November 2019

Welcome to our second newsletter aimed at keeping you up to date with developments in the new NHS Genomic Medicine Service.

It is now just over a year since the 100,000 Genomes Project drew to a close and the reconfiguration of genetic and genomic services across England was announced. So where are we now? We have made progress, albeit rather slower than we would have hoped, and for now the range of genetic tests available and the mechanism for ordering these tests remains as it has been for some years.

Here we give a brief update to keep you abreast with developments.

How are we progressing with consolidation?

After some consolidation both our rare disease and cancer labs are up and running. This has been challenging in the absence of contracts with NHSE and any clear indication of how the funding will work from next April. However, solid tumour cancer panel testing has been consolidated from some Trusts into the GLH lab at the Royal Marsden. In order to address some concerns that consolidation will adversely affect turnaround times, we will be piloting three runs a week of the large cancer panel mandated by NHSE to reduce the TAT to seven days (compared to the NHSE target of three weeks and Royal Marsden’s current average of 11-days). We hope that a number of our constituent labs will contribute to this pilot and if you are interested please contact Mike Hubank – michael.hubank@icr.ac.uk. The rare disease lab at GOSH has fully integrated the NW and NE Thames Regional Genetics laboratories, but we haven’t been able to progress the next stage of consolidation and bring in the Neurogenetics lab as the funding streams are still unclear. We hope this will be resolved soon as we still aim to complete this move before April next year.

Progress with whole genome sequencing

The go-live date for all GLHs to be delivering WGS has been pushed back due to delays in developing the National Genomics Informatic System (NGIS). We are now in the early testing phases but we won’t be trialling the system with patient samples until sometime in the Spring of 2020 with a view to being live for all WGS in the first wave soon after. None-the-less, our GMC teams have been very active, mapping pathways and identifying all those who need to be trained on NGIS before go-live so we are ready to roll when NGIS is ready.

What else is new in cancer?

NHSE are ‘tweaking’ the test directory slightly. One of the main changes is the incorporation of RNA panel testing to be functional early in 2020 in line with the likely introduction of NTRK fusion drugs, larotrectinib and entrectinib which is expected in early 2020. Funding is being made available for consolidated hub labs to develop and validate these panels urgently. Fortunately, RMH has been working on this for some time and has the relevant panels just about ready to go.

To address concerns about issues such as sample quantity, quality, transport of fresh frozen tissue, Louise Jones, our pathology lead is working with Mike Hubank, Scientific Director, to extend the work she has already done on the use of paxgene tubes for collection and transport of tumour samples for WGS. A protocol is being developed and Louise will be looking for sites to help with this work soon. This is an exciting development, not just because we need to address these issues but because it will be our first R&D project as a GLH.

Rapid exome sequencing.

Rapid exome sequencing for the very sick neonate and child has been launched. Any very sick child on NICU or PICU thought to have an underlying genetic condition where diagnosis may change management is eligible for testing. Requests must be made through clinical genetics and anyone needing more information of wishing to request a test should contact the relevant clinical genetics team through harry.leitch@nhs.net (07813 046071) or jan.cobben@nhs.net (07702 082170) For NW Thames Regional Clinical Geneticists or, for NE Thames Geneticists  gos-tr.londonnorthGLHrapidsequencing@nhs.net  or 0207 762 6886.

Rapid fetal exome sequencing is likely to be launched early in 2020.

News from the GMCs

Genomic Medicine Centres will no longer exist after April 2020, by which time the majority of 100,000 Genome results will have been analysed. However, Genomics England have announced that secondary findings will start to be returned in the Spring of 2020. There are three lines of work here i) the development of the bioinformatic pipeline at Genomics England, ii) the implementation group and iii) the evaluation group. We will update you on progress here in the next newsletter.

When will the new test directory be available?

Both the cancer and constitutional directories are now ‘locked down’, although there may be some changes to the cancer directory as discussed above. Both of these directories will be active from April 2020 and much work has gone, and still is going into validating the new tests. (https://www.england.nhs.uk/publication/national-genomic-test-directories/).

In summary, there is a lot happening to prepare for the changes needed to implement the new GMS but for now the testing available, requesting it and where to send it is largely unchanged. Progress is being made with one of the rapid sequencing services now live and WGS likely to be live before the end of this financial year. There is still a lot to do and if you have any queries please contact ldnnorth.glh@nhs.net.

Lyn Chitty, Medical Director,
James Fisher, Chief Operating Officer
Mike Hubank, Scientific Director

London North Genomic Laboratory Hub
29th November 2019