuivaniemi, H. Editorial: FDA-Approved Drug Repositioning for P-Glycoprotein Overexpressing Resistant Cancer. Front Oncol 11:632657, 2021. PMID: 33816271, PMC8018233, 10.3389/fonc.2021.632657.

 

2020

  1. Allwood, B.W., Maasdorp, E., Kim, G.J., Cooper, C.B., Goldin, J., van Zyl-Smit, R.N., Bateman, E.D., Dawson, R. Transition from Restrictive to Obstructive Lung Function Impairment During Treatment and Follow-Up of Active Tuberculosis. Int J Chron Obstruct Pulmon Dis 15:1039-1047, 2020. PMID: 32494129, PMC7227812, 10.2147/copd.S219731.
  2. Eribo, O.A., Leqheka, M.S., Malherbe, S.T., McAnda, S., Stanley, K., van der Spuy, G.D., Walzl, G., Chegou, N.N. Host urine immunological biomarkers as potential candidates for the diagnosis of tuberculosis. Int J Infect Dis 99:473-481, 2020. PMID: 32800854, 10.1016/j.ijid.2020.08.019.
  3. Madhvi, A., Mishra, H., Chegou, N.N., Tromp, G., Van Heerden, C.J., Pietersen, R.D., Leisching, G., Baker, B. Distinct host-immune response toward species related intracellular mycobacterial killing: A transcriptomic study. Virulence 11:170-182, 2020. PMID: 32052695, PMC7051142, 10.1080/21505594.2020.1726561.
  4. Malherbe, S.T., Chen, R.Y., Dupont, P., Kant, I., Kriel, M., Loxton, A.G., Smith, B., Beltran, C.G.G., van Zyl, S., McAnda, S., Abrahams, C., Maasdorp, E., Doruyter, A., Via, L.E., Barry, C.E., 3rd, Alland, D., Richards, S.G., Ellman, A., Peppard, T., Belisle, J., Tromp, G., Ronacher, K., Warwick, J.M., Winter, J., Walzl, G. Quantitative 18F-FDG PET-CT scan characteristics correlate with tuberculosis treatment response. EJNMMI Res 10:8, 2020. PMID: 32040770, PMC7010890, 10.1186/s13550-020-0591-9.
  5. Odia, T., Malherbe, S.T., Meier, S., Maasdorp, E., Kleynhans, L., du Plessis, N., Loxton, A.G., Zak, D.E., Thompson, E., Duffy, F.J., Kuivaniemi, H., Ronacher, K., Winter, J., Walzl, G., Tromp, G. The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment. Front Immunol 11:596173, 2020. PMID: 33643286, PMC7902901, 10.3389/fimmu.2020.596173.
  6. Oluwole, O.G., Kuivaniemi, H., Abrahams, S., Haylett, W.L., Vorster, A.A., van Heerden, C.J., Kenyon, C.P., Tabb, D.L., Fawale, M.B., Sunmonu, T.A., Ajose, A., Olaogun, M.O., Rossouw, A.C., van Hillegondsberg, L.S., Carr, J., Ross, O.A., Komolafe, M.A., Tromp, G., Bardien, S. Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson's disease in Black South African and Nigerian patients. BMC Med Genet 21:23, 2020. PMID: 32019516, PMC7001245, 10.1186/s12881-020-0953-1.
  7. Penn-Nicholson, A., Mbandi, S.K., Thompson, E., Mendelsohn, S.C., Suliman, S., Chegou, N.N., Malherbe, S.T., Darboe, F., Erasmus, M., Hanekom, W.A., Bilek, N., Fisher, M., Kaufmann, S.H.E., Winter, J., Murphy, M., Wood, R., Morrow, C., Van Rhijn, I., Moody, B., Murray, M., Andrade, B.B., Sterling, T.R., Sutherland, J., Naidoo, K., Padayatchi, N., Walzl, G., Hatherill, M., Zak, D., Scriba, T.J. RISK6, a 6-gene transcriptomic signature of TB disease risk, diagnosis and treatment response. Sci Rep 10:8629, 2020. PMID: 32451443, PMC7248089, 10.1038/s41598-020-65043-8. (Bioinformatics Unit members part of consortium)

 

