Human Studies Research Portal

LIMS application
HSU has purchased OpenSpecimen to underpin our sample tracking capability. The platform has been customised to suit HSU pipelines and is up and running with the Cell-O study the first to benefit from this new application.

Biomek i7
Ms Cynthia Burnett generously donated funding to HSU to purchase an automated workstation to facilitate new workflows in HSU. Specifically workflows for cell exposure experiments and genotyping. The robot has been installed and we have named it Cosmo in honour of Ms Burnett’s dog.

HSU has achieved international biobanking certification from the Canadian Tissue Repository Network (CTRNet). CTRNet certification is an internationally recognised certification available to biobanks who successfully demonstrate operations that align with biobanking best practices. All HSU staff successfully completed biobanking best practice education modules and essential biobank processes/documents have been aligned towards international best practice standards

IMB Family day, coinciding with UQ Open day, was held on the 6th of August 2023. The HSU team facilitated multiple lab tours and activities at the junior scientist's hub for kids.

n= 87 samples from the YODA study underwent methylation analysis via the Illumina MWAS platform. This data will provide valuable insights into youth mental health.

n= 479 samples from the PISA study underwent methylation analysis via the Illumina MWAS platform.

HSU has commenced collection and screening of MND participants from multiple sites nationally with a view for inclusion into a clinical trial determined via their genetic makeup.

The Human Studues Unit is excited to announce as of 1st January 2023 HSU is a facility within the division Population and Disease Genomics. We look forward to assisting IMB and wider UQ community with all your research genomics needs.

An exciting forum that HSU were able to attend to learn all about the research of others within the division

700 plasma samples from participants of the MND project have had lipidomics analysis performed at WEHI. This valuable information will provide insights to metabolism and progression of the disease

n= 6 participants with matched PAXgene RNA and EDTA-sourced RNA samples have been extracted, sequenced, and compared in an attempt to investigate the potential of a more economical method of RNA isolation in this pilot study.

Dr Fleur Garton and the HSU lab team have been busy performing CaptureSeq experiment on 200 samples of circulting cell free DNA to tease out novel biomarker to assist with MND diagnosis.

Centre for Population and Disease Genomics group leader Dr Sonia Shah has been awarded a prestigious MRFF grant to investigate cardiovascular risk factors and genes in South Asian Communities.

HSU staff extracted RNA from 250 PAXgene RNA collection tubes. All samples were progressed to sequencing. These samples were from a study led by Prof Marc Ruitenberg assessing effectiveness of immediate administration of bulk IgG for patients who have suffered spinal chord injury.

SALSA- SGC Data Explorer launches. Exciting new tool for researchers to query the MND sample cohort stored and managed by HSU. Researchers can apply for access to samples through the website. All queries are vetted by the custodian. https://hsu.imb.uq.edu.au/content/lauch-new-salsa-sgc-website

HSU has received 1239 samples from participants for womens health study led by Prof Gita Mishra.

HSU has designed a logo to represent our lab and service.

144 plasma samples collected from MND particpants have been selected based on phenotype and shared with researchers in Melbourne who will investgate a novel biomarker

Today marks the debut of Illumina GSAv3+UQvn1 custom content designed by PCTG and their collaborators. An additional 30,000 snps have been curated boosting research capabilites in the fields of cardiac helath, womens health, neurodegenerative, inflammation and infection genomics.

Opportunistic collection of stabilised RNA for our MND participant collections. Small cost compared to conventional method and smaller storage space.

COVID OZ_Genetics research study is actively recruiting participants. Looking to understand differences in symptom severity and duration. More information on participating click here: https://hsu.imb.uq.edu.au/covid-ozgenetics/

HSU staff attended a Genetics & Genomics symposium themed around personalised medicine with talks ranging from individualised medical approaches based on genetic risk score calculations to the use of nanotechnology for single molecule resolution diagnostics. Genomics has an exciting and important role to play in a persons future health management.

