GSE247146

Blood gene expression biomarkers of response to anti-TNF drugs in pediatric patients before initiation of treatment

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

24 case / 0 control samples elsewhere in the study have incomplete or conflicting evidence; they are not included above

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Source: GEO
Assay: bulk RNA-seq
Organism: Homo sapiens
Whole-study samples: 24 samples
Specimen: Biofluid
Reported/interpreted study design: Unclear study design Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: López-Fernández LA, Salvador-Martín S, Velosillo P, López Fernández LA
Contact name: Luis Andrés López Fernández
Submission date: 2023-11-06
Last update: 2025-09-25
Organization: Hospital General Universitario Gregorio Marañón
Department: Not available
Public date: 2024-02-26
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens); GPL30173 NextSeq 2000 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA1036291

Summary

Background/aims: Changes in gene expression profiles among individuals with inflammatory bowel diseases (IBDs) could potentially influence the responsiveness to anti-TNF treatment. The aim of this study was to identify genes that could serve as predictors of early response to anti-TNF therapies in pediatric IBD patients prior to the initiation of treatment.Methods: We conducted a prospective, longitudinal, and multicenter study, enrolling 24 pediatric IBD patients aged less than 18 years who were initiating treatment with either infliximab or adalimumab. RNA-seq from blood samples was analyzed using the DESeq2 library by comparing responders and non-responders to anti-TNF drugs. Results: Bioinformatic analyses unveiled 102 differentially expressed genes, with 99 genes exhibiting higher expression in responders compared to non-responders prior to the initiation of anti-TNF therapy. Functional enrichment analyses highlighted defense response to Gram-negative bacteria (FDR =2.3 ×10–7) as the most significant biological processes, and hemoglobin binding (FDR =0.002), as the most significant molecular function. Gene Set Enrichment Analysis (GSEA) revealed notable enrichment in transcriptional misregulation in cancer (FDR =0.016). Notably, 13 genes (CEACAM8, CEACAM6, CILP2, COL17A1, OLFM4, INHBA, LCN2, LTF, MMP8, DEFA4, PRTN3, AZU1, and ELANE) were selected for validation, and a consistent trend of increased expression in responders prior to drug administration was observed for most of these genes, with findings for 4 of them being statistically significant (CEACAM8, LCN2, LTF2, and PRTN3). Conclusions: We identified 102 differentially expressed genes involved in the response to anti-TNF drugs in children with IBDs and validated CEACAM8, LCN2, LTF2, and PRTN3. Genes participating in defense response to Gram-negative bacterium, serine-type endopeptidase activity, and transcriptional misregulation in cancer are good candidates for anticipating the response to anti-TNF drugs in children with IBDs.

Overall design

Expression profiling by high throughput sequencing. Whole gene expression profiles from total RNA isolated from whole-blood samples of children with inflammatory bowel disease of 12 responders and 12 non-responders taken before biologic administration were analyzed by RNA next-generation sequencing. The other 12 samples were taken from GSE159034.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 24 GSM samples	Primary source
recount3	Planned trusted source for processed count availability.	No match found
Expression Atlas	Planned source for curated expression experiment links.	No match found
PubMed	Primary GEO citations and related PubMed articles that mention this dataset. 1 linked publication 1 DOI Primary publication Blood gene expression biomarkers of response to anti-TNF drugs in pediatric inflammatory bowel diseases before initiation of treatment. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie, 2024 PubMed DOI	Available

Metadata Quality Components

Persisted metadata quality

93 pts

Clarity: 93%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Only one side of the comparison is clearly grouped. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Not ready

55% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No complete case/control contrast is available.
Critical dataset warnings must be resolved.

Next Steps

Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

Minimum sample count met

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

Critical dataset warnings are present.

Study design is model-system or unclear and should be reviewed before analysis.

Why This Is Ranked Here

Tumor vs normal

Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Disease context Inflammatory bowel disease Disease context came from Normalization rules.
Likely case group Inflammatory bowel disease 24 samples
Likely control group No control group detected 0 samples

Intent Interpretation

Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 38401525.
Publication context: Blood gene expression biomarkers of response to anti-TNF drugs in pediatric inflammatory bowel diseases before initiation of treatment.. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie, 2024. PMID 38401525. DOI 10.1016/j.biopha.2024.116299.

