Genetic laboratory service redesign

4 June 2015

The PHG Foundation is broadly supportive of efforts to harness the use of genomics and genetic technologies within the NHS, and to provide high quality, equitable and cost effective services with appropriate support for patients and families.

Genomic knowledge is increasing exponentially, but significant challenges remain to generate knowledge that is clinically useful for NHS patients. Interpreting genomic variants in ways that distinguish between those that are disease causing and those that are not, in a timely and affordable manner, remains the biggest challenge. For this reason it is vital that each of the GCLH’s systematically share their data, knowledge and expertise within the strategic network. It should be explicitly specified that GCLHs must work together as stated to share data, intelligence and expertise.

Thus we strongly endorse the aim (section 3.1) of driving improved quality “through collation and sharing of data for patient benefit by standardisation of and participation in minimum agreed datasets….”. Indeed the clinical interpretation of genomics data and variants relies on access to pre-existing knowledge and data. In addition to genomic/genetic data, interpretation of variants also requires phenotypic information not only on the patient under investigation, but also phenotype data linked with genetic data from previous cases. As most phenotype data and genotype data are generated and recorded in different places, it will be imperative for the GCLHs to collaboratively agree and determine the level / detail of phenotype data required to support their genome analysis activities, how this can be collected and recorded in a systematic way, and how this can be shared integrated with variant data.

Another important priority is to target the application of genomic sequencing technologies at those clinical specialities and phenotypes most likely to generate clinically useful knowledge, and to minimise the generation of variants of unknown significance or incidental findings that will then require further investigation or referral, particularly arising from areas of the genome that are not pertinent to the patient’s clinical presentation. This would complement the desired impact (on page 2 of the specification) of “safe and effective targeted treatment based on the genomic profile with minimised side effects as part of the overall move towards stratified and precision medicine”.

Specifically, emerging from our report on Realising Genomics, which is concerned with use of genomic sequencing in clinical settings, we recommend that the network should adopt as standard the use of targeted analysis of whole genomes using ‘gene lists’ that are nationally agreed following genome-based sequencing as the assay and using standardised evidence criteria, unless, in a particular class of cases, there are good clinical reasons for adopting whole genome or exome sequencing as a first line test.

In order to maintain public trust and confidence in these services, it is important that services are developed in ways that are both transparent and accountable.

Read the full response here

NHS England