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Processes

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Processes

Tissue collection and preparation

Tissue samples are collected by centres participating in the OCCAMS study. 

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 frozen 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.

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

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

A pathologist reviews the samples to confirm diagnosis and tumour cellularity. To be eligible 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 DNA sequencing, PCR and gene expression arrays.

DNA samples are sent to Illumina in California for DNA sequencing. Sequence information is then made available to Simon Tavare's bioinformatics group at the Cambridge Institute.

Bioinformatics

Bioinformatics is performed by Simon Tavare's group at the University of Cambridge Oncology Department's Cambridge Institute (CI).

An analysis pipeline, running on the CI's High Performance Computer Cluster (HPC), performs whole-genome analysis on the tumour and matched normal genomes.

The bulk of the analysis pipeline is concerned with identifying sequence variations between tumour and normal samples. A variety of software is employed to call inserts, deletions, loss of hetrozygosity and structural variations.

Submission to ICGC

As a part of the ICGC, Sequence and expression data is submitted to the DCC for download by other collaborators.