GEO DataSets

(Submitter supplied) Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculosis infection to tuberculosis disease might lead to interventions that combat the tuberculosis epidemic. We aimed to assess whether global gene expression measured in whole blood of healthy people allowed identification of prospective signatures of risk of active tuberculosis disease. RESULTS:Between July 6, 2005, and April 23, 2007, we enrolled 6363 from the ACS study and 4466 from independent South African and Gambian cohorts. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

355 Samples

Download data: XLSX

(Submitter supplied) The study aimed to define transcriptional signatures for detection of active TB (TB) compared to latent TB infection (LTBI) as well as to other diseases (OD) with similar clinical phenotypes in patients with and without HIV in two African adult populations. Transcriptional signatures were identified that distinguished active TB from LTBI, active TB from other diseases, and active TB from both LTBI and other diseases in HIV+/- patients.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

537 Samples

Download data: TXT

(Submitter supplied) Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculosis infection to tuberculosis disease might lead to interventions that combat the tuberculosis epidemic in the context of house hold contacts.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

434 Samples

Download data: CSV, TXT

(Submitter supplied) Exploratory RNA expression analysis during development of leprosy allows identification of RISK4LEP, a 4-gene blood RNA signature predicting leprosy years before clinical onset.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

120 Samples

Download data: CSV, TSV

(Submitter supplied) Background: Blood transcriptomic signatures for diagnosis of tuberculosis (TB) have shown promise in case-control studies but their diagnostic accuracy has not been prospectively validated in adults presenting with the full clinical spectrum of suspected TB, including extra-pulmonary TB, and its associated differential diagnoses with concomitant latent TB infection. Methods: Our study was nested within a prospective multi-center cohort study in secondary care in England. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

628 Samples

Download data: TXT

(Submitter supplied) We evaluated the predictive ability of various gene signatures in baseline peripheral blood mononuclear cell samples to distinguish Mtb-infected individuals who eventually progress to TB disease (progressors) or who remain asymptomatic (non-progressors) during clinical follow-up; we also compare long-term Mtb-infected non-progressors from patients with TB disease

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

51 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

491 Samples

Download data

(Submitter supplied) The study aimed to define transcriptional signatures for detection of active TB (TB) compared to latent TB infection (LTBI) as well as to other diseases (OD) with similar clinical phenotypes in patients with and without HIV in two African paediatric populations. Transcriptional signatures were identified that distinguished active TB from LTBI, and active TB from other diseases.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

334 Samples

Download data: TXT

(Submitter supplied) The study aimed to define transcriptional signatures for detection of active TB (TB) compared to latent TB infection (LTBI) as well as to other diseases (OD) with similar clinical phenotypes in patients with and without HIV in a paediatric cohort from Kenya Transcriptional signatures were identified that distinguished active TB from LTBI, active TB from other diseases, and active TB from both LTBI and other diseases in HIV+/- patients.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

157 Samples

Download data: TXT

(Submitter supplied) Knowing when a person was infected with Mycobacterium tuberculosis (M.tb) is critical as recent infection is the strongest clinical risk factor for progression to TB disease in immunocompetent individuals. However, time since M.tb infection is very difficult to determine in routine clinical practice. We determined whether gene expression patterns in blood RNA correlate with time since M.tb infection or exposure to develop a biomarker for recent exposure. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

26 Samples

Download data: TXT

(Submitter supplied) Whole blood gene expression profiling from well and malnourished Indian individuals with TB and severely malnourished household contacts with latent TB infection (LTBI). Severe malnutrition was defined as body mass index (BMI) <16. kg/m2 in adults and based on weight-for-height Z scores in children <18 years. Gene expression was measured using RNA-sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

48 Samples

Download data: TXT

(Submitter supplied) We report the accuracy of various existing blood transcriptional signatures in distinguishing TB and LTBI individuals in a South Indian cohort

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

44 Samples

Download data: XLSX

(Submitter supplied) Analysis of UK blood transcriptional profiles before treatment to indentify changes that occur during (2 weeks, 2 months), at the end of treatment (6 months) and after treatment (12 months) Analysis of South African blood transcriptional profiles before treatment to indentify changes that occur during (2 weeks, 2 months), at the end of treatment (6 months) and after treatment (12 months)

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

204 Samples

Download data: TXT

(Submitter supplied) In a prospective case-control study, we identified novel transcriptional classifiers for TB among US patients and systematically compared their accuracy to other classifiers in published studies.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL11532

109 Samples

Download data: CEL

(Submitter supplied) Genome wide DNA methylation profiling of PBMC from South African patients either infected with HIV only or coinfected with HIV and tuberculosis (TB). The Illumina Infinium 27k Human DNA methylation Beadchip was used to obtain DNA methylation profiles from PBMC samples. Samples included 19 HIV patients and 20 HIV/TB co-infected patients.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL8490

40 Samples

Download data: TXT

(Submitter supplied) Diagnosis of TB, especially in the presence of an HIV co-infection, can be challenging when using conventional diagnostic methods. In this study, we analyzed global gene expression data from PBMC of patients that were either mono-infected with HIV or co-infected with HIV and TB in order to identify a TB-specific gene signature.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4786

Platform:

GPL10558

44 Samples

Download data: TXT

Analysis of PBMCs from HIV patients with and without M. tuberculosis (TB) co-infection. Co-infection with TB is a cause of death in HIV-infected individuals. Results provide insight into a molecular signature to distinguish HIV/TB co-infected patients from HIV mono-infected patients.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 infection sets

Platform:

GPL10558

Series:

GSE50834

44 Samples

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(Submitter supplied) Background: Tuberculosis (TB) among persons living with HIV (PLWH) poses diagnostic challenges. Although several transcriptional signatures have recently been identified as promising tool for TB diagnosis, data are limited in persons with advanced HIV. Methodology: Reads were aligned to the human transcriptome (GRCh38 version 100), comprising both mRNA and ncRNA, with Salmon v1.2.0. A Random Forest algorithm with “leave-one-out” cross-validation was applied in the variance stabilizing transformation gene expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

25 Samples

Download data: TXT

(Submitter supplied) To define mechanisms that underlie progression of Mycobacterium tuberculosis (M.tb) infection to active tuberculosis (TB), we followed M.tb-infected adolescents longitudinally. Those who ultimately developed TB disease (“progressors”) were compared with matched controls, who remained healthy. Whole blood transcriptomic and plasma proteome analyses showed sequential modulation of immunological processes: type I/II interferon signalling and complement cascade were elevated 18 months before TB diagnosis, while changes in myeloid inflammation and lymphoid cell, monocyte and neutrophil gene modules occurred more proximally to TB disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

1650 Samples

Download data: TXT

(Submitter supplied) Identification of blood biomarkers that prospectively predict Mycobacterium tuberculosis treatment response.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

914 Samples

Download data: CSV, TXT