DNA and RNA Methodologies

The focus of the DNA and RNA Methodologies Group is the development of innovative methods and novel approaches to overcome current scientific limitations. For example, we applied targeted capture sequencing as a diagnostic for fusion genes in cancer (the RNA-based FuSeq tests) and to conventional DNA ChIP-seq for enhanced epigenetic studies (ChIP-CapSeq).

Established in 2019, this fledgling group was launched on the premise of realising the clinical potential of the FuSeq tests to accurately diagnose fusion genes in cancer patients, surpassing conventional testing methods such as FISH and qRT-PCR. With collaborations in place with key pathologists across Sydney, the current aim of the group is to complete the development of the FuSeq tests into accredited molecular assays, with transition to clinical practice within 3 years.

Other new methodologies under development by the group include improving sequencing library preparation methods for RNAs sourced from formalin-fixed tissues.

Selected Publications

Singh, M.*, Al-Eryani, G.*, Carswell, S., Ferguson, J.M., Blackburn, J., Barton, K., Roden, D., Luciani, F., Phan, T., Junankar, S., Jackson, K., Goodnow, C.C.†, Smith, M.A.†, Swarbrick, A.† 2019. High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes. Nat. Commun. (Accepted)

Trahair, T.N., Gifford, A.J., Fordham, A., Mayoh, C., Fadia, M., Lukeis, R., Wood, A.C., Valvi, S., Walker, R.D., Blackburn, J., Heyer, E.E., Mercer, T.R., Barbaric, D., Marshall, G.M., MacKenzie, K. 2019. Crizotinib and surgery for long term disease control in children and adolescents with ALK-positive inflammatory myofibroblastic tumors. JCO Precis. Oncol. (In Press)

Blackburn, J., Vecchiarelli, S., Heyer, E.E., Patrick, S.M., Lyons, R.J., Jaratlerdsiri, W., van Zyl, S., Bornman, M.S.R., Mercer, T.R., Hayes, V.M. 2019. TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa. Prostate 79:1191-1196

Heyer, E.E., Deveson, I.W., Wooi, D., Selinger, C.I., Lyons, R.J., Hayes, V.M., O’Toole, S.A., Ballinger, M.L., Gill, D., Thomas, D.M., Mercer, T.R.*, Blackburn, J.* 2019. Diagnosis of fusion genes using targeted RNA sequencing. Nat. Commun. 10:1388

Hardwick, S.A.*, Bassett, S.D.*  , Kaczorowski, D.C., Blackburn, J., Barton, K.M., Bartonicek, N., Carswell, S.L., Tilgner, H.U., Loy, C., Halliday, G., Mercer, T.R., Smith, M.A.†, Mattick, J.S.† 2019. Targeted, high-resolution RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions. Front. Genet. 10:309

Fleuren, E.D.G., Vlenterie, M., van der Graaf, W.T.A., Hillebrandt-Roeffen, M.H.S., Blackburn, J., Ma, X., Chan, H., Magias, M.C., van Erp, A., van Houdt, L., Cebeci, S.A.S., van de Ven, A., Flucke, U.E., Heyer, E.E., Thomas, D.M., Lord, C.J., Marini, K.D., Vaghjiani, V., Mercer, T.R., Cain, J.E., Wu, J., Versleijen-Jonkers, Y.M.H., Daly, R.J. 2017. Phosphoproteomic profiling across sarcoma subtypes reveals ALK and MET as novel actionable targets in synovial sarcomas. Cancer Res. 77:4279-4292

Blackburn, J., Deveson, I.W., Mercer, T.R. 2016. ChIP Capture Sequencing (ChIP-CapSeq): A protocol for targeted sequencing of immunoprecipitated DNA. Roche Sequencing Technical Note (https://www.n-genetics.com/products/1295/1024/13927.pdf)


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