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Diagnostic performance of transcriptomic signatures for the evaluation of suspected tuberculosis in routine clinical practice

ABSTRACT: Diagnostic performance of transcriptomic signatures for the evaluation of suspected tuberculosis in routine clinical practice

PROVIDER: PRJNA602856 | ENA |

REPOSITORIES: ENA

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Diagnostic performance of transcriptomic signatures for the evaluation of suspected tuberculosis in routine clinical practice

Project description: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. Patients had whole-blood taken for microarray to measure abundance of 47,275 transcripts and interferon-gamma release assays (IGRAs) at clinical presentation with suspected TB and were followed up for 6-12 months’ to determine final diagnoses based on pre-defined diagnostic criteria. The diagnostic accuracy of published transcriptomic signatures and a novel cohort-derived signature were assessed to generate area under the receiver-operating characteristic curves (AUC), sensitivities and specificities.

2021-01-26 | GSE144127 | GEO

Genomic Grade Index (GGI): Feasibility in routine practice and impact on treatment decisions in early breast cancer

Project description:Genomic Grade Index (GGI) is a 97-gene signature that improves histologic grade (HG) classification in invasive breast carcinoma. In this prospective study we sought to evaluate the feasibility of performing GGI in routine clinical practice and its impact on treatment recommendations. Patients with pT1pT2 or operable pT3, N0-3 invasive breast carcinoma were recruited from 8 centers in Belgium. Fresh surgical samples were sent at room temperature in the MapQuant DxM-bM-^DM-" PathKit for centralized genomic analysis. Genomic profiles were determined using Affymetrix U133 Plus 2.0 and GGI calculated using the MapQuant DxM-bM-^DM-" protocol, which defines tumors as low or high Genomic Grade (GG-1 and GG-3 respectively). 180 pts were recruited and 155 were eligible. The MapQuant test was performed in 142 cases and GGI was obtained in 78% of cases (n=111). Reasons for failures were 15 samples with <30% of invasive tumor cells (11%), 15 with insufficient RNA quality (10%), and 1 failed hybridization (<1%). For tumors with an available representative sample (M-bM-^IM-% 30% inv. tumor cells) (n=127), the success rate was 87.5 %. GGI reclassified 69% of the 54 HG2 tumors as GG-1 (54%) or GG-3 (46%). Changes in treatment recommendations occurred mainly in the subset of HG2 tumors reclassified into GG-3, with increased use of chemotherapy in this subset. The use of GGI is feasible in routine clinical practice and impacts treatment decisions in early-stage breast cancer. Total RNA was extracted from fresh tumor tissues comprising M-bM-^IM-%30% invasive tumor cells and hybridized on Affymetrix microarrays if the RIN was M-bM-^IM-% 7.

2013-06-03 | E-GEOD-43365 | biostudies-arrayexpress

Genomic Grade Index (GGI): Feasibility in routine practice and impact on treatment decisions in early breast cancer

Project description:Genomic Grade Index (GGI) is a 97-gene signature that improves histologic grade (HG) classification in invasive breast carcinoma. In this prospective study we sought to evaluate the feasibility of performing GGI in routine clinical practice and its impact on treatment recommendations. Patients with pT1pT2 or operable pT3, N0-3 invasive breast carcinoma were recruited from 8 centers in Belgium. Fresh surgical samples were sent at room temperature in the MapQuant Dx™ PathKit for centralized genomic analysis. Genomic profiles were determined using Affymetrix U133 Plus 2.0 and GGI calculated using the MapQuant Dx™ protocol, which defines tumors as low or high Genomic Grade (GG-1 and GG-3 respectively). 180 pts were recruited and 155 were eligible. The MapQuant test was performed in 142 cases and GGI was obtained in 78% of cases (n=111). Reasons for failures were 15 samples with <30% of invasive tumor cells (11%), 15 with insufficient RNA quality (10%), and 1 failed hybridization (<1%). For tumors with an available representative sample (≥ 30% inv. tumor cells) (n=127), the success rate was 87.5 %. GGI reclassified 69% of the 54 HG2 tumors as GG-1 (54%) or GG-3 (46%). Changes in treatment recommendations occurred mainly in the subset of HG2 tumors reclassified into GG-3, with increased use of chemotherapy in this subset. The use of GGI is feasible in routine clinical practice and impacts treatment decisions in early-stage breast cancer.

2013-06-03 | GSE43365 | GEO

Practice Programmatic Submission

Project description:Practice Programmatic Submission

| PRJEB26575 | ENA

Gene expression profiling in myeloproliferative neoplasms

Project description:Gene expression profiles were established for 50 MPNs samples. RNA extracted from 2 healthy people was used as control. All MPNs were screened for JAK2V617F mutation as part of routine diagnostic practice.

2011-12-31 | E-MTAB-510 | biostudies-arrayexpress

NGS zwc practice

Project description:to practice use ebi

| PRJEB28063 | ENA

Gene Expression Signatures for the Accurate Diagnosis of Peripheral T-Cell Lymphoma Entities in the Routine Clinical Practice

Project description:Gene Expression Signatures for the Accurate Diagnosis of Peripheral T-Cell Lymphoma Entities in the Routine Clinical Practice

| PRJNA937288 | ENA

Routine Surveillance

Project description:Strain from routine IMD surveillance in Belgium

| PRJEB37139 | ENA

Gene Expression Signatures for the Accurate Diagnosis of Peripheral T-Cell Lymphoma Entities in the Routine Clinical Practice [training]

Project description:Gene Expression Signatures for the Accurate Diagnosis of Peripheral T-Cell Lymphoma Entities in the Routine Clinical Practice [training]

| PRJNA937291 | ENA

Gene Expression Signatures for the Accurate Diagnosis of Peripheral T-Cell Lymphoma Entities in the Routine Clinical Practice [validation]

Project description:Gene Expression Signatures for the Accurate Diagnosis of Peripheral T-Cell Lymphoma Entities in the Routine Clinical Practice [validation]

| PRJNA937290 | ENA

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