The 100,000 Genomes Project (100KGP) was established to sequence genomes from people including around 85,000 UK National Health Service (NHS) patients affected by a rare disease, or cancer. Announced in 2012, the main aims were to:
- establish genomic medicine provision for the NHS
- create new personalised treatment options from clinical diagnoses
- provide materials and impetus for scientific discovery
- further develop the growing UK genomics industry
- engage patients with genomic medicine
A government owned company called Genomics England Ltd., was formed to complete the project aims. Illumina® was contracted for DNA sequencing and bioinformatic services. Patient recruitment started in 2014 at 13 Genomic Medicine Centres and was completed in 2018.
Fernanda Amary and Adrienne M. Flanagan of University College London Cancer Institute, and colleagues recently described their experience, lessons learned from participation in the project and their determination that genomic medicine will become standard practice within sarcoma management at the Royal National Orthopaedic Hospital (RNOH) and beyond. The paper was published in The Journal of Pathology: Clinical Research.
During the recruitment period 1256 patients were diagnosed with sarcoma at RNOH and in total 957 patients, including 76 children, treated at the hospital were consented to participate in 100KGP. Only 62% of the recruited patients were successfully sequenced, and 13% of these required a PCR amplification step due to lack of DNA. Cartilaginous tumours were the most difficult to sequence.
Neoadjuvant therapies tended to result in tumor necrosis, barring sequencing. This was most often the case with Ewing sarcoma. There was also a tendency to reject tumour freezing as samples were deemed too small or necrotic, when in fact further analysis revealed that they would have contained enough material for sequencing, had they been frozen. Out of hours, tumours were fixed in formalin, which prevented sequencing.
Several treatment relevant clinical findings, such as a high mutational burden in 3% of tumours was reported.
One of the key lessons learnt was that biopsy material was often more suitable for sequencing than tumour resections, as it had not yet been subjected to therapy and was less necrotic.
“The 100KGP established that patients and healthcare workers alike are eager to engage in genomic testing, and that WGS can readily be incorporated into clinical service as a standard of care. Nevertheless, challenges remain,” stated the authors.