The focus of the DNA and RNA Methodologies Group is the development and application of innovative methods and novel approaches to overcome current scientific limitations. Early work created two diagnostics for cancer-associated fusion genes using hybridisation capture sequencing (the RNA-based FuSeq tests), with the same technology applied to conventional DNA ChIP-seq for enhanced epigenetic studies (the ChIP-CapSeq protocol).
We initially focused on 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. Given our technical expertise, the group’s research portfolio has expanded to include hybridisation capture sequencing for the Molecular Screening and Therapeutics (MoST) program of Prof David Thomas, with the objective of translating genomic screening into health outcomes for Australian cancer patients with advanced disease and an unmet clinical need.
In line with our current projects, we are also currently developing new methodologies to improve sequencing library preparation methods for DNAs and RNAs sourced from formalin-fixed tissues.
Heyer, E.E., Blackburn, J. 2020. Sequencing strategies for fusion gene detection. BioEssays 42:e2000016
Singh, M., Jackson, K.J.L., Wang, J.J., Schofield, P., Field, M.A., Koppstein, D., Peters, T.J., Burnett, D.L., Rizzetto, S., Nevoltris, D., Masle-Farquhar, E., Faulks, M.L., Russell, A., Gokal, D., Hanioka, A., Horikawa, K., Colella, A.D., Chataway, T.K., Blackburn, J., Mercer, T.R., Langley, D.B., Goodall, D.M., Jefferis, R., Gangadharan Komala, M., Kelleher, A.D., Suan, D., Rischmueller, M., Christ, D., Brink, R., Luciani, F., Gordon, T.P., Goodnow, C.C.*, Reed, J.H.* 2020. Lymphoma driver mutations in the pathogenic evolution of an iconic human autoantibody. Cell 180:878-894
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. 10:3120
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. 3:1-11
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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Staff in the Group