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:
Exploring mitochondrial DNA mutational landscape in oesophageal adenocarcinoma at various stages of development, from pre-cancerous lesions, to primary cancer, lymph node spread and distant metastasis.
Explore whether mitochondrial DNA mutation burden and type affects response to chemo/chemoradiotherapy, understand if chemo/chemoradiotherapy impacts on mitochondrial DNA mutations to delineate if current chemo/chemoradiotherapy offer selective pressure to clones of oesophageal adenocarcinoma cells with certain mitochondrial DNA mutation profiles.
Linux based bioinformatics toolkits:
SAMtools - .bam file handing, viewing and interrogation of key aligned sequence file benchmarks.
BCFtools - .vcf file handling, normalisation and viewing of variant calls.
GATK mutect2 - variant calling, used for indel calls as part of my pipeline.
Mutserve - mitochondrial DNA specific variant caller, used for SNV calls as part of my pipeline.
Haplocheck - mitochondrial DNA sample contamination checker
Pyega3 - enables downloading of European Genome-Phenome Archive databses