HSU recently completed their first commercial contract, genotyping 284 samples using the Illumina Global Screening Array-24 v3.0 BeadChips. We are happy to report that 99% of samples passed genotyping QC.

Collaborations with Dr. Margie Wright at the Queensland Brain Institute has resulted in samples from adolescent twins having NextGen sequencing data generated. This study collects brain imaging and cognitive data, from twins 11- 12 years old and combines with genetic information collected from biological samples.

HSU is constantly reviewing and improving our in-house laboratory management systems. HSU IT team has implemented a new tier of data storage allowing the use of unique fraction IDs on every tube stored from a sample collection to improve sample trackability and management. We thank the research coordinators at the collection sites for transitioning seamlessly to this new data storage structure.

Supporting the Austism CRC the HSU laboratory completed screening of 800 individuals through three metabolomics assays (Neurotransmitters, Acylcarnitine’s, and Bile Acids,) as part of a broader systems genomics research programme. Lipidomics analysis was also completed on the same sample set as part of a collaboration with the Baker Institute in Melbourne.

PRISM 2 app has been launched on both Apple and Google play stores. Developed in conjunction with MNDandME this app supports individuals with MND to manage their disease journey.
More info: https://www.mndandme.com.au/mnd-me-app/

HSU has recently completed a project to extract DNA and perform genome wide methylation screening using the Illumina MethylationEPIC assay on 366 samples from the Staged Treatment in Early Psychosis (STEP) project. All samples passed our in-house QC checks and are now undergoing further analysis.

HSU have recently completed the Illumina MethylationEPIC array on 826 samples for a project investigating epigenetic changes in patients with Alzheimer's Disease. We are happy to report that all samples passed our standard QC.

We are proud to announce that thanks to our recent iScan Windows 10 computer upgrade, we have reduced our Illumina BeadChip scan time by approximately half! We would like to thank the Institute for Molecular Biosciences for their financial contribution.

We are excited to launch our latest research project on Endometriosis.
"Endometriosis: Pathogenesis And Treatment Response"
A Collaboration between The Royal Brisbane and Women’s Hospital and the Institute for Molecular Biosciences.
http://www.uq.edu.au/research/impact/stories/aiming-to-end-endo/

The lab team are about halfway through completing the Illumina MethylationEPIC arrays for a project investigating epigenetic changes in patients with Alzheimer’s Disease. This project is a continuation of another project we worked on 2 years ago looking at baseline samples for this cohort of people (BrainMend). This latest batch of DNA samples are from the second and third timepoint that these patients were assessed. The epigenetic data from both projects will be analysed together and compared to investigate any changes to the methylation status of DNA over time and how this may influence the disease or vice versa. So far, 4 plates of samples (~380) have been completed with the fifth plate currently in progress.

Over the last several weeks the HSU team have been busy extracting the DNA from 345 participant samples for the STEP (Staged Treatment in Early Psychosis) project, obtaining good-quality DNA which after further laboratory QC will be taken forward onto the Illumina MethylationEPIC arrays in early September 2020.

In June, 189 MND samples collected from participants across Australia and New Zealand were genotyped using the new Illumina Global Screening Array-24 v3.0 BeadChips, producing excellent call rates with an average >99%.

The Human Studies Unit is now back to full operations and we are now able to receipt all your research samples.

Australia Post is doing a great job of reducing their transit times so we are quite confident we will receive your samples within our optimal processing window.

Any questions please contact us on:
samples@imb.uq.edu.au

The HSU laboratory genotyped 110 Motor Neurone Disease DNA samples as part of a pilot study using Illumina’s new Infinium Global Diversity Array-8 v1.0 BeadChips targeting over 1.8 million variants! This run produced exceptional results with the average call rate over 99.7%.

We are back in the lab and the HSU team is getting ready to start receiving your research samples again.

As of now we can receipt your saliva collection kits for extraction or extracted DNA samples for genomics.

