Avner APGI BioResource: Introduction & Availability
From 2016 the APGI BioResource is proudly supported by a grant from the Avner Pancreatic Cancer Foundation. www.avnersfoundation.org.au
Our tissue and data resource contains fresh frozen tissue, formalin fixed paraffin embedded (FFPE) tissue, blood, blood products, tissue microarrays (TMAs), patient-derived xenografts and cell lines across a spectrum of pancreatic diseases. This resource has proven to be of consistent high-quality, and has been the foundation of several landmark publications in Pancreatic Cancer (Nature 2012, Nature 2013, Nature 2016).
A key APGI priority is to build capacity in translational research through the acquisition of tissue and blood samples coupled with detailed clinical data across Australia. This is providing an unparalleled base for ongoing studies in the future. APGI infrastructure consists of a dedicated team to coordinate sample collection, management, processing and distribution based at the Garvan Institute of Medical Research in Sydney.
We currently have over 4,000 pancreatic cancer patients in our database, with a range of prospectively collected and archived biospecimens. Every biospecimen is coupled with detailed clinico-pathological data, including past medical history, treatment data and detailed disease outcomes. Our resource is updated regularly and maintained by a dedicated team. This makes us one of the largest resources of pancreatic biological material in the world, and our samples have been used to support over 160 research studies globally.
We encourage you to read the APGI BioSpecimen and Data Access Policy, which outlined reuirements for distribution and use of our resource. For further information about how you can use the BioResource for your research, please contact us at firstname.lastname@example.org.
BioSpecimen Summary and Availability
We have been collecting, processing, analysing and storing biospecimens since 2006. Through this process we have developed state-of-the-science biospecimen resource practices, based on the guidelines from international bodies such as the NCI Best Practices for Biospecimen Resources. These practices and standard operating procedures outline the operational, technical, ethical, legal and policy best practices for the APGI BioResource, and are specific to the mission and scientific needs of the pancreatic cancer translational research community. Our best practices and detailed collection, processing and distribution protocols promote biospecimen and data quality and support adherence to ethical and legal requirements.
Tissue MicroArray (TMA)
The Avner APGI BioResource includes one of the world’s largest and most comprehensively annotated FFPE pancreatic tumour tissue cohort in micro-array format. This retrospectively acquired Australian surgical cohort spans over a decade, and is especially designed for rapid biomarker discovery studies. Prospectively collected FFPE tissue is currently being used to construct further TMAs. Pancreatic tumour types include pancreatic ductal adenocarcinomas, ampullary carcinomas, intraductal papillary mucinous neoplasms, pancreatic endocrine tumours and solid pseudo papillary tumours.
Each TMA* contains triplicates of each core as well as controls. TMA maps* displaying the location and minimal relevant information of each core will be provided once samples are distributed.
*Excludes Test Arrays
|BioSpecimen Type||Patient count||TMA count||Restricted|
|Pancreatic Ductal Adenocarcinoma (PDAC) Test Array||20 cases||1 TMA||No|
|Normal Pancreas Test Array||20 cases||1 TMA||No|
|Pancreatic Ductal Adenocarcinoma (PDAC) Training Set Arrays||96 cases||3 TMAs||No|
|Pancreatic Ductal Adenocarcinoma (PDAC) Validation Set Arrays||352 cases||11 TMAs||No|
|Ampullary Carcinoma Set Arrays||96 cases||3 TMAs||No|
|Intraductal Papillary Mucinous Neoplasm (IPMN) Set Arrays||56 cases||2 TMAs||No|
|Solid Pseudopapillary Tumour (SPT) Set Array||32 cases||1 TMA||No|
|Pancreatic Intraductal Neoplasm (PanIN) Array||32 cases||1 TMA||No|
|Chronic Pancreatitis Set Arrays||64 cases||2 TMAs||No|
|Pancreatic Neuroendocrine (PNET) Set Arrays||64 cases||2 TMAs||No|
|International Cancer Genome Consortium (ICGC) Set Arrays||232 cases||8 TMAs||Yes|
|International Cancer Genome Consortium (ICGC) Refined Set Arrays||39 cases||2 TMAs||No|
Formalin Fixed Paraffin Embedded (FFPE) Tissue
A wide range of FFPE tissue is available from our BioResource. We do not provide whole FFPE tissue blocks but can arrange whole sections (either on slides or in cigars) or cores for downstream processes such as nucleic acid extraction or staining.
Many of our prospectively collected FFPE tissue have matched snap frozen and blood component material, accompanied by a rich clinicopathological dataset.
Surgically resected tissue of various histological types, including limited metastases, have been collected and snap frozen in liquid nitrogen. In some cases, tissue in DMSO may be available as well as patient-derived xenograft (PDX) tissue.
Patient-derived cell lines (PDCL’s) have been created on 18 patients. Some patients have multiple cell lines grown under different environments. If you are requesting PDCL’s only, without any clinical information, the approval process may be expedited. Read more about accessing PDCL’s here.
Received whole blood is centrifuged and divided into resulting blood components – plasma, buffy coat, red blood cells, and serum (where applicable) – and snap frozen in liquid nitrogen.
Whole blood may also be available, sometimes in the form of PAXgene DNA Blood Tubes.
Nucleic Acid Analytes
DNA and RNA analytes extracted from various BioSpecimen types are stored in buffer at -80°C, with accompanying BioSpecimen data (concentration, volume, A260/280, etc) recorded for later aliquot creation.
High Risk Cohorts
As part of the Australian familial Pancreatic Cancer Cohort (AFPaCC) 2011-2016 we have accrued a cohort of over 200 families with a history of pancreatic cancer through a dedicated registry. The cohort includes blood, tissue samples (mostly FFPE) and detailed clinical, pathological and family history information on families deemed High risk. This is cohort of patients and samples are available for the research community to access and would be a valuable adjunct to genetic or clinical studies on familial cancer. Further details are available on our Familial pages.
Scanned H&E images are available for the majority of the ICGC sequenced fresh tissue BioSpecimens as TIFF (thumbnail) files with a dimension of about 1024x768 pixels.
Full resolution SVS files may be available upon request however sufficient time and storage (approximately 3 GB per image) needs to be made available.
- Clinical Presentation
- Risk Factors
- Family History