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DAC for the access to IMMUcan data

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Mrs bianca colleoni
bianca.colleoni@eortc.org

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This DAC controls 12 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
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