Transforming pathology & diagnostic practice

Sampling posters for the clinic

Download sampling posters here

Pathology Videos

We have videos available both describing tumour-specific sampling procedures and from an event discussing pathology in detail; please see tabs below.

Prostate Tumour Sampling

Breast Tumour Sampling

Renal Tumour Sampling

 View all videos in our Tumour Sampling collection (opens in new tab)

You can view a day’s talks and discussion around tissue handling in our playlist (opens in new tab). This event was held here at Genomics England in partnership with NHS England and the Royal College of Pathologists on July 19th 2017. Watch individual talks (with slides):

The Future Face of Pathology - Prof. J. Martin

Implementing a Fresh Tissue Path Service - Prof. G. Bussolati Legality of Tissue Handling - Dr. C. Craig Sampling Small Tumours - Dr. C. Craig Tumour Assessment - J. Moorhead

CM Path badging of laboratories for quality - Prof. G. Thomas


Our aim is to drive up the quality of cancer DNA samples for molecular testing in the NHS. This will not only serve the 100,000 Genomes Project but also have a positive impact on cancer testing in the NHS more broadly.

Whole genome sequencing (WGS) in cancer can improve diagnosis and aid in treatment selection for clinicians. Often, the methods used to process tumour samples in routine NHS settings are unsuitable to extract DNA for WGS.

We are working with GMCs to change practice and enable WGS in the NHS. See below for the latest updates on our experiments.

Fresh, frozen tissue

Gaining DNA of high enough quality for whole genome sequencing, from routine clinical care, is not an issue unique to the 100,000 Genomes Project. Our work will help to inform other clinical and research studies in the NHS and around the world.

We are working with research collaborators, partners in NHS pathology services, and NHS England to introduce the fresh frozen (FF) method of collecting and storing cancer biopsy samples. We are extremely grateful for all the GMCs ground breaking work in this area.

Please contact us if you are interested in collaborative experiments in this area.

Updates / latest experiments

We have several experiments underway, with four overarching aims

  • Facilitating biopsy collection pathways
  • Enabling of collection of fresh tissue
  • Optimising DNA extraction from FFPE
  • Pre-sequencing QC

A full report on all the experiments and results to date is currently being prepared.

View Experiment summaries
Experiment 5 results - FFPE optimisation

The results showed that although normal buffer formalin (NBF) fixation & decrosslinking at 65°C may have some advantages in the data quality, DNA was not being extracted in large enough quantities for WGS (decrosslinking failure was discussed as the likely cause).

The NBF fixation, decrosslinking at 80°C provided the next best sequencing quality (current conditions) but there were still significant issues with the quality of the data.

False negative and false positive indel, single nucleotide variant (SNV) calling, structural variant (SV) and translocations were adversely affected compared to FF.


Background

For background information and an introduction to cancer pathology and diagnostics, please see our pages on the 100,000 Genomes Project.

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