DAC for the access to IMMUcan data

Contact Information

Mrs bianca colleoni
bianca.colleoni@eortc.org

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This DAC controls 30 datasets

Dataset ID	Description	Technology	Samples
EGAD50000002178	Tumor versus Germline variant calling on UPST-SCCHN3 cohort	Illumina Genome Analyzer II Illumina NovaSeq 6000	460
EGAD50000002179	Transcriptomics of Tumor samples on UPST-SCCHN3 cohort	Illumina Genome Analyzer II	217
EGAD50000002205	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with confirmed locally recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) who receive first-line treatment with immune checkpoint inhibitors (ICI) or ICI combined with chemotherapy. This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.	Illumina Genome Analyzer II	499
EGAD50000002206	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with confirmed locally recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) who receive first-line treatment with immune checkpoint inhibitors (ICI) or ICI combined with chemotherapy. This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities.	Illumina Genome Analyzer II	202
EGAD50000002235	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with non-small cell lung cancer who had surgical resection. This is a subcohort of the EORTC SPECTAlung study. This dataset contains whole exome sequencing data from tumor samples processed with the Vegan pipeline. In the absence of matching germline samples, variant calling is performed using two panel of normals (one for female and one for male). It includes SNP and CNV calling.	Illumina Genome Analyzer II	191
EGAD50000002236	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with non-small cell lung cancer who had surgical resection. This is a subcohort of the EORTC SPECTAlung study. This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities.	Illumina Genome Analyzer II	125
EGAD50000002269	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes metastatic Triple Negative Breast Cancer (mTNBC) patients, naïve of treatment in the metastatic settings, treated in 1st line with chemotherapy or chemo-immunotherapy This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.	Illumina Genome Analyzer II	34
EGAD50000002270	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes metastatic Triple Negative Breast Cancer (mTNBC) patients, naïve of treatment in the metastatic settings, treated in 1st line with chemotherapy or chemo-immunotherapy This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.	Illumina Genome Analyzer II	76
EGAD50000002753	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patient with confirmed metastatic NSCLC, naïve of treatment in the metastatic settings, to be treated in 1st line. This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.	Illumina Genome Analyzer II	447
EGAD50000002754	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patient with confirmed metastatic NSCLC, naïve of treatment in the metastatic settings, to be treated in 1st line. This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.	Illumina Genome Analyzer II	157
EGAD50000002810	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with confirmed localized TNBC (stages I to III) treated with neo-adjuvant therapy This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.	Illumina Genome Analyzer II	417
EGAD50000002811	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with confirmed localized TNBC (stages I to III) treated with neo-adjuvant therapy This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.	Illumina Genome Analyzer II	865
EGAD50000002896	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.	Illumina Genome Analyzer II	99
EGAD50000002897	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.	Illumina Genome Analyzer II	179
EGAD50000002916	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patient with confirmed metastatic RCC, naïve of treatment in the metastatic settings, to be treated in 1st line. This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.	Illumina Genome Analyzer II	204
EGAD50000002917	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patient with confirmed metastatic RCC, naïve of treatment in the metastatic settings, to be treated in 1st line. This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.	Illumina Genome Analyzer II	69
EGAD50000002946	The IMMUcan project aims to characterize the interactions between the immune system and tumors, and to evaluate how therapeutic interventions modulate these interactions. This cohort includes patients enrolled in UroCCR, the French Research Network on Kidney Cancer, a multicenter database established to advance kidney cancer research and improve patient care.This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.	Illumina Genome Analyzer II	245
EGAD50000002947	The IMMUcan project aims to characterize the interactions between the immune system and tumors, and to evaluate how therapeutic interventions modulate these interactions. This cohort includes patients enrolled in UroCCR, the French Research Network on Kidney Cancer, a multicenter database established to advance kidney cancer research and improve patient care. This dataset contains whole-exome sequencing (WES) data generated from tumor samples and processed using the Vegan pipeline. The analysis includes both single-nucleotide variant (SNV) and copy number variant (CNV) calling. As no matched germline samples were available, somatic variant calling was performed using sex-specific Panels of Normals (PoNs), one for male and one for female samples. These PoNs were generated from germline samples of IMMUcan participants and applied according to GATK best-practice recommendations for somatic analysis without matched normal samples (https://gatk.broadinstitute.org/hc/en-us/articles/360037058172-CreateSomaticPanelOfNormals-BETA).	Illumina Genome Analyzer II	246
EGAD50000003044	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients from the Nirvana (NCT03774732) trial treated with PD-1 Inhibitor and Chemotherapy with Concurrent Irradiation at Varied Tumour Sites in Advanced Non-small Cell Lung Cancer. This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.	Illumina Genome Analyzer II	53
EGAD50000003045	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients from the Nirvana (NCT03774732) trial treated with PD-1 Inhibitor and Chemotherapy with Concurrent Irradiation at Varied Tumour Sites in Advanced Non-small Cell Lung Cancer. This dataset contains whole exome sequencing data from tumor samples processed with the Vegan pipeline. Variant calling is performed against two Panel of Normals (one for each biological sex) computed (https://gatk.broadinstitute.org/hc/en-us/articles/360035531132) using 60 samples from the same sex, from the IMMUcan study. It includes SNP and CNV calling.	Illumina Genome Analyzer II	52
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
EGAD50000003096	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with a confirmed diagnostic of metastatic colorectal adenocarcinoma This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.	Illumina Genome Analyzer II	246
EGAD50000003097	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with a confirmed diagnostic of metastatic colorectal adenocarcinoma This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.	Illumina Genome Analyzer II	123
EGAD50000003103	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with early-stage colorectal adenocarcinoma. This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.	Illumina Genome Analyzer II	40
EGAD50000003104	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with early-stage colorectal adenocarcinoma . This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.	Illumina Genome Analyzer II	20
EGAD50000003113	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence these interactions. This cohort comprises patients with metastatic colorectal adenocarcinoma treated at the Centre Léon Bérard Hospital (Lyon, France). The dataset contains whole-exome sequencing (WES) data generated from tumor samples and analyzed against a sex-matched panel of normals consisting of 60 samples processed within the IMMUcan study using the VEGAN pipeline. The dataset includes single nucleotide variant (SNV) and copy number variant (CNV) calling results.	Illumina Genome Analyzer II	210
EGAD50000003114	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes metastatic colorectal Adenocarcinoma from Hopital Centre Leon Berard (Lyon, France) . This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.	Illumina Genome Analyzer II	171
EGAD50000003131	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence these interactions. This cohort comprises patients with metastatic colorectal adenocarcinoma treated at Hôpital Saint-Luc (Brussels, Belgium). The dataset contains transcriptomic data processed using the STAR RNA-seq alignment pipeline. Samples were sequenced using the Takara SMART-Seq Stranded kit, and the data are provided as gene-level count matrices.	Illumina Genome Analyzer II	230
EGAD50000003132	The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence these interactions. This cohort comprises patients with metastatic colorectal adenocarcinoma treated at Hôpital Saint-Luc (Brussels, Belgium). The dataset contains whole-exome sequencing (WES) data from tumor samples and matched germline controls, processed using the Vegan pipeline. It includes single-nucleotide polymorphism (SNP) and copy number variation (CNV) calls.	Illumina Genome Analyzer II	300