Thank you for your continued partnership with the Australian Pancreatic Cancer Genome Initiative (APGI). We appreciate your support and collaboration and hope you enjoy our 2016 research update.




Thank you for your continued partnership with the Australian Pancreatic Cancer Genome Initiative (APGI). We appreciate your support and collaboration and hope you enjoy our 2016 research update.

Project Updates

Long Term Survivors (LTS)

The APGI is driving a global study to characterise the molecular landscape of PDAC long term survivors (LTS). We hypothesise that LTS’s display distinct genetic and transcriptomic features previously unexplored by clinical or pathological based studies. We are looking to recruit patients who have survived 5 years or greater disease-free post resection and have available tumour tissue and a normal sample (tissue or blood) suitable for whole exome sequencing. Ethical approval is in place centrally for this study.


If you have patients whom fit this criteria, or you are a long term survivor yourself please email APGI Project Manager to discuss participation.

IPMN Study
The APGI is co-coordinating an international collaborative effort to characterise the evolutionary landscape of 100 intraductal papillary mucinous neoplasms (IPMN’s) from benign to invasive tumours. Whole genome sequencing will be employed over the IPMN component and matched invasive samples, where available, along with germline material. A subset of mucinous cystic neoplasms will also be included. One key aim is to investigate the different pathways to invasive cancer.
Ethics Review Equivalency (ERE) Task Force
Despite significant advances in genome sciences and technology, there has not been a co-evolution of the ethics review system. Duplication of ethics review for data intensive research has become strikingly problematic; in particular it unduly delays research and drains financial resources that should be devoted to research. The ERE Task Force as part of the Global Alliance for Genomics and Health are working towards developing a policy which provides Essential Elements for the ethics review process to foster recognition of ethics reviews globally. The APGI are playing a key role in its development through our experiences and expertise developed in genomic related ethical issues.
Other exciting projects in the pipeline include:
  • KRAS wildtype – a clinical and genomic analysis of this molecularly unique subset of PDAC’s
  • Metastases vs primary – a pilot study analysing genomic correlation of primary and metastatic disease within the same patient.


The Avner APGI BioResource

From 2016, the APGI BioResource is proudly supported by an Avner Pancreatic Cancer Foundation Accelerator GrantThe APGI strives to support translational pancreatic cancer research by providing samples and data via a governed and transparent process.

A total of 12 national and international studies were supported this year including:

  • A “big data” study using cutting-edge informatic methods to integrate the APGI cancer genomics data and the corresponding clinical records to identify novel genes and gene groups that may help explain both common and idiosyncratic presentations in pancreatic cancer patients (Dr Frank Lin, Kinghorn Cancer Centre for Clinical Genomics)


  • An expression study using the APGI Training and Validation Set TMA’s to assess the prognostic and predictive value of SLC7A11 and MutY-Homolog in human pancreatic cancer cells. When inhibited, these 2 proteins can kill pancreatic cancer cells and cancer-promoting pancreatic stellate cells, increasing the effectiveness of existing cancer drugs (Dr Phoebe Phillips, Lowy Cancer Research Centre).
To access this world-class resource, which includes ICGC-grade DNA samples and highly-annotated constructed TMA’s, please visit
APGI BioResource Summary

APGI Publications

Hypermutation in pancreatic cancer. Humphris JL, Patch A, Nones K, Bailey PJ, Johns AL, McKay S, Chang DK, Miller DK, Pajic M, Kassahn KS, Quinn MCJ, Bruxner TJC, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Stone A, et al. Gastroenterology. Nov 2016; doi: 10.1053/j.gastro.2016.09.060 [Epub ahead of print]This APGI-led study interrogated 385 pancreatic cancer genomes to define hypermutation and its causes. Mismatch repair deficiency was identified in 1% of tumors harboring different mechanisms of somatic inactivation of MLH1 and MSH2. Defining mutation load in individual pancreatic cancers has the potential to inform immunotherapy clinical trial design in pancreatic cancer.


Genomic analyses identify molecular subtypes of pancreatic cancer. Bailey P, Chang DK, Nones K, Johns AL, Patch A, Gingras M, Miller DK, Christ AN, Bruxner TJC, Quinn MC, Nourse C, Murtaugh LC, et al.   Nature. Mar 2016; 531:47-52 doi:10.1038/nature16965

This ground-breaking study demonstrated that by incorporating genomic and expression data, pancreatic cancer can be classified into four district disease sub-types – Squamous, Progenitor, ADEX and Immunogenic. We now have a deeper understanding of pancreatic cancer biology, and the unique characteristics of each sub-type have the potential to be exploited in the clinic with more targeted therapies. Read more about what this means for pancreatic cancer patients on our website.

APGI Leadership Team

At the end of 2015, we introduced you to the APGI’s newly appointed Chairman, Professor Anthony Gill. Since then, the APGI Leadership Team has further expanded and we welcomed the following new members in 2016:

Lorraine Chantrill – Lorraine has recently been appointed as Senior Staff Specialist Medical Oncologist at St Vincent’s Hospital. She is clinical lead for Oncology Clinical Trials and is working towards establishing new pancreatic cancer clinical trials, such as the Phase 3 HALO trial. Lorraine is a Director of the AGITG and has an active interest in translational cancer medicine.

Dr Paul Timpson – Paul and his team are using cutting edge in vitro and in vivo imaging technology and fluorescent bio-sensor mouse models to pinpoint molecular drivers of pancreatic cancer progression, invasion and metastases in real time.

John Pearson – John is a well-established bioinformatician with over 20 years experience creating software for medical researchers. John currently manages the Genome Informatics Group at QIMR Berghofer Medical Research

Nature 2016: Pancreatic cancer subtypes