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NGS for Solid Tumour Profiling

Dr. Rachel Butler, FRCPath, All Wales Genetics Laboratory
| Feb 02, 2016

I’m frequently asked about what factors we considered before making the decision to adopt NGS for profiling solid tumours in our laboratory practice. As every lab knows, implementing a new technology means investing time, money and human resources, so you need convincing arguments that there will be significant benefits in return.

My laboratory was seeing an increase in the need to assess mutations in more than one gene. When multiple assessments are required, often they end up being requested sequentially, which leads to an increase in both cost and time to answer. Time management in the lab becomes difficult to streamline, not to mention the delays involved when we need additional sample material.

We’ve found that the NGS workflow allows us to synchronise on a single, operational process for all of our gene targets, which is a huge benefit for improving productivity and overall cost savings.

In the webinar that I presented for Illumina, I shared some of our laboratory’s experience with NGS, including the factors to consider during panel design. Another very important aspect, that I discuss, is how we worked with our bioinformatics team to create a simplified interface for data analysis.

Understanding the technical aspects of NGS technology has allowed us to overcome some of the challenges in quantity and variability of FFPE samples. We worked with the CR-UK SMP Technology Hubs to develop standardized sequencing coverage requirements for 95% confidence level of variant detection.

More recently, we started working with circulating tumour DNA (ctDNA) in our clinical trial studies. ctDNA presents numerous advantages but also poses new challenges, because there is significantly less DNA available. In the webinar, I discuss the potential of NGS data taken at multiple time points in the FOCUS4 trial, which really illustrates the utility of ctDNA in mapping the appearance of resistance mutations.

The future looks promising for NGS technology in molecular pathology services using gene panel testing to deliver patient stratification to help direct patients to an appropriate clinical trial. In the UK, we started the Clinical NGS Consortium for Solid Tumours (CNCST), led by David Gonzales de Castro, Head of the Molecular Diagnostics Laboratory at The Royal Marsden, as a forum to discuss and establish NGS best practices; in 2016, we plan to expand the geographic scope of the consortium to include other laboratories in Europe.

If you are interested in viewing the full presentation, the webinar recording can be streamed here.