Making the case for Centralised Biobanking in WA
Careful management of bio-specimens for current and future research is fundamental for high quality and reproducible research. There’s a need in WA to establish a harmonised sample collection, storage, curation and management system which will allow ethically acceptable standardisation across cohorts and registries. This will assist with avoiding duplication of effort and investment.
With Medical Research Future Funds (MRFF), WAHTN commissioned a scoping project in 2018 to develop recommendations for national guidelines and piloting infrastructure for a scalable, shared, and standardised data repository of clinical and research genomics resource facility in WA. The project, overseen by Dr Aron Chakera, has the potential to be scaled nationally and has produced an international scan of Biobank resources, facility ethics and economics across Australia, the UK and Japan. To inform the Report a questionnaire was sent out to a number of WA stakeholders to gather information and feedback on the establishment of a centralised biobank in WA. With follow up interviews, the project team were able to clarify and understand the data and specimen banking requirements across different studies and Biobanks in WA.
A stakeholder engagement workshop was held in October 2018 with the aim of developing working groups to further advance the discussion points around:
- Quality Assurance
- Data Management
The minutes and slides presented at the workshop are available online.
What are the next steps? In order to further develop a plan for a centralised Biobank in WA, interested parties were invited to join one of the six working groups listed above. Each working group addressed the issues and defined actions which need to occur to create the Biobank hub in the context of each specific group. The Chair for each working group is responsible for compiling key messages and summarise recommendations, tasks, and actions as discrete projects (small / medium / large, short term / mid term / long term etc). Subsequently a WA Biobank Committee chaired by Aron Chakera was formed in late 2019.
Trialling of a Biobanking Informatics Platform for WA
WAHTN has contributed funds towards the costs of a Telethon Kids Institute (TKI) initiated project which purchased OpenSpecimen and configured it within TKI servers for supporting complex Biobanking operations. WAHTN funding contributed to the training of IT and Biobanking personnel in the configuration and use of the platform. OpenSpecimen was used initially to support the Joondalup Heath Campus based ORIGINS Biobank and proved to be of great benefit.
As such, the Steering Committee has agreed to make OpenSpecimen the default software for WA biobanking. The challenges of COVID-19 have realised funding for research infrastructure and allowed the purchase of a new OpenSpecimen licence for WA with the long term goal to use OpenSpecimen to support other research across WA.
WAHTN Biobank Registry
|Biobank Name||Contact||Phone||Type of biobank||Description||Number of samples||Sample types||Data types||Institution||Website||User type||Collection period|
|Nicotine Dependence Study||Sulev Koks||08 6457 email@example.com||Cohort||This a collection of DNA from 1800 male subjects who all filled in questionnaires on smoking behaviour with the Fagerström Test for Nicotine Dependence. This cohort is from Vietnam.||1,001 - 10,000||DNA||Patient Questionnaires||Perron Institute for Neurological and Translational Research||Oligo: A biobank that supports several research groups or clinical trials, may or may not be designed to release biospecimens outside their collaborative group.||2014 - 2016|
|NCARD Biobank||Jenette Creaney||08 6151 firstname.lastname@example.org||Case Control, Longitudinal, Disease Specific, Cohort||Based at SCGH, the NCARD Biobank is dedicated to medical research focused on improving diagnosis and treatment of asbestos related diseases such as mesothelioma, as well as other health conditions. Over the past 25 years, 3000 Western Australians have donated clinical samples to the NCARD Biobank. The biobank has supported over 30 different projects with approximately 10,000 biospecimens used in medical research.||10,001 - 100,000||Blood, Plasma, Serum, DNA, RNA, Urine, Immortalised Cell Lines, Tissue (Frozen), Primary Cells, Pleural Effusions||Demographic Data, Medical Records||Sir Charles Gairdner Hospital, University of Western Australia||resphealth.org.au/ncard-biobank||Oligo: A biobank that supports several research groups or clinical trials, may or may not be designed to release biospecimens outside their collaborative group.||1994 - ongoing|
