Transforming cancer pathology and diagnostic services
Whole genome sequencing (WGS) in cancer can improve diagnosis and aid in treatment selection for clinicians. Currently, 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.
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. 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.
For background information and an introduction to cancer pathology and diagnostics, please see our pages on the 100,000 Genomes Project.
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. A meeting with all NHS GMC experimental leads, molecular pathology leads and NHS England collaborators is being planned for early 2017. At the meeting, data will be discussed and decisions taken about the next steps and any future experiments.
Experiment 1- Alternative Freezing Strategies – Shallow sequencing data on cryospray and storage of tissue prior to freezing showed promising results with no indications of DNA damage. Samples are to be sequenced and somatic calling carried out to ensure that the somatic calling is not affected by processing. Final data available in late 2016.
Experiment 2- Determination of Optimal Fixation Time. Samples collected from different fixation conditions experiments. Results will be available in late 2016.
Experiment 3- Alternative Fixatives – Samples fixed using alternative fixative (Paxgene) are being sequenced. Initial data will be reviewed by October and final results will be available later in 2016.
Experiment 4 – Vacuum packing. This experiment will resume in 2017.
Experiment 5 – Optimised FFPE vs non-optimised FFPE/ DNA Extraction conditions (temperature) for FFPE. Experiment completed. 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.
Experiment 6 – Promega Presequencing. DNA samples will be analysed using a presequencing kit and QC data compared with already acquired sequenced data for the same samples. Results will be available in late 2016.