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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CTCF Binding Site Mutations: Linking Topologically Associated Domains Dysregulation to Cutaneous Squamous Cell Carcinoma Progression

Fresh tumor tissue from nodal metastases (n = 41) was harvested during surgery and immediately snap-frozen. A total of 72/75 cSCC, WGS samples were included in the analysis (refer to QC section), comprising primary tumors (both metastatic (PM (n = 16)) and non-metastatic (PNM (n = 15)), as well as lymph node metastases (LNM (n = 41)). The metastatic cohort included matched PM and LNM samples for 13 patients. The PNM group had to meet the following criteria: absence of metastases at > 24 months follow-up after resection of the primary or negative sentinel lymph node biopsy at time of resection or histologically negative neck dissection. Somatic variant analysis was performed using DRAGEN pipeline version 4.3.6 on the Illumina Connected Analytics (ICA) v2 environment using in house shell scripting. Tumor-normal paired analyses were carried out in three stages: alignment, variant calling, and integrative somatic analysis. Further information on the somatic calling is available at https://help.dragen.illumina.com/product-guides/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/somatic-mode.

Request Access

Every data user requires approval from DAC, however academic researcher are encouraged to request. Primary code = DUO:0000026 user-specific restriction Secondary code = DUO:0000019: publication required

Primary code = DUO:0000026 user-specific restriction This requirement indicates that use is limited to use by approved users. Secondary code = DUO:0000019: publication required This requirement indicates that the requestor agrees to make results of studies using the data available to the larger scientific community.

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
EGAS50000001686 Whole Genome Sequencing

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
EGAF00009006013 vcf.gz 87.1 MB Report
EGAF00009006014 vcf.gz 47.6 MB Report
EGAF00009007596 vcf.gz 40.1 MB Report
EGAF00009007602 vcf.gz 24.6 MB Report
EGAF00009007606 vcf.gz 29.7 MB Report
EGAF00009007607 vcf.gz 43.6 MB Report
EGAF00009007618 vcf.gz 74.6 MB Report
EGAF00009007620 vcf.gz 99.6 MB Report
EGAF00009007621 vcf.gz 30.9 MB Report
EGAF00009007625 vcf.gz 89.7 MB Report
EGAF00009007628 vcf.gz 27.0 MB Report
EGAF00009007629 vcf.gz 10.0 MB Report
EGAF00009007638 vcf.gz 45.4 MB Report
EGAF00009007641 vcf.gz 22.4 MB Report
EGAF00009007645 vcf.gz 5.3 MB Report
EGAF00009007704 vcf.gz 4.0 MB Report
EGAF00009007728 vcf.gz 10.8 MB Report
EGAF00009007738 vcf.gz 11.1 MB
EGAF00009007739 vcf.gz 28.6 MB Report
EGAF00009007798 vcf.gz 10.5 MB Report
EGAF00009007829 vcf.gz 60.6 MB Report
EGAF00009007832 vcf.gz 77.3 MB Report
EGAF00009007876 vcf.gz 51.2 MB Report
EGAF00009007886 vcf.gz 16.4 MB Report
EGAF00009007887 vcf.gz 13.2 MB Report
EGAF00009007892 vcf.gz 23.3 MB Report
EGAF00009007894 vcf.gz 78.8 MB Report
EGAF00009007988 vcf.gz 32.3 MB Report
EGAF00009007989 vcf.gz 33.5 MB Report
EGAF00009008064 vcf.gz 13.7 MB Report
EGAF00009012694 vcf.gz 6.5 MB Report
EGAF00009012695 vcf.gz 2.1 MB
EGAF00009012696 vcf.gz 20.4 MB Report
EGAF00009012699 vcf.gz 1.9 MB Report
EGAF00009012701 vcf.gz 27.6 MB Report
EGAF00009012707 vcf.gz 27.2 MB Report
EGAF00009012708 vcf.gz 2.2 MB Report
EGAF00009012711 vcf.gz 64.9 MB Report
EGAF00009012713 vcf.gz 7.3 MB Report
EGAF00009012714 vcf.gz 53.1 MB Report
EGAF00009012716 vcf.gz 13.3 MB Report
EGAF00009012719 vcf.gz 15.2 MB Report
EGAF00009012721 vcf.gz 35.0 MB Report
EGAF00009012723 vcf.gz 13.2 MB Report
EGAF00009012727 vcf.gz 30.3 MB Report
EGAF00009012728 vcf.gz 2.0 MB Report
EGAF00009012729 vcf.gz 149.9 MB Report
EGAF00009012730 vcf.gz 30.3 MB Report
EGAF00009012732 vcf.gz 15.0 MB Report
EGAF00009012734 vcf.gz 29.2 MB Report
EGAF00009012736 vcf.gz 27.9 MB Report
EGAF00009012738 vcf.gz 8.7 MB Report
EGAF00009012740 vcf.gz 8.4 MB Report
EGAF00009012745 vcf.gz 9.8 MB Report
EGAF00009012746 vcf.gz 4.5 MB Report
EGAF00009012895 vcf.gz 100.2 MB Report
EGAF00009012899 vcf.gz 61.4 MB Report
EGAF00009013619 vcf.gz 1.7 MB Report
EGAF00009013622 vcf.gz 38.0 MB Report
EGAF00009013624 vcf.gz 70.1 MB Report
EGAF00009013625 vcf.gz 1.7 MB Report
EGAF00009013627 vcf.gz 47.9 MB Report
EGAF00009013628 vcf.gz 17.7 MB Report
EGAF00009013634 vcf.gz 25.9 MB Report
EGAF00009013641 vcf.gz 7.1 MB Report
EGAF00009013643 vcf.gz 19.3 MB Report
EGAF00009013649 vcf.gz 86.4 MB Report
EGAF00009013651 vcf.gz 28.5 MB Report
EGAF00009013652 vcf.gz 17.5 MB Report
EGAF00009013653 vcf.gz 145.3 MB Report
EGAF00009014945 vcf.gz 22.1 MB Report
EGAF00009014971 vcf.gz 182.7 MB Report
EGAF00009015111 vcf.gz 3.0 MB Report
EGAF00009015171 vcf.gz 81.4 MB Report
EGAF00009015737 vcf.gz 21.7 MB Report
75 Files (2.7 GB)