Dr James   Blackburn
Conjoint Senior Lecturer

Dr James Blackburn

2004 – PhD Human Molecular Genetics, University of London (Imperial College) - UK 
2000 – BSc (Hons) Genetics, University of Manchester - UK

medicine-health
St Vincent's Clinical School

Dr Blackburn leads the DNA and RNA Methodologies team at the Garvan Institute of Medical Research. With a diverse background in a variety of molecular techniques and research disciplines, he is an expert in the clinical implementation of next-generation sequencing and targeted sequencing technologies. The focus of Dr Blackburn’s research group is the development and application of innovative methods and novel approaches to overcome current scientific limitations. This includes the creation of two novel tests for the detection of fusion genes in cancer, and undertaking the Garvan-based sequencing for the Molecular Screening and Therapeutics (MoST) program of Omico Australia – the objective of which is to translate genomic screening into health outcomes for cancer patients with advanced or metastatic disease and an unmet clinical need.

Keywords: cancer genomics; cancer transcriptomics; haematological malignancies; solid tumours

Phone
+61 2 9355 5722
Location
The Kinghorn Cancer Centre 370 Victoria Street Darlinghurst NSW 2010

Publications

  • Book Chapters | 2017
    Dr James Blackburn
    Kawasaki M; Kawasaki K; Blackburn J; Ohazama A, 2017, 'Molecular Mechanisms Regulating Tooth Number', in Interface Oral Health Science 2016, Springer Singapore, pp. 147 - 162, http://dx.doi.org/10.1007/978-981-10-1560-1_13
  • Journal articles | 2021
    Dr James Blackburn
    Gong B; Li D; Kusko R; Novoradovskaya N; Zhang Y; Wang S; Pabón-Peña C; Zhang Z; Lai K; Cai W; LoCoco JS; Lader E; Richmond TA; Mittal VK; Liu LC; Johann DJ; Willey JC; Bushel PR; Yu Y; Xu C; Chen G; Burgess D; Cawley S; Giorda K; Haseley N; Qiu F; Wilkins K; Arib H; Attwooll C; Babson K; Bao L; Bao W; Lucas AB; Best H; Bhandari A; Bisgin H; Blackburn J; Blomquist TM; Boardman L; Burgher B; Butler DJ; Chang CJ; Chaubey A; Chen T; Chierici M; Chin CR; Close D; Conroy J; Coleman JC; Craig DJ; Crawford E; del Pozo A; Deveson IW; Duncan D; Eterovic AK; Fan X; Foox J; Furlanello C; Ghosal A; Glenn S; Guan M; Haag C; Hang X; Happe S; Hennigan B; Hipp J; Hong H; Horvath K; Hu J; Hung LY; Jarosz M; Kerkhof J; Kipp B; Kreil DP; Łabaj P; Lapunzina P; Li P; Li QZ; Li W; Li Z; Liang Y; Liu S; Liu Z; Ma C; Marella N; Martín-Arenas R; Megherbi DB; Meng Q; Mieczkowski PA; Morrison T; Muzny D; Ning B; Parsons BL; Paweletz CP; Pirooznia M; Qu W; Raymond A; Rindler P; Ringler R; Sadikovic B, 2021, 'Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions', Genome Biology, vol. 22, pp. 109, http://dx.doi.org/10.1186/s13059-021-02315-0
    Journal articles | 2021
    Dr James Blackburn
    Deveson IW; Gong B; Lai K; LoCoco JS; Richmond TA; Schageman J; Zhang Z; Novoradovskaya N; Willey JC; Jones W; Kusko R; Chen G; Madala BS; Blackburn J; Stevanovski I; Bhandari A; Close D; Conroy J; Hubank M; Marella N; Mieczkowski PA; Qiu F; Sebra R; Stetson D; Sun L; Szankasi P; Tan H; Tang LY; Arib H; Best H; Burgher B; Bushel PR; Casey F; Cawley S; Chang CJ; Choi J; Dinis J; Duncan D; Eterovic AK; Feng L; Ghosal A; Giorda K; Glenn S; Happe S; Haseley N; Horvath K; Hung LY; Jarosz M; Kushwaha G; Li D; Li QZ; Li Z; Liu LC; Liu Z; Ma C; Mason CE; Megherbi DB; Morrison T; Pabón-Peña C; Pirooznia M; Proszek PZ; Raymond A; Rindler P; Ringler R; Scherer A; Shaknovich R; Shi T; Smith M; Song P; Strahl M; Thodima VJ; Tom N; Verma S; Wang J; Wu L; Xiao W; Xu C; Yang M; Zhang G; Zhang S; Zhang Y; Shi L; Tong W; Johann DJ; Mercer TR; Xu J, 2021, 'Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology', Nature Biotechnology, http://dx.doi.org/10.1038/s41587-021-00857-z
    Journal articles | 2021
    Dr James Blackburn
