About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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Variant calling for IMMU-SCCHN2 cohort

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.

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DUO:0000007
version: 2021-02-23

disease specific research

This data use permission indicates that use is allowed provided it is related to the specified disease.

ModifiersMONDO:0045054

DUO:0000019
version: 2021-02-23

publication required

This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community.

DUO:0000021
version: 2021-02-23

ethics approval required

This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.

DUO:0000026
version: 2021-02-23

user specific restriction

This data use modifier indicates that use is limited to use by approved users.

DUO:0000027
version: 2021-02-23

project specific restriction

This data use modifier indicates that use is limited to use within an approved project.

DUO:0000028
version: 2021-02-23

institution specific restriction

This data use modifier indicates that use is limited to use within an approved institution.

Terms of use to access IMMUcan data v2.0

The applicant needs to agree with the Terms of use to access IMMUcan data through EGA.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000002147 Cancer Genomics

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
i
EGAF50000984924 fastq.gz 4.2 GB
EGAF50000984925 fastq.gz 5.1 GB
EGAF50000984926 fastq.gz 4.8 GB
EGAF50000984927 fastq.gz 4.4 GB
EGAF50000984928 fastq.gz 3.7 GB
EGAF50000984929 fastq.gz 3.0 GB
EGAF50000984930 fastq.gz 4.3 GB
EGAF50000984931 fastq.gz 4.6 GB
EGAF50000984932 fastq.gz 4.7 GB
EGAF50000984933 fastq.gz 2.9 GB
EGAF50000984934 fastq.gz 5.0 GB
EGAF50000984935 fastq.gz 3.7 GB
EGAF50000984936 fastq.gz 3.8 GB
EGAF50000984937 fastq.gz 4.5 GB
EGAF50000984938 fastq.gz 2.9 GB
EGAF50000984939 fastq.gz 3.0 GB
EGAF50000984940 fastq.gz 2.7 GB
EGAF50000984941 fastq.gz 3.2 GB
EGAF50000984942 fastq.gz 3.0 GB
EGAF50000984943 fastq.gz 5.2 GB
EGAF50000984944 fastq.gz 4.5 GB
EGAF50000984945 fastq.gz 4.3 GB
EGAF50000984946 fastq.gz 2.8 GB
EGAF50000984947 fastq.gz 5.0 GB
EGAF50000984948 fastq.gz 4.5 GB
EGAF50000984949 fastq.gz 3.7 GB
EGAF50000984950 fastq.gz 3.8 GB
EGAF50000984951 fastq.gz 4.3 GB
EGAF50000984952 fastq.gz 2.8 GB
EGAF50000984953 fastq.gz 4.3 GB
EGAF50000984954 fastq.gz 4.6 GB
EGAF50000984955 fastq.gz 2.8 GB
EGAF50000984956 fastq.gz 5.3 GB
EGAF50000984957 fastq.gz 4.5 GB
EGAF50000984958 fastq.gz 5.1 GB
EGAF50000984959 fastq.gz 3.1 GB
EGAF50000984960 fastq.gz 4.2 GB
EGAF50000984961 fastq.gz 4.9 GB
EGAF50000984962 fastq.gz 4.1 GB
EGAF50000984963 fastq.gz 4.3 GB
EGAF50000984964 fastq.gz 5.9 GB
EGAF50000984965 fastq.gz 4.5 GB
EGAF50000984966 fastq.gz 2.8 GB
EGAF50000984967 fastq.gz 5.8 GB
EGAF50000984968 fastq.gz 3.1 GB
EGAF50000984969 fastq.gz 3.0 GB
EGAF50000984970 fastq.gz 3.1 GB
EGAF50000984971 fastq.gz 3.8 GB
EGAF50000984972 fastq.gz 3.1 GB
EGAF50000984974 fastq.gz 4.2 GB
EGAF50000985004 fastq.gz 4.3 GB
EGAF50000985005 fastq.gz 4.4 GB
EGAF50000985006 fastq.gz 4.5 GB
EGAF50000985007 fastq.gz 4.6 GB
EGAF50000985008 vcf.gz 21.9 kB
EGAF50000985009 vcf.gz 11.1 kB
EGAF50000985010 vcf.gz 5.8 kB
EGAF50000985011 vcf.gz 27.8 kB
EGAF50000985012 vcf.gz 6.4 kB
EGAF50000985013 vcf.gz 6.4 kB
EGAF50000985014 vcf.gz 25.5 kB
EGAF50000985015 vcf.gz 24.6 kB
EGAF50000985016 vcf.gz 12.8 kB
EGAF50000985017 vcf.gz 32.4 kB
EGAF50000985018 vcf.gz 3.0 kB
EGAF50000985019 vcf.gz 28.4 kB
EGAF50000985020 vcf.gz 6.0 kB
EGAF50000985021 vcf.gz 40.0 kB
EGAF50000985022 vcf.gz 6.2 kB
EGAF50000985023 vcf.gz 43.7 kB
EGAF50000985024 vcf.gz 5.2 kB
EGAF50000985025 vcf.gz 38.9 kB
EGAF50000985026 vcf.gz 4.4 kB
EGAF50000985027 vcf.gz 62.6 kB
EGAF50000985028 vcf.gz 7.5 kB
EGAF50000985029 vcf.gz 75.1 kB
EGAF50000985030 vcf.gz 5.6 kB
EGAF50000985031 vcf.gz 105.5 kB
EGAF50000985032 vcf.gz 6.1 kB
EGAF50000985033 vcf.gz 30.8 kB
EGAF50000985034 vcf.gz 6.6 kB
EGAF50000985035 vcf.gz 28.2 kB
EGAF50000985036 vcf.gz 6.9 kB
EGAF50000985037 vcf.gz 35.2 kB
EGAF50000985038 vcf.gz 5.1 kB
EGAF50000985039 vcf.gz 83.4 kB
EGAF50000985040 vcf.gz 9.0 kB
EGAF50000985041 vcf.gz 83.3 kB
EGAF50000985042 vcf.gz 13.2 kB
EGAF50000985043 vcf.gz 60.7 kB
90 Files (218.8 GB)