|LIBI (lifelong impact of burn injury)||Mark Fear||0411 355 email@example.com||Longitudinal, Disease Specific||Samples collected from children attending PCH for treatment for a burn injury. Longitudinal sample collection across clinical follow-up.||101 - 1,000||Plasma, DNA, RNA, Faeces, Urine, Primary Cells, Hair||Demographic Data, Patient Questionnaires, Medical Records||University of Western Australia||Oligo: A biobank that supports several research groups or clinical trials, may or may not be designed to release biospecimens outside their collaborative group.||2020 - ongoing|
|Helicobacter Research Biobank||Alfred Chin Yen Tay||08 6457 firstname.lastname@example.org||Cohort, Cross Sectional, Population Based, Disease Specific||Clinical Helicobacter pylori strains.||1,001 - 10,000||Microbiological, Tissue (Frozen)||Medical Records, Physiological / Biochemical Measurements||University of Western Australia||Mono: A biobank that supports a specific research project, may have few staff members, a small-scale accrual scope with little to no initial intention of releasing or distributing biospecimens to secondary parties.||1997 - 2018|
|PlusLife (Perth Bone & Tissue Bank Inc)||Anne Cowie||08 6144 email@example.com||Donated human musculoskeletal tissue for transplant purposes. Some tissue deemed not suitable for Tx is available for research purposes.||1,001 - 10,000||Tissue (Frozen)||Demographic Data, Patient Questionnaires, Medical Records||pluslife.org.au||Mono: A biobank that supports a specific research project, may have few staff members, a small-scale accrual scope with little to no initial intention of releasing or distributing biospecimens to secondary parties.||1990 - ongoing|
|Neurodegenerative Disease Biobank||Sue Fletcher||0403 079 firstname.lastname@example.org||Disease Specific||Collection of dermal fibroblasts, lymphocytes, DNA, whole blood from patients with neurodegenerative disease, plus some healthy controls.||101 - 1,000||Blood, DNA, Immortalised Cell Lines, Primary Cells||Medical Records, Physiological / Biochemical Measurements||Murdoch University||Poly: A biobank that generally has a larger accrual scope, resources and multiple users outside the biobank proper.||2016 - ongoing|
|Health in Men Study||Leon Flicker||08 9224 email@example.com||Cohort, Longitudinal, Population Based||The Health In Men Study (HIMS) arose out of a population-based randomized trial of screening for abdominal aortic aneurysms conducted in Perth in 1996-99. All men were identified from an electronic copy of the electoral roll, the target age range was 65-79 years. In total, 12,203 men attended for baseline screening and of these 4,249 returned for a resurvey and provided a blood sample in 2001-4. Cholesterol, HDL, LDL, triglycerides, glucose, creatinine, C-reactive protein and homocysteine were all measured.||1,001 - 10,000||Plasma, Serum, DNA||Demographic Data, Patient Questionnaires, Medical Records, Physiological / Biochemical Measurements||University of Western Australia||Poly: A biobank that generally has a larger accrual scope, resources and multiple users outside the biobank proper.||2001 - 2017|
|Fremantle Diabetes Study||Timothy Davis||08 9431 firstname.lastname@example.org||Cohort, Longitudinal, Population Based, Disease Specific||Serum/plasma and DNA/RNA from approximately 3,000 people with diabetes recruited between 1993 and 2011.||10,001 - 100,000||Plasma, Serum, DNA, RNA||Demographic Data, Patient Questionnaires, Physiological / Biochemical Measurements||University of Western Australia||Mono: A biobank that supports a specific research project, may have few staff members, a small-scale accrual scope with little to no initial intention of releasing or distributing biospecimens to secondary parties.||1993 - 2019|