    Whiteley SL; Holleley CE; Wagner S; Blackburn J; Deveson IW; Marshall Graves JA; Georges A, 2021, 'Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination', PLoS Genetics, vol. 17, pp. e1009465, http://dx.doi.org/10.1371/journal.pgen.1009465
    Journal articles | 2020
    Dr James Blackburn
    Heyer EE; Deveson IW; Wooi D; Selinger CI; Lyons RJ; Hayes VM; O’Toole SA; Ballinger ML; Gill D; Thomas DM; Mercer TR; Blackburn J, 2020, 'Author Correction: Diagnosis of fusion genes using targeted RNA sequencing (Nature Communications, (2019), 10, 1, (1388), 10.1038/s41467-019-09374-9)', Nature Communications, vol. 11, http://dx.doi.org/10.1038/s41467-020-15697-9
    Journal articles | 2020
    Dr James Blackburn
    Heyer EE; Blackburn J, 2020, 'Sequencing Strategies for Fusion Gene Detection', BioEssays, vol. 42, pp. e2000016, http://dx.doi.org/10.1002/bies.202000016
    Journal articles | 2020
    Dr James Blackburn
    Reis ALM; Deveson IW; Wong T; Madala BS; Barker C; Blackburn J; Marcellin E; Mercer TR, 2020, 'A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features', Nature Communications, vol. 11, http://dx.doi.org/10.1038/s41467-020-17445-5
    Journal articles | 2020
    Dr James Blackburn
    Singh M; Jackson KJL; Wang JJ; Schofield P; Field MA; Koppstein D; Peters TJ; Burnett DL; Rizzetto S; Nevoltris D; Masle-Farquhar E; Faulks ML; Russell A; Gokal D; Hanioka A; Horikawa K; Colella AD; Chataway TK; Blackburn J; Mercer TR; Langley DB; Goodall DM; Jefferis R; Gangadharan Komala M; Kelleher AD; Suan D; Rischmueller M; Christ D; Brink R; Luciani F; Gordon TP; Goodnow CC; Reed JH, 2020, 'Lymphoma Driver Mutations in the Pathogenic Evolution of an Iconic Human Autoantibody', Cell, vol. 180, pp. 878 - 894.e19, http://dx.doi.org/10.1016/j.cell.2020.01.029
    Journal articles | 2020
    Dr James Blackburn
    Mueller SA; Gauthier MEA; Blackburn J; Grady JP; Kraitsek S; Hajdu E; Dettmer MS; Dahlstrom JE; Lee CS; Luk PP; Yu B; Giger R; Kummerfeld S; Clark JR; Gupta R; Cowley MJ, 2020, 'Molecular patterns in salivary duct carcinoma identify prognostic subgroups', Modern Pathology, vol. 33, pp. 1896 - 1909, http://dx.doi.org/10.1038/s41379-020-0576-2
    Journal articles | 2020
    Dr James Blackburn
    Yamada A; Kawasaki M; Miake Y; Yamada Y; Blackburn J; Kawasaki K; Trakanant S; Nagai T; Nihara J; Kudo T; Meguro F; Schmidt-Ullrich R; Liu B; Hu Y; Page A; Ramírez Á; Sharpe PT; Maeda T; Takagi R; Ohazama A, 2020, 'Overactivation of the NF-κB pathway impairs molar enamel formation', Oral Diseases, vol. 26, pp. 1513 - 1522, http://dx.doi.org/10.1111/odi.13384
    Journal articles | 2019
    Dr James Blackburn
    Nagai T; Trakanant S; Kawasaki M; Kawasaki K; Yamada Y; Watanabe M; Blackburn J; Otsuka-Tanaka Y; Hishinuma M; Kitatmura A; Meguro F; Yamada A; Kodama Y; Maeda T; Zhou Q; Saijo Y; Yasue A; Sharpe PT; Hindges R; Takagi R; Ohazama A, 2019, 'MicroRNAs control eyelid development through regulating Wnt signaling', Developmental Dynamics, vol. 248, pp. 201 - 210, http://dx.doi.org/10.1002/dvdy.10
    Journal articles | 2019
    Dr James Blackburn
    Blackburn J; Wong T; Madala BS; Barker C; Hardwick SA; Reis ALM; Deveson IW; Mercer TR, 2019, 'Use of synthetic DNA spike-in controls (sequins) for human genome sequencing', Nature Protocols, vol. 14, pp. 2119 - 2151, http://dx.doi.org/10.1038/s41596-019-0175-1
    Journal articles | 2019
    Dr James Blackburn
    Blackburn J; Vecchiarelli S; Heyer EE; Patrick SM; Lyons RJ; Jaratlerdsiri W; van Zyl S; Bornman MSR; Mercer TR; Hayes VM, 2019, 'TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa', Prostate, vol. 79, pp. 1191 - 1196, http://dx.doi.org/10.1002/pros.23823
    Journal articles | 2019
    Dr James Blackburn
    Hardwick SA; Bassett SD; Kaczorowski D; Blackburn J; Barton K; Bartonicek N; Carswell SL; Tilgner HU; Loy C; Halliday G; Mercer TR; Smith MA; Mattick JS, 2019, 'Targeted, high-resolution RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions', Frontiers in Genetics, vol. 10, http://dx.doi.org/10.3389/fgene.2019.00309
