Genomics England searches for tumor sample processing improvements to boost data quality

Genomics England has run into teething problems in the first few months of its massive genome sequencing initiative. About half of tumor samples sequenced to date have yielded substandard data, a shortcoming Genomics England is trying to overcome by trialing new processes and working with hospitals to incorporate the practices into their day-to-day tasks.

The difficulties encountered by Genomics England are indicative of the scale of the challenge it faces, which entails working with the country's healthcare system to sequence 100,000 genomes over the next few years. So far, the team has sequenced 2,300 whole genomes, some of which are from cancer patients. These have proven to be problematic. The issue--which Genomics England is far from alone in facing--is how to gather sequencing-quality DNA at standard healthcare facilities. To date, half of tumor samples have fallen short of this standard, dragging down data quality.

Genomics England is exploring a variety of ways of gathering samples that will yield the quality data it needs to make a success of the program. The standard formalin-fixed, paraffin-embedded (FFPE) process for handling samples can damage DNA, and results from the first batch of genomes suggest this is happening frequently in the 100,000 Genomes Project. Genomics England thinks the shortage of cancer cells in samples that go through the fresh frozen (FF) process makes it equally problematic. In their current forms, neither FFPE or FF is a panacea.

The aim now is to improve both processes to increase the percentage of samples that yield quality sequencing data. Once Genomics England has settled on the best ways to handle samples, it will work with operating theaters and laboratories within the National Health Service to incorporate these processes into day-to-day activities. The new procedures could be in place in the next few weeks.

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