An Effective Pipeline for Whole Genome Sequencing for Research in a Tertiary Cancer Centre


Year:

Session type:

Theme:

George Morrissey1,Alison Berner2,Tracy Odigie3,Alice Rendall3,Keith Rogerson3,Rahul Kurup3,Glen Brice3,Helen Hanson3,John Short3,Katie Snape3,Ruth Pettengel3,Nirupa Murugaesu2
1,2Genomics England,3St George's University Hospital NHS Trust

Abstract

Background

The 100,000 Genomes Project is performing whole genome sequencing (WGS) on paired tumour and germline DNA from patients with cancer. It aims to provide genomic data to inform patient management, contribute to a database for future research, and establish new diagnostic pathways in histopathology and genetics. We describe the experience of St Georges University Hospital, part of South London Genomic Medicine Centre. 

Method

Patients are identified as eligible by screening of biopsy and theatre lists and multidisciplinary team meetings (MDTs). After liaising with the clinical team and histopathology, a fresh tumour sample is obtained. Patients are approached prospectively or retrospectively, for consent and blood or saliva for germline testing. If adequate DNA is extracted, it is sent to Illumina for sequencing and Genomics England (GEL) for annotation. Resulting genomic reports provide detailed information on somatic and germline single nucleotide variants, copy number and mutational signatures. These are discussed at a Genomic MDT consisting of Consultant Oncologist, Consultant Clinical Geneticist and Consultant Clinical Scientist. A summary report of actionable or potentially actionable findings is produced and sent to the referring clinician.  

Results

From 1st June 2016 to 11th May 2018, we collected 873 samples, 324 biopsies and 549 resections. 1060 patients were consented and 556 patients had DNA extracted. To date, 492 cases have been submitted to GEL, of which 121 have been discussed at MDT and had results returned.  57 patients (47%) had clinically actionable or potentially actionable mutations. The most frequently occurring were mutations in KRAS and PIK3CA, each found in 16.5% of patients. Two patients had germline findings, one in BRCA2 and one in MSH2. 

Conclusion

We demonstrate an effective pipeline for tumour WGS and review of results. Our data suggests that WGS has the potential to affect patient management and increase recruitment to trials.