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GMS Cancer-specific clinical dataΒΆ

Name of Table/Data view Description
cancer_analysis Once tumour and germline whole genome sequencing data is delivered by our sequencing partners it is run through the Genomics England interpretation pipeline, which realigns the data, and applies further QC, annotation and variant prioritisation steps, together with additional analyses, such as estimating tumour mutation burden and generating mutational signatures. This information is then made available in the cancer_analysis table, where each entry corresponds to one tumour sample that has been sequenced and interpreted.

Samples are uniquely identified by their tumour_sample_platekey number, and matched to the information of their germline, as well as disease type, quality control measures, tumour mutational burden, signatures and paths to the alignment and variant calling files. Note that one participant may have more than one tumour sample, for the same or different tumours.
tumour Data associated with a tumour in the NHS GMS.
tumour_morphology Morphology data associated with a tumour in the NHS GMS.
tumour_topography Topography data associated with a tumour in the NHS GMS.

Last update: November 3, 2023