Hi-Plex: simple, low-cost, modular targeted DNA sequencing technology
Hi-Plex was developed by our Molecular Biologist, Assoc Prof Daniel Park and Computer Scientist, Dr Bernard Pope, co-leads of our Human Genomics Group at Melbourne Bioinformatics, to simplify processes and reduce costs on projects needing targeted sequencing of panels of genes across large numbers of specimens. It brings greater efficiency and accuracy to all such research projects – big and small.
Hi-Plex is suitable for an extensive range of clinical and research applications and is complemented by software for primer design and variant calling. It enables a PCR-based target-enrichment system, unrivalled in terms of simplicity, accuracy and cost.
Although per-base sequencing costs have decreased during recent years, library preparation for targeted massively parallel sequencing remains constrained by high reagent costs, limited design flexibility and protocol complexity. Hi-Plex addresses these limitations.
Hi-Plex is invaluable when looking into candidate cancer predisposition in large breast and colon cancer datasets involving thousands of samples.
It’s currently being applied in a nationwide study of approximately 10,000 women affected with breast/ovarian cancer who have tested negative for mutations in BRCA1 and BRCA2, known as the Brca Refined Analysis of Sequence Tests: Risk And Penetrance (BRA-STRAP). For this our team is using Hi-Plex to study a panel of breast cancer genes and candidate genes to determine prevalence and penetrance of mutations in the Australian population. This will facilitate translation of the panel testing approach into Familial Cancer Centres. The data can then be pooled with international data to build a more comprehensive, shared database to inform new genetic testing models for clinical practice worldwide.
University of Melbourne collaborator Prof Melissa Southey employs Hi-Plex in studies of prostate cancer susceptibility, with a current study involving in the order of 7,000 DNAs provided by participants of population based studies and it is also being used as part of a long term collaboration between Prof Southey and colleagues at the University of Pennsylvania.
Collaborator Assoc Prof Daniel Buchanan’s Oncogenomics laboratory at the University of Melbourne uses Hi-Plex to find associations between mutations in certain genes and predisposition for serrated polyposis, a type of colorectal cancer. Daniel will present this work in the Presidential Plenary Abstract Session at the forthcoming 2017 Collaborative Group of the Americas on Inherited Colorectal Cancer Annual Meeting in Orlando, Florida, USA.
In April 2016, HiPlex featured in a presentation by Sean Wen, part of the Breast Cancer Research team from Cancer Research, Malaysia, at the Global Breast Cancer Conference, one of the biggest conferences of its kind in Asia. Link to Sean’s slides here: Hi-Plex for High-Throughput Mutation Screening of BRCA1, BRCA2, TP53, and PALB2 in Breast and Ovarian Cancer Patients.
How it works:
Hi-Plex detects genetic variants and reports them in formats that work with complementary annotation tools. In this way, variants can be broadly categorised according to their likely clinical significance. This is a typical Hi-Plex workflow:
While developed for large-scale cancer projects, Hi-Plex is now being demonstrated in diverse settings, such as the population genetics of non-model organism snails and crayfish.
Contact the Hi-Plex team for information and collaboration enquiries from tech transfer, reagent design, methods, data analysis, including bespoke analysis pipelines.
Related Journal References:
Park, D. J., Li, R., Lau, E., Georgeson, P., Nguyen-Dumont, T. & Pope, B. J. UNDR ROVER – a fast and accurate variant caller for targeted DNA sequencing. BMC Bioinformatics 17, 165 (2016).
Nguyen-Dumont, T., Hammet, F., Mahmoodi, M., Pope, B. J., Giles, G. G., Hopper, J. L., Southey, M. C. & Park, D. J. Abridged adapter primers increase the target scope of Hi-Plex. Biotechniques 58, 33–36 (2015).
Nguyen-Dumont, T., Mahmoodi, M., Hammet, F., Tran, T., Tsimiklis, H., Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Giles, G. G., Hopper, J. L., Australian Breast Cancer Family Registry, Southey, M. C. & Park, D. J. Hi-Plex targeted sequencing is effective using DNA derived from archival dried blood spots. Anal. Biochem. 470, 48–51 (2015).
Pope, B. J., Nguyen-Dumont, T., Hammet, F. & Park, D. J. ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets. Source Code Biol. Med. 9, 3 (2014).
Nguyen-Dumont, T., Pope, B. J., Hammet, F., Mahmoodi, M., Tsimiklis, H., Southey, M. C. & Park, D. J. Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing. Anal. Biochem. 442, 127–129 (2013).
Nguyen-Dumont, T., Teo, Z. L., Pope, B. J., Hammet, F., Mahmoodi, M., Tsimiklis, H., Sabbaghian, N., Tischkowitz, M., Foulkes, W. D., Kathleen Cuningham Foundation Consortium for research into Familial Breast cancer (kConFab), Giles, G. G., Hopper, J. L., Australian Breast Cancer Family Registry, Southey, M. C. & Park, D. J. Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2. BMC Med. Genomics 6, 48 (2013).