Oesophageal Cancer Clinical and Molecular Stratification

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Tissue collection and preparation

Tissue collection and preparation

Any hospital that is a specialist centre for oesophago-gastric cancer is eligible to join the OCCAMS consortium.

Recruitment

Patients are recruited at the time of diagnosis and samples taken at times of clinically indicated interventions. The clinicians collecting the sample provide clinical and demographic information and tumour material for one or more time points. Collection of blood provides a genomic reference and a potential resource to look for biomarkers present in the blood.

Barrett's

In addition to tumour and blood, lymph node and Barrett's tissue may be collected where appropriate.

Processing

Depending on sample type, samples are embedded in paraffin or frozen. Samples are transported to Cambridge for further processing and analysis.

Pathology review

A pathologist reviews the samples to confirm diagnosis and tumour cellularity. As per ICGC criteria to be eligable for analysis, samples must be a minimum of 70% tumour cells. DNA and RNA are extracted using a strict QC process. DNA and RNA samples that meet required standards are used for Whole Genome Sequencing (WGS), and where tissue is sufficient for RNAseq and methylation arrays. For specific studies ATAC-seq and Nanopore sequencing may be conducted.

ctDNA

Longitudinal blood samples are taken for ctDNA analysis.

Organoids

Fresh samples may be processed for organoids in a collaboration with the Sanger Institute.