DNA and RNA Methodologies Group

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.

Selected Publications

Mueller, S.A., Gauthier, M.E.A., Blackburn, J., Grady, J.P., Kraitsek, S., Hajdu, E., Dettmer, M.S., Dahlstrom, J.E., Lee, C.S., Luk, P.P., Yu, B., Giger, R., Kummerfeld, S., Clark, J.R., Gupta, R.*, Cowley, M.J.* 2020. Molecular patterns in salivary duct carcinoma identify prognostic subgroups. Mod. Pathol. 33:1896-1909

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)

More Garvan Publications

Staff in the Group

Andrew Berg

Research Assistant

Danson Wooi

PhD Student

Qianyu YE

Research Assistant