Concise gene signature for point-of-care classification of tuberculosis

EMBO Molecular Medicine

Volumn 8, Issue 2, 2016, Pages 86-95

  Maertzdorf, Jeroen ^a   Mcewen, Gayle ^a   Weiner, January ^a   Tian, Song ^b   Lader, Eric ^b   Schriek, Ulrich ^c   Mayanja Kizza, Harriet ^d   Ota, Martin ^e   Kenneth, John ^f   Kaufmann, Stefan H E ^a  

^a MAX PLANCK INSTITUTE FOR INFECTION BIOLOGY   (Germany)

^b QIAGEN   (United States)

^c QIAGEN GMBH   (Germany)

^d MAKERERE UNIVERSITY   (Uganda)

^e MEDICAL RESEARCH COUNCIL LABORATORIES   (Gambia)

^f ST JOHN'S NATIONAL ACADEMY OF HEALTH SCIENCES   (India)

Author keywords

Disease classification; Genomics; Molecular diagnosis; Real time PCR; Tuberculosis

Indexed keywords

ACCURACY; ARTICLE; COHORT ANALYSIS; CONTROLLED STUDY; DISEASE CLASSIFICATION; ENDEMIC DISEASE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC IDENTIFICATION; HUMAN; INDIAN; MAJOR CLINICAL STUDY; PANDEMIC; POINT OF CARE TESTING; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; TUBERCULOSIS; VALIDATION PROCESS; MOLECULAR DIAGNOSIS; PATHOLOGY; POINT OF CARE SYSTEM; PREDICTIVE VALUE; PROCEDURES; VALIDATION STUDY;

GENE EXPRESSION PROFILING; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; POINT-OF-CARE SYSTEMS; PREDICTIVE VALUE OF TESTS; SENSITIVITY AND SPECIFICITY; TUBERCULOSIS;

EID: 84957943318     PISSN: 17574676     EISSN: 17574684     Source Type: Journal    
DOI: 10.15252/emmm.201505790     Document Type: Article

References (29)

