This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
For further information about this project, please contact:
We have developed and are actively enhancing microsatellite instability (MSI) assays that can be used to detect loss of DNA mismatch repair function, an important cancer biomarker. These use amplicon sequencing and custom bioinformatics pipelines to call MSI status and to call variants at mutation hotspots that complement MSI analysis. Applications include the detection of mismatch repair deficiency in cancer tissues and in normal tissues, as well as testing liquid biopsies for early cancer detection.
The MSI analysis pipelines use state of the art applications for DNA sequence analysis, such as BWA, SAMtools, Picard, GATK, and VEP, as well as bespoke software for specific tasks such as trimming primer sequences from reads (BAMclipper) and custom R scripts for variant calling and MSI classification. Pipelines are executed as shell scripts that call to these different software, using fastq files as input and giving variant calls and interpretation as output.