2019

  1. Darboe, F., Mbandi, S.K., Naidoo, K., Yende-Zuma, N., Lewis, L., Thompson, E.G., Duffy, F.J., Fisher, M., Filander, E., van Rooyen, M., Bilek, N., Mabwe, S., McKinnon, L.R., Chegou, N., Loxton, A., Walzl, G., Tromp, G., Padayatchi, N., Govender, D., Hatherill, M., Karim, S.A., Zak, D.E., Penn-Nicholson, A., Scriba, T.J. Detection of Tuberculosis Recurrence, Diagnosis and Treatment Response by a Blood Transcriptomic Risk Signature in HIV-Infected Persons on Antiretroviral Therapy. Front Microbiol 10:1441, 2019. PMID: 31297103, PMC6608601, 10.3389/fmicb.2019.01441.
  2. Duffy, F.J., Weiner, J., 3rd, Hansen, S., Tabb, D.L., Suliman, S., Thompson, E., Maertzdorf, J., Shankar, S., Tromp, G., Parida, S., Dover, D., Axthelm, M.K., Sutherland, J.S., Dockrell, H.M., Ottenhoff, T.H.M., Scriba, T.J., Picker, L.J., Walzl, G., Kaufmann, S.H.E., Zak, D.E. Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome. Front Immunol 10:527, 2019. PMID: 30967866, PMC6440524, 10.3389/fimmu.2019.00527.
  3. Edwards, T.L., Giri, A., Hellwege, J.N., Hartmann, K.E., Stewart, E.A., Jeff, J.M., Bray, M.J., Pendergrass, S.A., Torstenson, E.S., Keaton, J.M., Jones, S.H., Gogoi, R.P., Kuivaniemi, H., Jackson, K.L., Kho, A.N., Kullo, I.J., McCarty, C.A., Im, H.K., Pacheco, J.A., Pathak, J., Williams, M.S., Tromp, G., Kenny, E.E., Peissig, P.L., Denny, J.C., Roden, D.M., Velez Edwards, D.R. A Trans-Ethnic Genome-Wide Association Study of Uterine Fibroids. Front Genet 10:511, 2019. PMID: 31249589, PMC6582231, 10.3389/fgene.2019.00511.
  4. Kuivaniemi, H., Tromp, G. Type III collagen (COL3A1): Gene and protein structure, tissue distribution, and associated diseases. Gene 707:151-171, 2019. PMID: 31075413, PMC6579750, 10.1016/j.gene.2019.05.003.
  5. Penn-Nicholson, A., Hraha, T., Thompson, E.G., Sterling, D., Mbandi, S.K., Wall, K.M., Fisher, M., Suliman, S., Shankar, S., Hanekom, W.A., Janjic, N., Hatherill, M., Kaufmann, S.H.E., Sutherland, J., Walzl, G., De Groote, M.A., Ochsner, U., Zak, D.E., Scriba, T.J. Discovery and validation of a prognostic proteomic signature for tuberculosis progression: A prospective cohort study. PLoS Med 16:e1002781, 2019. PMID: 30990820, PMC6467365, 10.1371/journal.pmed.1002781. (Bioinformatics Unit members part of consortium)
  6. Ronacher, K., Chegou, N.N., Kleynhans, L., Djoba Siawaya, J.F., du Plessis, N., Loxton, A.G., Maasdorp, E., Tromp, G., Kidd, M., Stanley, K., Kriel, M., Menezes, A., Gutschmidt, A., van der Spuy, G.D., Warren, R.M., Dietze, R., Okwera, A., Thiel, B., Belisle, J.T., Cliff, J.M., Boom, W.H., Johnson, J.L., van Helden, P.D., Dockrell, H.M., Walzl, G. Distinct serum biosignatures are associated with different tuberculosis treatment outcomes. Tuberculosis (Edinb) 118:101859, 2019. PMID: 31434026, PMC6839616, 10.1016/j.tube.2019.101859.
  7. Schurz, H., Müller, S.J., van Helden, P.D., Tromp, G., Hoal, E.G., Kinnear, C.J., M?ller, M. Evaluating the Accuracy of Imputation Methods in a Five-Way Admixed Population. Front Genet 10:34, 2019. PMID: 30804980, PMC6370942, 10.3389/fgene.2019.00034.
  8. Schurz, H., Salie, M., Tromp, G., Hoal, E.G., Kinnear, C.J., M?ller, M. The X chromosome and sex-specific effects in infectious disease susceptibility. Hum Genomics 13:2, 2019. PMID: 30621780, PMC6325731, 10.1186/s40246-018-0185-z.
  9. Simba, H., Kuivaniemi, H., Lutje, V., Tromp, G., Sewram, V. Systematic Review of Genetic Factors in the Etiology of Esophageal Squamous Cell Carcinoma in African Populations. Front Genet 10:642, 2019. PMID: 31428123, PMC6687768, 10.3389/fgene.2019.00642.
  10. Warren, R., Ismail, N., Chegou, N.N., Theron, G., Walzl, G., Malherbe, S.T., Kinnear, C.J., Van der Spuy, G.D., Goosen, W., Miller, M.A., Diacon, A.H., Van Helden, P.D. Tuberculosis research in South Africa over the past 30 years: From bench to bedside. S Afr Med J 109:45-52, 2019. PMID: 32252868, 10.7196/SAMJ.2019.v109i11b.14249.