|Curtin CCRE Biobank||Christopher Reid||0419 319 email@example.com||Cohort, Population Based||Biobanking samples from volunteers participating in CCRE studies: PACIFIC / STAREE.||1 - 100||Blood, Plasma, Serum||Demographic Data, Patient Questionnaires, Physiological / Biochemical Measurements||Curtin University||2019 - ongoing|
|A follow-up of the WA Kidskin Study||Professor David Mackey||08 9381 firstname.lastname@example.org||Cohort||We are assessing myopia rates in approximately 900 of 1776 original young adult participants who were part of the Western Australian Kidskin Study while they were in primary school in the 1990s. The Kidskin Study intervention resulted in a reduction in time spent outdoors and an increase in the use of sun protection while outdoors. We wish to now investigate the possible impact that this intervention has had on the development of myopia in these participants who are now young adults.||101 - 1,000||Blood, DNA||Patient Questionnaires, Imaging Data, Physiological / Biochemical Measurements||Lions Eye Institute||2015 - ongoing|
|WA Family Study of Schizophrenia||Winthrop Professor Vera A Morgan||08 6488 email@example.com||Case Control, Cohort, Population Based||The West Australian Family Study of Schizophrenia biobank is an invaluable collection of biological samples and a uniquely rich phenotype and genotype database of more than 1400 individuals, comprising schizophrenia cases, first degree relatives and unrelated controls. The data and samples have been collected over the past 20 years from participants that have been assessed using various cognitive, diagnostic, neurological, biological, and personality measurements.||1,001 - 10,000||Plasma, Serum, DNA, RNA, Immortalised Cell Lines||Demographic Data, Patient Questionnaires, Imaging Data, Genealogical Records, Physiological / Biochemical Measurements||University of Western Australia||uwa.edu.au/facilities/centre-for-clinical-research-in-neuropsychiatry||1996 - 2017|
|TARRGET Glaucoma Study||Professor David Mackey||08 9381 firstname.lastname@example.org||Population Based, Disease Specific||The TARRGET pilot study selected 100 families in SA from advanced glaucoma index cases in the Australian & New Zealand Registry of Advanced Glaucoma (ANZRAG). The data showed that >50% of screened firstdegree relatives (FDRs) had signs suspicious of glaucoma or definite glaucoma, as well as detecting new suspect and definite glaucoma. The study has now expanded nationally to educate and screen FDRs. We will audit uptake rates of families and relatives with information incorporated into ANZRAG.||101 - 1,000||Blood, DNA, Saliva||Demographic Data, Patient Questionnaires, Imaging Data, Genealogical Records, Physiological / Biochemical Measurements||Lions Eye Institute, Flinders University, University of Western Australia||2017 - ongoing|
|Ophthalmic Western Australian Biobank||Professor David Mackey||08 9381 email@example.com||Cohort, Longitudinal, Twin Study, Disease Specific||OWAB is a resource for research into eye disease incorporating clinical data and biological specimens. It facilitates core research projects into eye disease aetiology, prevention and detection, development of new therapies and genetic risk. Participants include patients with an eye condition who have attended a clinical appointment at the Lions Eye Institute as well as a control group, i.e. those with normal healthy eyes recruited from unaffected relatives and individuals attending the clinic.||1,001 - 10,000||Blood, DNA, Saliva, Urine, Tissue (Frozen)||Patient Questionnaires, Imaging Data, Genealogical Records, Physiological / Biochemical Measurements||Lions Eye Institute||2012 - ongoing|
|Glaucoma Inheritance Study in Tasmania||Professor David Mackey||08 9381 firstname.lastname@example.org||Longitudinal, Population Based, Disease Specific||Glaucoma Inheritance Study in Tasmania has created one of the largest glaucoma biobanks in the world, with over 5,000 DNA samples and clinical material from familial and sporadic cases of glaucoma stored in OWAB. This study resulted in the discovery of the myocilin gene and its association with glaucoma and has also examined the impact of providing DNA testing and results to glaucoma families and currently working on models of cascade family screening for glaucoma.||1,001 - 10,000||Blood, DNA, Primary Cells||Imaging Data, National Registries, Genealogical Records||Flinders University, University of Tasmania, University of Western Australia||1993 - ongoing|
