Australian Melanoma Genome Project

James S Wilmott1, Peter Johansson2, Matthew A. Field3, Valerie Jakrot1, John

V. Pearson2, Nicola Waddell2, Catherine A. Shang4, Andrew Gilbert4, Jonathan Cebon5, Mark Shackleton6, Anna Fitzgerald4, John F Thompson1, Nicholas K Hayward2, Richard A Scolyer1,7, Graham J Mann1,8

1Melanoma Institute Australia, North Sydney, NSW, Australia

2Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Qld, Australia

3Immunogenomics Laboratory, Australian National University, Canberra, ACT, Australia

4Bioplatforms Australia, Macquarie University, North Ryde, NSW, Australia

5Ludwig Institute for Cancer Research, Olivia Newton-John Cancer and Wellness Centre, Austin Health, Heidelberg, Vic, Australia

6Melanoma Research Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Vic, Australia

7Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia

8Centre for Cancer Research, The University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia

Abstract

Australia has the highest incidence of cutaneous melanoma worldwide, where it is the fourth most common cancer and a leading cause of cancer death in young adults. Late stage metastatic melanoma was until very recently usually rapidly fatal. However, inhibitors of the MAP kinase pathway and of immune checkpoint mechanisms have dramatically extended patient survival, highlightingthe importance ofidentification of therapeutic targets in cancer through molecularcharacterization. Melanomas typically havevery large numbers ofsomatic mutations, including some now understood to affect key driver genes both within and outside of coding regions. To comprehensively extend the molecular characterization of melanoma, the Australian Melanoma Genome Project (AMGP) was launched in August 2012 with the support of Melanoma Institute Australia (MIA), the Australian Government via Bioplatforms Australia, NSW Health and the Cancer Council NSW. The AMGPaims to analyse whole genomes from 500 primary and metastatic melanomas.To date, the majority of samples hasbeen sourced from the MIA Biospecimen Bank, and thushave comprehensive, prospectively collected clinical annotation.Whole genome sequencing (WGS) has been performed and analysed to date on 220 samples from 202 patients: including 79 primary melanomas, 15 cell lines, and 126 metastasesfrom various sites; 250 cases will be sequenced by the end of 2014, and the remaining 250 by mid-2015. WGS is being performed on theIllumina HiSeq2000 and Xtenplatforms at Australian and Korean sequencing centres. Tumours are being analysed at ≥60X coverage, germline DNA at 40X, and cell lines at 40X. Mapping, alignment, variant calling and structural variant determination are being carried out with ICGC-compatible pipelines. Complementary RNAseq and methylome data are being obtained on a subset of cases, facilitating an integrated ‘omics’ approach to analysis. Data will be released in the public domain.

Presenting author name and contact information:

ProfGrahamJMann

Melanoma Institute Australia

40 Rocklands Rd, North Sydney, NSW 2060

+61 2 8627 3777

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