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:
This project investigates genomic centromeres and telomeres as drivers of childhood cancer. This seeks to find recurrent genomic and structural changes in a pan-cancer study, centring around childhood ALL, medulloblastoma, and neuroblastoma. Using short, long and ultra‑long read sequencing, centromere and telomere variants will be investigated in patient samples with matched germline material. The results of validation studies and functional studies may also be analysed to support the main results of the project.
The workflows are implemented using bash, Snakemake, or Nextflow, and incorporate bioinformatics tools such as Jellyfish, Samtools, BCFTools, Minimap2, and Verkko. Custom R scripts, built on packages including BiocManager, tidyverse, and Biostrings, provide additional functionality. The pipelines are modular and can be executed in parallel, allowing large genomic datasets to be processed efficiently. Because the research is exploratory, both the choice of packages and the pipeline structure may change over time as new methods are developed or adapted to suit specific analytical requirements.