|Twins Eye Study||Professor David Mackey||08 9381 email@example.com||Cohort, Twin Study, Population Based||Twins Eye Study in Tasmania, QLD and WA links in with other twins work in Australia, with over 1000 pairs of twins and 200 siblings extensively phenotyped for ocular biometry. DNA samples and clinical material is stored in OWAB. Analysis of their 610K SNP DNA is providing insight into genetics of factors such as central corneal thickness, intraocular pressure and optic disc cup size. Results of the Genome Wide Association Study on this cohort are now deposited in the NIH dbGaP data repository.||1,001 - 10,000||Blood, DNA||Imaging Data, Genealogical Records, Physiological / Biochemical Measurements||University of Tasmania, QIMR Berghofer MIR, Lions Eye Institute||2000 - ongoing|
|Eye Protection Study||Professor David Mackey||08 9381 firstname.lastname@example.org||Population Based||Outdoor activity involves exposure to sun, which has both beneficial and potentially harmful effects on the eye. In this study, we are evaluating the use of eye protection by those involved in sporting and outdoor activities; determining evidence of any sun damage to the eye in these groups; and assessing the early glaucomatous damage to eye. Biological data for this study is stored in the Ophthalmic Western Australian Biobank.||101 - 1,000||DNA, Microbiological||Imaging Data, Physiological / Biochemical Measurements||Lions Eye Institute, University of Western Australia||2012 - ongoing|
|Colour Vision Deficiency||Professor David Mackey||08 9381 email@example.com||Population Based, Disease Specific||The aim of this study was to compare the structure and anatomy of eyes of people who are 'colour blind' or who have a colour vision deficiency (CVD) with the eyes of people with normal colour vision. We also tested whether there are skills and tasks that people who are 'colour blind' or who have a colour vision deficiency (CVD) can perform faster or more accurately that people with normal colour vision. The DNA samples for this study are stored in the Ophthalmic Western Australian Biobank.||1 - 100||DNA, Saliva||Patient Questionnaires, Physiological / Biochemical Measurements||Lions Eye Institute, University of Western Australia||2015 - 2018|
|Western Australia Retinal Degeneration Study||Fred Chen||0466 646 firstname.lastname@example.org||Case Control, Cohort, Disease Specific||This is a natural history study of retinal degeneration. Patients provide skin and blood samples for research into the pathogenesis of retinal degeneration and development of personalised therapy.||101 - 1,000||Blood, Plasma, Serum, DNA, RNA, Immortalised Cell Lines, Primary Cells||Demographic Data, Imaging Data, Medical Records||Lions Eye Institute||2015 - ongoing|
|Western Australian Pregnancy Biobank||Professor Jeffrey Keelan||08 6458 email@example.com||Cross Sectional||Western Australian Pregnancy Biobank (WAPB) is a biorepository of samples and associated clinical data from pregnancies at high risk of preterm delivery and related complications. The WAPB is an invaluable database used to assist researchers - both local and external - to expand knowledge and understanding of the causes of preterm birth, its prediction and effective treatment therewith aiming to reduce the rates of prematurity and other pregnancy complications.||1,001 - 10,000||Blood, Plasma, Serum, RNA, Saliva, Urine, Microbiological, Tissue (Frozen), Tissue (FFPE)||Demographic Data, Patient Questionnaires, Medical Records||Women and Infants Research Foundation, University of Western Australia||thewholeninemonths.com.au/biobank||2015 - 2018|
|WA DNA Bank||Michael Epis||0413 303 firstname.lastname@example.org||Cohort, Longitudinal, Disease Specific||The Western Australian DNA Bank is a state-of-the-art national processing and long-term secure storage facility for biospecimens (including DNA, RNA, serum and plasma) that have been collected from participants of medical research projects. The WA DNA Bank itself does not recruit these participants, but processes and stores biospecimens for medical researchers who have collected a sample from consenting donors. A key aim of the WA DNA Bank is to facilitate access to human DNA collections in WA.||10,001 - 100,000||Blood, Plasma, Serum, DNA, RNA, Saliva, Urine||Demographic Data||University of Western Australia||gohad.uwa.edu.au/enabling-resources/biobanking||2004 - ongoing|
