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Detection of Microsatellite Instability in Colonoscopic Biopsies and Postal Urine Samples from Lynch Syndrome Cancer Patients Using a Multiplex PCR Assay

Lookup NU author(s): Rachel Phelps, Dr Richard Gallon, Christine Hayes, Dr Tom Lee, Professor Rakesh Heer, Dr Ciaron McAnulty, Dr Mauro Santibanez Koref, Professor Sir John BurnORCiD, Dr Michael Jackson



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


© 2022 by the authors. Identification of mismatch repair (MMR)-deficient colorectal cancers (CRCs) is recommended for Lynch syndrome (LS) screening, and supports targeting of immune checkpoint inhibitors. Microsatellite instability (MSI) analysis is commonly used to test for MMR deficiency. Testing biopsies prior to tumour resection can inform surgical and therapeutic decisions, but can be limited by DNA quantity. MSI analysis of voided urine could also provide much needed surveillance for genitourinary tract cancers in LS. Here, we reconfigure an existing molecular inversion probe-based MSI and BRAF c.1799T > A assay to a multiplex PCR (mPCR) format, and demonstrate that it can sample >140 unique molecules per marker from <1 ng of DNA and classify CRCs with 96–100% sensitivity and specificity. We also show that it can detect increased MSI within individual and composite CRC biopsies from LS patients, and within preoperative urine cell free DNA (cfDNA) from two LS patients, one with an upper tract urothelial cancer, the other an undiagnosed endometrial cancer. Approximately 60–70% of the urine cfDNAs were tumour-derived. Our results suggest that mPCR sequence-based analysis of MSI and mutation hotspots in CRC biopsies could facilitate presurgery decision making, and could enable postal-based screening for urinary tract and endometrial tumours in LS patients.

Publication metadata

Author(s): Phelps R, Gallon R, Hayes C, Glover E, Gibson P, Edidi I, Lee T, Mills S, Shaw A, Heer R, Ralte A, McAnulty C, Santibanez-Koref M, Burn J, Jackson MS

Publication type: Article

Publication status: Published

Journal: Cancers

Year: 2022

Volume: 14

Issue: 15

Online publication date: 08/08/2022

Acceptance date: 21/07/2022

Date deposited: 20/09/2022

ISSN (electronic): 2072-6694

Publisher: MDPI


DOI: 10.3390/cancers14153838


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Funder referenceFunder name
Barbour Foundation
C1297/A15934Cancer Research UK CRUK (open competition)
MC_PC_17168Medical Research Council (MRC)