Performing an Analytical Validation for an NGS Workflow: Q&A with Liverpool Clinical Laboratories

A. The Molecular Pathology Service at LCL has been providing a regional service in Cheshire and Merseyside for over ten years. Originally, our lab was performing single gene molecular profiling of EGFR variants, ALK and ROS1 gene fusions, and PD-L1 protein expression. This required the use of a combination of multiple techniques, including RT-PCR, IHC, and FISH. We currently examine approximately 1200 NSCLC samples per year and, with the increase in molecular biomarkers, we decided to explore the possibility of implementing local next-generation sequencing (NGS).

A. LCL is based in a large teaching hospital and referral centre for other laboratories. With this comes a fair amount of projects, and we have been involved in a number of these, including for IHC, FISH, RT-PCR, etc. The time it takes to complete a validation can be dependent on several factors, including the availability of staff to undertake testing activities whilst delivering other commitments and access to a dynamic range of material to include in testing. Validation costs vary but include the cost of reagents, scientific/consultant staff time, and the cost of commercial control material.

A. Working with the analytical validation (AV) team helped with project planning, run planning, and the analysis of results. This reduced the burden on the scientific staff involved in the project and allowed us to perform project work alongside our daily activities. The AV consultation package is also cost-effective as it includes all reagents, commercial control material, and the consulting services of the AV team.

The support we received from the Thermo Fisher AV team was excellent. The run plans provided were clear and simple to follow. The weekly project meetings were very friendly, and the results/progress were all clearly explained. The Customer Concierge team were also very helpful with documentation and the delivery of reagents and controls.

A. As we had used the Genexus and the Oncomine Precision Assay before, it was not the first time we had seen results from the assay. However, the number of runs and samples included in the project generated a considerable amount of data. The AV consultation service assisted significantly in the analysis of the run data, comparing against expected results and providing detailed updates.

We would advise to take some time to select the samples you wish to include in your project. We were fortunate that we had a large number of samples previously tested by NGS and so had access to a wide range to choose from, which included some rare variants, rare fusions, and CNVs.

A. We would certainly recommend the AV consulting service to labs looking to introduce NGS. It can save you time completing your validation, and it is cost effective with regards to the reagents, commercial controls, and the service included.