|Perkins Cancer Biobank||Louise Winteringham||08 6151 email@example.com||Disease Specific||The Perkins Cancer Biobank is a biobank of extensively characterised tumour samples with associated clinical information. Fresh tumour samples collected during surgical or diagnostic procedures undergo a set of core molecular assays prior to cryopreservation. Stored data and biospecimens will be used for ethically and scientifically approved research that is consistent with our overall goal of improving the outcomes of cancer treatment.||1 - 100||Serum, Tissue (Frozen)||Demographic Data, Imaging Data, Medical Records, Physiological / Biochemical Measurements||Harry Perkins Institute of Medical Research||Poly: A biobank that generally has a larger accrual scope, resources and multiple users outside the biobank proper.||2020 - ongoing|
|ICAD Study||Virginie Lam||08 9266 firstname.lastname@example.org||Cohort, Cross Sectional, Population Based||A cohort of 347 West Australians (20-80 years) were recruited between 2011-2012 to determine whether certain plasma biomarkers, related to dietary influences, were associated with mild cognitive impairment. We have a substantive databank of plasma biomarkers, neuropsychological performance data specific to age-related cognitive decline, and information on dietary patterns, anthropometric measurements, lifestyle (work/exercise patterns), supplement use, and medical history/current medications.||101 - 1,000||Plasma, Serum||Demographic Data, Patient Questionnaires, Medical Records, Physiological / Biochemical Measurements||Curtin University||2011 - 2013|
|National SHIP||Anna Waterreus||08 9347 email@example.com||Cross Sectional, Population Based, Disease Specific||The 2010 national psychosis prevalence survey (Survey of High Impact Psychosis-SHIP covered: psychopathology, functioning and disability, cognition, substance use, education, employment, income, accommodation, medication use, service utilisation and needs, and physical health (including fasting blood tests). About 1/4 of the survey sample of 1825 participants with psychotic disorders, including schizophrenia, also consented to providing a blood sample for DNA and plasma.||101 - 1,000||Plasma, DNA||Demographic Data, Patient Questionnaires, National Registries, Physiological / Biochemical Measurements||Neuroscience Research Australia||2010 - 2010|
|The Raine Study||Alex D'Vauz||08 6488 firstname.lastname@example.org||Cohort, Longitudinal, Population Based, Birth Cohort||The Raine Study is a longitunal cohort study that has collected biosamples for over 30 years from pregnancy to early adulthood and across multiple generations.||10,001 - 100,000||Blood, Plasma, Serum, DNA, Faeces, Urine||Demographic Data, Patient Questionnaires, Imaging Data, Medical Records, Physiological / Biochemical Measurements||University of Western Australia||rainestudy.org.au||1989 - ongoing|
|WARTBANC||Dr Jenny McCloskey||08 9224 3560||jenny.mcCloskey@health.wa.gov.au||Disease Specific||The WA Research Team Biobank of Anogenital Neoplasia and Condylomata (WARTBANC) was developed for research into HPV-associated anogenital disease. This Biobank compiles excised tissues, blood and clinical data from patients treated surgically for anogenital condylomata and assessment for AIN at RPH and longitudinal data and samples from patients previously treated/ assessed at RPHSHS and prospectively consented for use of their data and samples in unspecified future research.||10,001 - 100,000||Blood, Serum, Microbiological, Tissue (Frozen)||Demographic Data, Medical Records||Royal Perth Hospital||1995 - ongoing|
