Mechanistic and functional drivers of cancer neochromosomes

Mechanistic and functional drivers of cancer neochromosomes

Project details

Neochromosomes are massive extra chromosomes that frequently occur in certain rare cancers, such as sarcomas. They are composed of hundreds of genomic segments that are amplified, rearranged and stitched together into “Frankenstein chromosomes”. We recently discovered the chaotic molecular processes, which underlie their formation and evolution—chromosome shattering and breakage-fusion-bridge. (Papenfuss & Thomas, Molecular and Cellular Oncology 2015, 2:4, e1000698; Garsed et al, Cancer Cell 2014,10;26(5):653-67). 

This exciting research project will involve the analysis of second and third generation DNA sequencing data (Illumina short read, Genomics 10X Chromium, Oxford Nanopore, and PacBio), integration of epigenetic, transcriptomic and proteomics data, as well as mathematical modeling, to refine our understanding of how these processes are initiated; whether they operate non-randomly; and what role they play in other cancers.

The research student will learn about biological sequencing analysis, develop expertise in computational biology and bioinformatics, and gain insight into analysis of cancer data, especially second and third generation DNA sequencing data.

About our research group

The Papenfuss lab uses mathematics, statistics and computation to understand the evolution  of cancer, as well as other diseases. This frequently entails the development of novel bioinformatics, computational and mathematical methods to make sense of complex biological data, for example tools for discovering genomic rearrangements. Lab members comprise mathematicians, statisticians, computer scientists, physicists, as well as biologists. Our work is enabled by the Institutes new high performance computing resources.

The lab is joint between the Institute and the Peter MacCallum Cancer Centre. We collaborate widely, and this project is a collaboration with Professor David Thomas, Dr Tim Mercer at the Garvan Institute, and Dr Andrew Webb and Dr Alan Rubin at the Institute.

Researchers:

Associate Professor Tony Papenfuss

Tony Papenfuss
Associate Professor
Tony
Papenfuss
Head, Computational Biology; Laboratory Head

Project Type: