DNA and RNA Methodologies

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 research-validated diagnostics for cancer-associated fusion genes using hybridisation capture sequencing (targeted RNAseq), with the same technology applied to conventional chromatin sequencing to enhance epigenetic studies (ChIP-CapSeq).

As fusion genes drive 20% of all cancer incidence, we initially focused on realising the clinical potential of our fusion gene tests to accurately diagnose fusions in cancer patients, surpassing conventional testing methods such as FISH and qRT-PCR. Given our technical expertise, the group’s research portfolio expanded to include sequencing for the Molecular Screening and Therapeutics (MoST) program of Omico Australia, with the objective of translating genomic screening into health outcomes for Australian cancer patients with advanced or metastatic disease and an unmet clinical need.

In line with our current projects, we are additionally developing new methodologies to improve next-generation sequencing library preparation for formalin-fixed and degraded tissues. These enhancements also have the potential to be deployed in a clinical context to improve patient sample sequencing eligibility and success.

Selected Publications

Bartonicek, N., Rouet, R., Warren, J., Loetsch, C., Rodriguez, G.S., Walters, S., Lin, F., Zahra, D., Blackburn, J., Hammond, J.M., Reis, A.L.M., Deveson, I.W., Zammit, N., Zeraati, M., Grey, S., Christ, D., Mattick, J.S., Chtanova, T., Brink, R., Dinger, M., Weatheritt, R.J., Sprent, J., King, C. 2022. The retroelement Lx9 puts a brake on the immune response to virus infection. Nature 608:757-765

Bournazos, A.M., ... ... ... Australasian Consortium for RNA Diagnostics. 2022. Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genet. Med. 24:130-145

Gong, B., ... <SEQC2 Oncopanel Sequencing Working Group> ... Xu, J. 2021. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biol. 22:109

Deveson, I.W., ... <SEQC2 Oncopanel Sequencing Working Group> ... Shi, L. 2021. Evaluating the analytical validity of circulating tumor DNA sequencing for precision oncology. Nat. Biotechnol. [In Press; DOI: 10.1038/s41587-021-00857-z]

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)

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