|Busselton Population Medical Research Institute||Jennie Hui||08 6383 email@example.com||Cohort, Cross Sectional, Longitudinal, Quality Control, Population Based||BPMRI's medical and population health research aims for a better understanding and management of disease and illness. The institute's research activities are diverse and encompass a wide range of health conditions and measures. Our areas of study include sleep disorders, respiratory diseases, cardiovascular diseases, diabetes, genetics and others.||> 1,000,000||Blood, Plasma, Serum, DNA, RNA, Urine, Immortalised Cell Lines, Microbiological, Sputum, Throat Swabs||Demographic Data, Patient Questionnaires, Imaging Data, Medical Records, Physiological / Biochemical Measurements||Busselton Population Medical Research Institute||bpmri.org.au||1966 - ongoing|
|Charles Day Tissue Bank||Dr Carolyn Grove||08 6383 4247||PathWest.QEIIHaemR&DTissueBanking|
|Cross Sectional, Longitudinal, Disease Specific||The Charles Day Tissue Bank comprises samples of blood, bone marrow, lymph node or other tissue from patients being investigated for haematological cancers and other blood disorders. It is situated in the Haematology Department at PathWest, Queen Elizabeth II Medical Centre, but runs as a cross-site collaboration with contribution of samples from the adult tertiary hospitals in Western Australia. It aims to support high quality research and diagnostic innovation in the field of haematology.||10,001 - 100,000||Blood, Serum, Primary Cells, Tissue (Frozen)||Demographic Data, Physiological / Biochemical Measurements||PathWest||2012 - ongoing|
|Neuromuscular and other rare diseases||Sue Fletcher||0403 079 firstname.lastname@example.org||Case Control, Cross Sectional, Disease Specific||Collection of myogenic cells, dermal fibroblasts, lymphocytes, DNA, whole blood from patients with inherited disease, plus some healthy controls.||1,001 - 10,000||Blood, DNA, Immortalised Cell Lines, Primary Cells, Tissue (Frozen)||Medical Records, Physiological / Biochemical Measurements||Murdoch University||2000 - ongoing|
|CMV & CVD||Patricia Price||0438 480 email@example.com||Case Control, Cohort, Cross Sectional, Longitudinal, Population Based||The biobank comprises plasma, DNA, PBMC and saliva from ~80 renal transplant recipients and 80 healthy controls collected in 2014. In 2017, 100 participants donated follow-up samples. Biomarkers and cardiovascular health were assessed at both time points. We also have measures of the burden and footprint of CMV.||101 - 1,000||Blood, Plasma, DNA, Saliva, Primary Cells||Demographic Data, Physiological / Biochemical Measurements||Curtin University||2014 - 2017|
|The Australian IPF Registry - blood substudy||A/Prof Yuben Moodley||08 6152 6568||Yuben.firstname.lastname@example.org||Cohort, Cross Sectional, Longitudinal, Disease Specific||Little is known about the mechanisms of lung fibrosis. Earlier studies suggest that there may be blood or genetic markers, which may contribute to the development and progression of lung fibrosis. Our biobank stores blood samples (e.g. plasma and serum) from IPF patients at 0, 3, 6 and 12 months after enrolment to investigate the changes in these markers over time, and their relationship to lung fibrosis. We hope that this will improve the understanding of the underlying cause of lung fibrosis.||10,000 - 100,000||Plasma, Serum, RNA, DNA, Primary Cells||Demographic Data, Patient Questionnaires, National Registries, Physiological / Biochemical Measurements||Institute for Respiratory Health||2014-ongoing|
|Type 1 and 2 Diabetes Plasma and Serum Repository||Joanne O'Dea||08 6456 4606||Joanne.O'Dea@health.wa.gov.au||Longitudinal, Disease Specific||The primary aim is to establish and maintain a plasma and serum repository to enable proteomic research. The secondary aims include identification of risk factors implicated in the complications of diabetes and to ID new risk factors associated with developing complications.||1,001 - 10,000||Plasma, Serum||Demographic Data||Perth Children's Hospital||2006-ongoing|
|Type 1 and 2 Diabetes DNA Bank||Joanne O'Dea||08 6456 4606||Joanne.O'Dea@health.wa.gov.au||Longitudinal, Disease Specific||This project involves the acquisition of DNA samples from patients newly diagnosed with Type 1 and Type 2 diabetes in Western Australia. These samples form a biobank to serve research into diabetes pathogenesis, its complications and related autoimmune conditions.||1,001-10,000||DNA||Demographic Data||Perth Children's Hospital||2000-ongoing|