Cautions

Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
Downgraded for tissue search because it is a biofluid cohort.
Downgraded for tissue search because study design or specimen source is unclear.
Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Overall score capped because comparison suitability is weak for the selected search intent.
Missing or unclear metadata. Comparison - Unclear study design. Specimen - Biofluid. Comparison suitability: 0%.
Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No clear control group was detected from normalized metadata.
Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Normalized Fields

76 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM7884318 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884319 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884320 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884321 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884322 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884323 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884324 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884325 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884326 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884327 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884328 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884329 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884330 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884331 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884332 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884333 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884334 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884335 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884336 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884337 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884338 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884339 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884340 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7884341 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE247146 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE247146 dataset_title: Blood gene expression biomarkers of response to anti-TNF drugs in pediatric patients before initiation of treatment organism: Homo sa... keyword match keyword match: bulk rna-seq

disease inflammatory bowel disease GSE247146 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease dataset_accession: GSE247146 dataset_title: Blood gene expression biomarkers of response to anti-TNF drugs in pediatric patients before initiation of treatment organism: Homo sa... controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884318 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease SAL008 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884319 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease NJ035 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884320 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease JC022 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884321 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease PT015 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884322 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease NJ029 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884323 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease NJ037 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884324 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease IL008 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884325 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease H12003 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884326 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease H12004 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884327 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease VR019 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884328 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease PAZ021 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884329 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease SJ039 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884330 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease VV0011 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884331 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease GM0031 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884332 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease JC0121 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884333 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease RM0171 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884334 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease RM0101 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884335 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease VR0161 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884336 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease PAZ0161 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884337 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease PM005_1 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884338 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease VR0131 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884339 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease RM0161 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884340 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease D0051 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease inflammatory bowel disease GSM7884341 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease RS0041 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

organism Homo sapiens GSE247146 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE247146 dataset_title: Blood gene expression biomarkers of response to anti-TNF drugs in pediatric patients before initiation of treatment organism: Homo sa... keyword match keyword match: homo sapiens

tissue blood GSE247146 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE247146 dataset_title: Blood gene expression biomarkers of response to anti-TNF drugs in pediatric patients before initiation of treatment organism: Homo sa... controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884318 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood SAL008 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884319 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood NJ035 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884320 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood JC022 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884321 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PT015 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884322 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood NJ029 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884323 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood NJ037 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884324 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood IL008 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884325 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood H12003 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884326 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood H12004 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884327 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood VR019 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884328 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PAZ021 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884329 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood SJ039 Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884330 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood VV0011 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884331 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood GM0031 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884332 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood JC0121 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884333 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RM0171 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884334 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RM0101 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884335 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood VR0161 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884336 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PAZ0161 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884337 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PM005_1 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884338 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood VR0131 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884339 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RM0161 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884340 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood D0051 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7884341 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RS0041 (re-analysis) Blood tissue: Blood; disease state: pediatric inflammatory bowel disease; treatment: Anti-TNF; response: Non-responder; time: before initiation of treatment controlled vocabulary controlled vocabulary tissue match: blood

Sample Group Preview

24 rows shown Show Hide

Study totals: Case 24 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 24 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Inflammatory bowel disease	Case	GSM7884318	SAL008	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884319	NJ035	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884320	JC022	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884321	PT015	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884322	NJ029	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884323	NJ037	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884324	IL008	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884325	H12003	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884326	H12004	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884327	VR019	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884328	PAZ021	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884329	SJ039	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884330	VV0011 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884331	GM0031 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884332	JC0121 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884333	RM0171 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884334	RM0101 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884335	VR0161 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884336	PAZ0161 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884337	PM005_1 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884338	VR0131 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884339	RM0161 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884340	D0051 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.
Inflammatory bowel disease	Case	GSM7884341	RS0041 (re-analysis)	Blood Tissue: Blood; Disease state: Pediatric inflammatory bowel disease; Treatment: Anti-TNF; Response: Non-responder; Time: Before initiation of treatment	Case marker detected.

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Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.

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Use as Discovery Cohort