From 1st June 2020 we will be able to extend our receipt and processing to whole blood samples, stool and urine.

Any questions please contact us on:
samples@imq.uq.edu.au

HSU has completed a project to extract DNA and generate genomic data from 152 saliva samples collected by Dr Dominic Tran, University of Sydney. Dr Tran is studying the effects of transcranial magnetic stimulation (TMS) on movement. HSU received the saliva samples that were collected using the Oragene Saliva collection kits. DNA was extracted from the 2ml saliva samples, DNA concentration measured and finally samples were normalised to ~100ng/ul. All 152 DNA samples were run on Illumina Global Screening Array generating data for ~650,000 snps across the genome for each individual. The average call rate for the samples was 99%.

In February 2020, our laboratory genotyped 332 DNA samples using the Illumina PsychArray-24 BeadChips as part of a project researching the Biomarkers of Anxiety Disorders and Prediction of Treatment Response. The samples included in this project resulted in an average call rate of >0.98.

Over the last month, 190 samples were run on the Illumina MethylationEPIC array. Samples were incorporated from a variety of projects including Motor Neurone Disease, Parkinson’s Disease, and the Queensland Twin and Adolescent Brain study. Our lab is happy to report the majority of samples (including all MND samples) passed our standard QC.

Recently the HSU laboratory genotyped a number of samples from the Early Psychosis, Endometriosis, Endometrial Cell Lines, and Outcomes of Mental Health projects using the Illumina Global Screening Array-24 BeadChips, with the majority of samples producing pass rates of over 98%.

Starting August 2nd, 475 DNA samples have been genotyped on Illumina® OmniExpress-24 BeadChips as part of the endometriosis disease stratification and risk prediction project. DNA samples originated from the Reproductive Sciences Laboratory at the San Raffaele Scientific Institute in Milan, Italy, and The Royal Women’s Hospital in Melbourne, Australia. This project introduced a new Illumina beadchip into our lab and we are happy to report pass rates of >98% for all samples.

We have completed the whole genome methylation screening of our Autism CRC cohort. We processed 475 samples using the Illumina Epic arrays in record time. We started 13 May 2019 and were all done by 28 June 2019 – 6 weeks running time allowing for time away on our HSU retreat.

Last week the HSU team attended an overnight retreat on North Stradbroke Island. We each presented a short talk about our area of expertise, and we completed workshops on human ethics, project planning and data management. We also enjoyed watching the humpback whales on their annual migration past the island.

Over the last 3 years, between 23/3/2016 and 31/5/2019 we have processed a total of 4286 blood, 759 stool, 660 hair, 1010 urine and 345 saliva samples across 12 projects. Our busiest month was April 2018 when we receipted and processed 211 blood, 56 stool, 90 hair and 29 saliva samples.

The 2015 – 2019 SALSA project funded by the MND Australia Ice Bucket Challenge Grant came to an end today. During the project we deposited blood samples from 651 MND cases, 230 controls, a total of 1967 sample collections and storage of > 22,000 sample aliquots. The work of the SALSA project will be continued by the NHMRC Partnership Grant.

During the first quarter of 2019 we receipted and processed 214 blood, 81 stool, 44 urine and 44 saliva samples across seven research projects.

We have just completed a GWAS (Genome-Wide Association Study) for Endometriosis, using samples from 3 Endometriosis projects. In total we processed 553 samples with an Average Call Rate of 0.99 (range 0.975-0.999).

We have just completed a GWAS for Autism. We processed a total of 2490 samples.

A total of 231 new SALSA participants were recruited into this project in 2018. 93 from Victoria, 61 from Queensland, 39 from Western Australia, 20 from South Australia and 18 from New South Wales.

Our MND Cognition project was launched. This project is conducted by Prof. Gail Robinson and Amelia Ceslis through the RBWH MND Research Clinic under the direction of Dr. Robert Henderson.