This is a historic project which has previously made use of HPC facilities at Newcastle University.
For further information about this project, please contact:
The aim of the project is to analyse sequencing data to identify and characterise mismatch repair deficient samples. The sequencing data were mainly generated using amplicon sequencing but include whole genome sequencing data.
The project requires mainly batch processing using aligner such as BWA, programs for sequencing quality assessment and the GATK suite of programs. R and its associated libraries are also used. This has led in excess of 20 publication including:
Gallon et al "Constitutional Microsatellite Instability, Genotype, and Phenotype Correlations in Constitutional Mismatch Repair Deficiency" 2023 PMID: 36586540
Gallon et al. "Detection of constitutional mismatch repair deficiency in children and adolescents with acute lymphoblastic leukemia. " 2023 Leuk Lymphoma. PMID: 36272172
Gallon et al. "How Should We Test for Lynch Syndrome? A Review of Current Guidelines and Future Strategies. " 2021 Cancers PMID: 33499123
Gallon et al. "Novel microsatellite instability test of sebaceous tumours to facilitate low-cost universal screening for Lynch syndrome" 2025 Clin Exp Dermatol. PMID: 39847610
Hall et al "Detection of urothelial carcinoma in Lynch syndrome using microsatellite instability analysis of urine cell-free DNA." EBioMedicine. PMID: 41138669