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IMMUcan SCCHN2 cohort

The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes HNSCC patients with confirmed progression, after treatment with curative chemo-radiation, to receive salvage surgery. Comprehensive profiling data are integrated with longitudinally collected clinical information. Cellular profiling of the same tumor samples was performed using multiplex immunofluorescence imaging, imaging mass cytometry, and H&E staining.

Type: Cancer Genomics
Archive: European Genome-phenome Archive (EGA)

2 Datasets

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
EGAD50000003080	The goal of IMMUcan is to improve our understanding of the interactions between the immune system and tumors, and to investigate how therapeutic interventions modulate these interactions. This cohort comprises patients with head and neck squamous cell carcinoma (HNSCC) who experienced disease progression following curative chemoradiotherapy and subsequently underwent salvage surgery. The dataset contains whole-exome sequencing (WES) data from 27 tumor samples and their matched germline controls, processed using the VEGAN analysis pipeline. The dataset includes the results of single nucleotide variant (SNV/SNP) and copy number variation (CNV) calling, enabling comprehensive characterization of the somatic genomic landscape of these tumors.	Illumina Genome Analyzer II	27
EGAD50000003081	The goal of IMMUcan is to improve our understanding of the interactions between the immune system and tumors, and to investigate how therapeutic interventions modulate these interactions. This cohort comprises patients with head and neck squamous cell carcinoma (HNSCC) who experienced disease progression following curative chemoradiotherapy and subsequently underwent salvage surgery. The dataset contains transcriptomic data from 15 tumor samples, processed using the STAR RNA-seq analysis pipeline. Two library preparation protocols were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA input. The dataset provides gene-level expression counts for downstream analyses.	Illumina Genome Analyzer II	15