1. Abu-Raddad LJ, Sabatelli L, Achterberg JT, Sugimoto JD, Longini IM Jr, Dye C, Halloran ME (2009) Epidemiological benefits of more-effective tuberculosis vaccines, drugs, and diagnostics. Proc Natl Acad Sci USA 106: 13980-13985
2. Babu K (2013) Sarcoidosis in tuberculosis-endemic regions: India. J Ophthalmic Inflamm Infect 3: 53
3. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 57: 289-300
4. Berry MP, Graham CM, McNab FW, Xu Z, Bloch SA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ et al (2010) An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466: 973-977
5. Bloom CI, Graham CM, Berry MP, Rozakeas F, Redford PS, Wang Y, Xu Z, Wilkinson KA, Wilkinson RJ, Kendrick Y et al (2013) Transcriptional blood signatures distinguish pulmonary tuberculosis, pulmonary sarcoidosis, pneumonias and lung cancers. PLoS ONE 8: e70630
6. Boehme CC, Nicol MP, Nabeta P, Michael JS, Gotuzzo E, Tahirli R, Gler MT, Blakemore R, Worodria W, Gray C et al (2011) Feasibility, diagnostic accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of tuberculosis and multidrug resistance: a multicentre implementation study. Lancet 377: 1495-1505
7. Chaussabel D, Baldwin N (2014) Democratizing systems immunology with modular transcriptional repertoire analyses. Nat Rev Immunol 14: 271-280
8. Dawany N, Showe LC, Kossenkov AV, Chang C, Ive P, Conradie F, Stevens W, Sanne I, Azzoni L, Montaner LJ (2014) Identification of a 251 gene expression signature that can accurately detect M. tuberculosis in patients with and without HIV co-infection. PLoS ONE 9: e89925
9. Fu S, Qu G, Guo S, Ma L, Zhang N, Zhang S, Gao S, Shen Z (2011) Applications of loop-mediated isothermal DNA amplification. Appl Biochem Biotechnol 163: 845-850
10. Hothorn T, Hornik K, Zeileis A (2006) Unbiased recursive partitioning: a conditional inference framework. J Comput Graph Stat 15: 651-674
11. Kaforou M, Wright VJ, Oni T, French N, Anderson ST, Bangani N, Banwell CM, Brent AJ, Crampin AC, Dockrell HM et al (2013) Detection of tuberculosis in HIV-infected and -uninfected African adults using whole blood RNA expression signatures: a case-control study. PLoS Med 10: e1001538
12. Lee SH, Kim SW, Kang JY, Ahn CH (2008) A polymer lab-on-a-chip for reverse transcription (RT)-PCR based point-of-care clinical diagnostics. Lab Chip 8: 2121-2127
13. Liaw A, Wiener M (2002) Classification and regression by randomForest. R News 2: 18-22
14. Maertzdorf J, Kaufmann SH, Weiner J III (2015) Toward a unified biosignature for tuberculosis. Cold Spring Harb Perspect Med 5: a018531
15. Maertzdorf J, Ota M, Repsilber D, Mollenkopf HJ, Weiner J, Hill PC, Kaufmann SH (2011a) Functional correlations of pathogenesis-driven gene expression signatures in tuberculosis. PLoS ONE 6: e26938
16. Maertzdorf J, Repsilber D, Parida SK, Stanley K, Roberts T, Black G, Walzl G, Kaufmann SH (2011b) Human gene expression profiles of susceptibility and resistance in tuberculosis. Genes Immun 12: 15-22
17. Maertzdorf J, Weiner J III, Mollenkopf HJ, Bauer T, Prasse A, Muller-Quernheim J, Kaufmann SH (2012) Common patterns and disease-related signatures in tuberculosis and sarcoidosis. Proc Natl Acad Sci USA 109: 7853-7858
18. Maurin M (2012) Real-time PCR as a diagnostic tool for bacterial diseases. Expert Rev Mol Diagn 12: 731-754
19. Naito T, Tanaka H, Naoe Y, Taniuchi I (2011) Transcriptional control of T-cell development. Int Immunol 23: 661-668
20. Norbis L, Miotto P, Alagna R, Cirillo DM (2013) Tuberculosis: lights and shadows in the current diagnostic landscape. New Microbiol 36: 111-120
21. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28: E63
22. Pai M, Schito M (2015) Tuberculosis diagnostics in 2015: landscape, priorities, needs, and prospects. J Infect Dis 211: S21-S28
23. Perkins JR, Dawes JM, Orengo C, McMahon SB, Bennett DL, Kohl M (2012) ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. BMC Genom 13: 296
24. Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez JC, Muller M (2011) pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics 12: 77
25. Satproedprai N, Wichukchinda N, Suphankong S, Inunchot W, Kuntima T, Kumpeerasart S, Wattanapokayakit S, Nedsuwan S, Yanai H, Higuchi K et al (2015) Diagnostic value of blood gene expression signatures in active tuberculosis in Thais: a pilot study. Genes Immun 16: 253-260
26. Scrivens M, Dickenson JM (2005) Functional expression of the P2Y14 receptor in murine T-lymphocytes. Br J Pharmacol 146: 435-444
27. Song HO, Kim JH, Ryu HS, Lee DH, Kim SJ, Kim DJ, Suh IB, Choi DY, In KH, Kim SW et al (2012) Polymeric LabChip real-time PCR as a point-of-care-potential diagnostic tool for rapid detection of influenza A/H1N1 virus in human clinical specimens. PLoS ONE 7: e53325
28. Weiner J, Maertzdorf J, Kaufmann SH (2013) The dual role of biomarkers for understanding basic principles and devising novel intervention strategies in tuberculosis. Ann NY Acad Sci 1283: 22-29
29. World Health Organization (2015) Global Tuberculosis Report 2015. Geneva: WHO