Germline mismatch repair (MMR) gene analyses from English NHS regional molecular genomics laboratories 1996–2020

Dec 26, 2022 | Publications, Published 2023

Home » Publications » Germline mismatch repair (MMR) gene analyses from English NHS regional molecular genomics laboratories 1996–2020

Lucy Loong, Catherine Huntley, Fiona McRonald, Francesco Santaniello, Joanna Pethick, Bethany Torr, Sophie Allen, Oliver Tulloch, Shilpi Goel, Brian Shand, Tameera Rahman, Margreet Luchtenborg, Alice Garrett, Richard Barber, Tina Bedenham, David Bourn, Kirsty Bradshaw, Claire Brooks, Jonathan Bruty, George J Burghel, Samantha Butler, Chris Buxton, Alison Callaway, Jonathan Callaway, James Drummond, Miranda Durkie, Joanne Field, Lucy Jenkins, Terri P McVeigh, Roger Mountford, Rodney Nyanhete, Evgenia Petrides, Rachel Robinson, Tracy Scott, Victoria Stinton, James Tellez, Andrew J Wallace, Laura Yarram-Smith, Kate Sahan, Nina Hallowell, Diana M Eccles, Paul Pharoah, Marc Tischkowitz, Antonis C Antoniou, D Gareth Evans, Fiona Lalloo, Gail Norbury, Eva Morris, John Burn, Steven Hardy, Clare Turnbull (2022). Germline mismatch repair (MMR) gene analyses from English NHS regional molecular genomics laboratories 1996–2020: development of a national resource of patient-level genomics laboratory records. Journal of Medical Genetics. 60. jmg-2022. 10.1136/jmg-2022-108800. https://pubmed.ncbi.nlm.nih.gov/36572524/

Abstract:

Objective: To describe national patterns of National Health Service (NHS) analysis of mismatch repair (MMR) genes in England using individual-level data submitted to the National Disease Registration Service (NDRS) by the NHS regional molecular genetics laboratories.

Design: Laboratories submitted individual-level patient data to NDRS against a prescribed data model, including (1) patient identifiers, (2) test episode data, (3) per-gene results and (4) detected sequence variants. Individualised per-laboratory algorithms were designed and applied in NDRS to extract and map the data to the common data model. Laboratory-level MMR activity audit data from the Clinical Molecular Genetics Society/Association of Clinical Genomic Science were used to assess early years’ missing data.

Results: Individual-level data from patients undergoing NHS MMR germline genetic testing were submitted from all 13 English laboratories performing MMR analyses, comprising in total 16 722 patients (9649 full-gene, 7073 targeted), with the earliest submission from 2000. The NDRS dataset is estimated to comprise >60% of NHS MMR analyses performed since inception of NHS MMR analysis, with complete national data for full-gene analyses for 2016 onwards. Out of 9649 full-gene tests, 2724 had an abnormal result, approximately 70% of which were (likely) pathogenic. Data linkage to the National Cancer Registry demonstrated colorectal cancer was the most frequent cancer type in which full-gene analysis was performed.

Conclusion: The NDRS MMR dataset is a unique national pan-laboratory amalgamation of individual-level clinical and genomic patient data with pseudonymised identifiers enabling linkage to other national datasets. This growing resource will enable longitudinal research and can form the basis of a live national genomic disease registry.

Tags: Brian Shand | National Lynch Syndrome Registry | Oliver Tulloch | Shilpi Goel | Tameera Rahman