The Cancer Molecular Diagnostics Laboratory (CMDL) was established in 2015 to develop new technologies in relation to detailed molecular genetic profiling using next generation sequencing and for sequencing modified bases in DNA. The CMDL is a shared resource that provides clinically actionable genomic results for patients enrolled on clinical trials and clinical studies led by researchers across the Centre.
The CMDL is currently operating under Good Clinical Laboratory Practice (GCLP) standards and, in collaboration with Cambridge University Hospitals, is working towards ISO accreditation.
CMDL experimental workflows include processing and analysing fresh frozen and formalin-fixed paraffin embedded tissue (FFPE) as well as ctDNA; these workflows are easily translated into standardised protocols for routine analysis.
The CMDL operates from two locations on the Cambridge Biomedical Campus. The main laboratory is in the Clifford Allbutt Building and a satellite Blood Processing Laboratory (BPL) is in the Cambridge Breast Cancer Research Unit (CBCRU) in Addenbrooke’s Hospital.
The BPL is mainly responsible for collecting and processing clinical trials samples and liaises with clinical teams and research nurses to efficiently collect blood, serum, buffy coats, mononuclear cells (PBMCs), ascites and plasma. All these patients are tracked by the BPL team using Addenbrooke’s electronic patient record system (Epic) and logged in Achiever (LIMS system).
As part of the Integrative Cancer Programme, CMDL is developing protocols for small (targeted re-sequencing) to medium scale projects (analysis of hundreds of genes in one sequencing experiment) that will enable Centre scientists and clinicians to molecularly characterise cancer patients.
The CMDL is led by Shubha Anand. We currently have a team of 13; ten in CMDL and three in BPL. Pictured below left to right: Ezequiel Martin, Natasha Moore, Shubha Anand, Francesca Nice, Lorena Di Lisio, Mark Lucas, Maribel Lara, Nell Baiioud, Sharyar Hadi, Pippa Martin
We work very closely with other teams on the campus. Addenbrooke's Tissue Bank, the Cambridge Clinical Trials Unit Laboratory, the Cambridge Breast Cancer Unit and the Cancer Research UK Cambridge Institute Biorepository dispatch all patient tumour material to us. All these units use the Achiever database, which facilitates efficient sample tracking and dispatch. We perform our sequencing at the Stratified Medicine Core Laboratory, located in the Academic Department of Medical Genetics.
The CMDL team performs further work on samples collected either in BPL or on samples which are directly received in the laboratory. This includes:
- Genomic DNA extractions from blood or tissue (both FFPE, and Fresh Frozen)
- Circulating free DNA (cfDNA) extractions on the Qiasymphony
- RNA extractions from tissues
- Next Generation Sequencing (NGS) and data analysis on cfDNA, tumour and matched germline DNA with custom capture based pan cancer 350 gene as well as smaller targeted amplicon panels
- Digital droplet PCR with commercially available and custom probes
We are currently also working to adapt and validate some new technologies in CMDL:
- Shallow whole genome sequencing for cfDNA for copy number and tumour burden
- A custom Lymphoma specific 110-gene panel for ctDNA, FFPE and matched germline DNA. Along with SNVs, this panel will also be able to detect the most common translocations reported in lymphomas
- Simultaneous extraction of DNA and RNA from FFPE material using a sonication based method.