Diagnostic ‘omics’ for active tuberculosis

Haas, Carolin T.; Roe, Jennifer K.; Pollara, Gabriele; Mehta, Meera; Noursadeghi, Mahdad

doi:10.1186/s12916-016-0583-9

Table 1 Transcriptomic studies

From: Diagnostic ‘omics’ for active tuberculosis

Study	Sample	Dataset GSE number	Country	Classes	Number	HIV status	Case definition					Independent test set^c	Validation set^d	Evaluation of accuracy	Signature size
Study	Sample	Dataset GSE number	Country	Classes	Number	HIV status	Prior TB treatment^a	TB location	Microbiologically proven^b	TST	IGRA	Independent test set^c	Validation set^d	Evaluation of accuracy	Signature size
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
Dawany et al., 2014 [63]	PBMC	50834	South Africa	HC	22	+						N	Y	Y	HIV vs. HIV/TB 251
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
Ottenhof et al., 2012 [52]	PBMC	56153	Indonesia	HC	23							N	N	N
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
Bloom et al., 2012 [55]	WB	40553	South Africa, UK	LTBI	38	–					+	Y	Y	N	TB vs. LTBI 664 treatment 320
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	–

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
^aNumber of days (d), weeks (w) or months (m) on treatment at time of sampling
^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
^cNever involved in training the model
^dNew, independent set of samples

Back to article page

ISSN: 1741-7015

Contact us

Submission enquiries: bmcmedicineeditorial@biomedcentral.com
General enquiries: info@biomedcentral.com

BMC Medicine

Contact us