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Table 1 Transcriptomic studies

From: Diagnostic ‘omics’ for active tuberculosis

Study Sample Dataset GSE number Country Classes Number HIV status Case definition Independent test setc Validation setd Evaluation of accuracy Signature size
Prior TB treatmenta TB location Microbiologically provenb TST IGRA
Maertzdorf et al., 2015 [62] WB 74092 India TB 113 0 P Y    Y Y Y TB vs. LTB/HV 4
LTBI 56     +/– +/–
HC 20     
Walter et al., 2015 [61] WB 73408 USA TB 109   P Y    Y Y Y  
LTBI      +
Pneumonia     
Anderson et al., 2014 [60] WB 39941 South Africa, Malawi, Kenya CCTB 95   P, EP Y    Y Y Y TB vs. LTBI 42 TB vs. OD 51
CNTB 27   P, EP U   
LTBI 68     + +
OD 140     
CCTB 51 +   P, EP Y   
CNTB 17 +   P, EP U   
LTBI 0 +     + +
OD 93 +     
Cai et al., 2014 [58] PBMC 54992 China TB 173   0 P Y    Y N Y TB vs. HV 1, TB vs. LTBI 1
LTBI 148       +
HC 51      
Dawany et al., 2014 [63] PBMC 50834 South Africa TB 21 + Y P Y    N Y Y HIV vs. HIV/TB 251
HC 22 +      
Kaforou et al., 2013 [59] WB 37250 South Africa, Malawi TB 97 <1d P, EP Y    Y Y Y TB vs. LTBI 27, TB vs. OD 44
LTBI 83     + +
OD 83      +/–
TB 97 + <1d P, EP Y   
LTBI 84 +     + +
OD 92 +      +/–
Bloom et al., 2013 [48] WB 42834 UK & France TB 35 0 P Y    Y Y Y TB vs. OD 144
Sarcoid 61      
Pneumonia 14      
Lung cancer 16      
HC 113     
Verhagen et al., 2013 [98] WB 41055 Venezuela TB 9 0 P   + + N Y Y TB vs. LTBI 5
LTBI 29     + +
HC 25    
Pneumonia 18      
Cliff et al., 2012 [54] WB 3134836238 South Africa TB 27 0, 1/4/26 w P Y    Y Y Y Treatment 62
Maertzdorf et al., 2012 [51] WB 34608 Germany TB 8 0 P U    N N Y  
LTBI 4      +
HC 14     
Sarcoid 18      
Ottenhof et al., 2012 [52] PBMC 56153 Indonesia TB 23 0, 8w, 28w P Y    N N N  
HC 23       
Bloom et al., 2012 [55] WB 40553 South Africa, UK TB 37 0, 2w, 2 m, 6 m, 12 m P Y    Y Y N TB vs. LTBI 664 treatment 320
LTBI 38      +
Lesho et al., 2011 [99] PBMC N/A USA TB 5   P Y +   N N Y TB vs. LTBI vs. BCG vacc vs. HC 127
LTBI 6     +  
BCG vacc 5      
HC 7     
Maertzdorf et al., 2011 [56] WB 25534 South Africa TB 33 0 P Y    N N Y TB vs. LTBI 5
LTBI 34      
HC 9      
Maertzdorf et al., 2011 [50] WB 28623 The Gambia TB 46 0 P Y    N N N  
LTBI 25     +  
HC 37     0  
Lu et al., 2011 [100] PBMC 27984 China TB 46 <4w P Y    Y Y Y TB vs. LTBI 3
LTBI 59      +
HC 26     
Berry et al., 2010 [57] WB 19491194441944319442194391943522098 UK, South Africa PTB 54   0 P Y    Y Y Y TB vs. health 393 TB vs. OD 86
LTBI 69      + +
HC 24     
OD 96       
Stern et al., 2009 [53] PBMC N/A Colombia TB 1    P Y +   N N N  
LTBI 1      +  
HC 1      
Jacobsen et al., 2007 [101] PBMC 6112 Germany TB 37 Y P, EP Y +   N Y N TB vs. LTBI vs. HC 3
LTBI 22      +  
HC 15      
Mistry et al., 2007 [47] WB N/A South Africa TB 10 0 Y     N N Y TB vs. cured vs. LTBI vs. recurrent 9
Cured TB 10      
LTBI 10     +  
Rec TB 10      
  1. WB Whole blood, PBMC Peripheral blood mononuclear cells, TB Active tuberculosis, LTBI Latent TB infection, HC Healthy controls, OD Other diseases, CCTB Culture-confirmed TB, CNTB Culture-negative TB, EP Extrapulmonary, P Pulmonary, Y Yes, N No
  2. aNumber of days (d), weeks (w) or months (m) on treatment at time of sampling
  3. bU if unclear whether all TB cases were microbiologically confirmed, e.g. if diagnosis was based on Mtb culture or chest X-ray or TB symptoms, or if microbiologically proven and unproven TB cases were grouped together
  4. cNever involved in training the model
  5. dNew, independent set of samples