Variant analysis on FFPE specimen from NSCLC patients (OCAPlus)

This study assessed the presence of somatic variants via the Oncomine Comprehensive Panel Plus panel (ThermoFisher) for commonly mutated cancer genes and measure tumor mutational burden using next-generation sequencing. It was performed on genomic DNA from FFPE tissue of tumor resections. Mutations were used to draw OncoPrints and to assess TMB in relation with response metrics.

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000001630	This dataset comprises molecular and immunogenomic profiles from 60 individual NSCLC patients (30 male, 30 female), with samples collected at multiple timepoints including initial biopsies (IB), resections (RES), and peripheral blood mononuclear cells (PBMC) at different timepoints during treatment. It includes 32 FFPE tumor samples sequenced on Illumina with the FoundationOne panel, 20 FFPE samples sequenced on IonTorrent with the Oncomine Comphrehensive Assay Plus, and 41 samples assessed with IonTorrent via Oncomine Immune Response Research Assay panel for targeted gene expression. T-cell receptor (TCR) repertoire profiling was performed on 62 tumor samples (initial biopsies and resections, Oncomine TCR Beta-SR Assay), and 155 blood-derived samples were sequenced with Oncomine TCR Beta-LR Assay. Data files include processed sequencing results in bam format.	Ion GeneStudio S5 Prime Ion Torrent S5 unspecified	310

Publications	Citations
Tumor immune dynamics and long-term clinical outcome of stage IIIA NSCLC patients treated with neoadjuvant chemoimmunotherapy. Schmid D, Sobottka B, Manzo M, Trüb M, Leonards K, Herzig P, Oyewole OR, Jermann P, Hayoz S, Savic Prince S, Tochtermann G, Natoli M, Pless M, Bettini A, Früh M, Mauti LA, Britschgi C, Peters S, Mark M, Ochsenbein AF, Janthur WD, Waibel C, Mach N, Froesch P, Buess M, Bohanes P, Gonzalez M, Alborelli I, Rothschild SI, Koelzer VH, Zippelius A. Nat Commun 16: 2025 8673	0

Publications

Citations

Tumor immune dynamics and long-term clinical outcome of stage IIIA NSCLC patients treated with neoadjuvant chemoimmunotherapy.
Schmid D, Sobottka B, Manzo M, Trüb M, Leonards K, Herzig P, Oyewole OR, Jermann P, Hayoz S, Savic Prince S, Tochtermann G, Natoli M, Pless M, Bettini A, Früh M, Mauti LA, Britschgi C, Peters S, Mark M, Ochsenbein AF, Janthur WD, Waibel C, Mach N, Froesch P, Buess M, Bohanes P, Gonzalez M, Alborelli I, Rothschild SI, Koelzer VH, Zippelius A. Nat Commun 16: 2025 8673