    Journal articles | 2019
    Dr James Blackburn
    Heyer EE; Deveson IW; Wooi D; Selinger CI; Lyons RJ; Hayes VM; O’Toole SA; Ballinger ML; Gill D; Thomas DM; Mercer TR; Blackburn J, 2019, 'Diagnosis of fusion genes using targeted RNA sequencing', Nature Communications, vol. 10, http://dx.doi.org/10.1038/s41467-019-09374-9
    Journal articles | 2019
    Dr James Blackburn
    Deveson IW; Madala BS; Blackburn J; Barker C; Wong T; Barton KM; Smith MA; Watkins DN; Mercer TR, 2019, 'Chiral DNA sequences as commutable controls for clinical genomics', Nature Communications, vol. 10, pp. 1342, http://dx.doi.org/10.1038/s41467-019-09272-0
    Journal articles | 2019
    Dr James Blackburn
    Trahair T; Gifford AJ; Fordham A; Mayoh C; Fadia M; Lukeis R; Wood AC; Valvi S; Walker RD; Blackburn J; Heyer EE; Mercer TR; Barbaric D; Marshall GM; MacKenzie KL, 2019, 'Crizotinib and surgery for long-term disease control in children and adolescents with ALK-positive inflammatory myofibroblastic tumors', JCO Precision Oncology, vol. 3, pp. 1 - 11, http://dx.doi.org/10.1200/PO.18.00297
    Journal articles | 2019
    Dr James Blackburn
    Singh M; Al-Eryani G; Carswell S; Ferguson JM; Blackburn J; Barton K; Roden D; Luciani F; Giang Phan T; Junankar S; Jackson K; Goodnow CC; Smith MA; Swarbrick A, 2019, 'High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes', Nature Communications, vol. 10, pp. 3120, http://dx.doi.org/10.1038/s41467-019-11049-4
    Journal articles | 2019
    Dr James Blackburn
    Mueller SA; Grady J; Dettmer M; Gauthier M-EA; Hajdu E; Blackburn J; Giger R; Dahlstrom JE; Luk P; Lee S; Kratisek S; Yu B; Clark JR; Cowley MJ; Gupta R, 2019, 'The targetable genomic landscape of salivary duct carcinoma', Pathology, vol. 51, pp. S83 - S83, http://dx.doi.org/10.1016/j.pathol.2018.12.210
    Journal articles | 2018
    Dr James Blackburn
    Kawasaki M; Kawasaki K; Meguro F; Yamada A; Ishikawa R; Porntaveetus T; Blackburn J; Otsuka-Tanaka Y; Saito N; Ota MS; Sharpe PT; Kessler JA; Herz J; Cobourne MT; Maeda T; Ohazama A, 2018, 'Lrp4/Wise regulates palatal rugae development through turing-type reaction-diffusion mechanisms', PLoS ONE, vol. 13, http://dx.doi.org/10.1371/journal.pone.0204126
    Journal articles | 2018
    Dr James Blackburn
    Deveson IW; Brunck ME; Blackburn J; Tseng E; Hon T; Clark TA; Clark MB; Crawford J; Dinger ME; Nielsen LK; Mattick JS; Mercer TR, 2018, 'Universal Alternative Splicing of Noncoding Exons', Cell Systems, vol. 6, pp. 245 - 255.e5, http://dx.doi.org/10.1016/j.cels.2017.12.005
    Journal articles | 2018
    Dr James Blackburn
    Deveson I; Madala BS; Blackburn J; Barker C; Wong T; Barton K; Smith M; Watkins N; Mercer T, 2018, 'Chiral DNA sequences as commutable reference standards for clinical genomics', BIORXIV, http://dx.doi.org/10.1101/404285
    Journal articles | 2017
    Dr James Blackburn
    Fleuren EDG; Vlenterie M; Van Der Graaf WTA; Hillebrandt-Roeffen MHS; Blackburn J; Ma X; Chan H; Magias MC; Van Erp A; Van Houdt L; Cebeci SAS; Van De Ven A; Flucke UE; Heyer EE; Thomas DM; Lord CJ; Marini KD; Vaghjiani V; Mercer TR; Cain JE; Wu J; Versleijen-Jonkers YMH; Daly RJ, 2017, 'Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes', Cancer Research, vol. 77, pp. 4279 - 4292, http://dx.doi.org/10.1158/0008-5472.CAN-16-2550
    Journal articles | 2017
    Dr James Blackburn
    Deveson IW; Holleley CE; Blackburn J; Marshall Graves JA; Mattick JS; Waters PD; Georges A, 2017, 'Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination', Science Advances, vol. 3, http://dx.doi.org/10.1126/sciadv.1700731
    Journal articles | 2016
    Dr James Blackburn
    Watanabe M; Kawasaki K; Kawasaki M; Portaveetus T; Oommen S; Blackburn J; Nagai T; Kitamura A; Nishikawa A; Kodama Y; Takagi R; Maeda T; Sharpe PT; Ohazama A, 2016, 'Spatio-temporal expression of Sox genes in murine palatogenesis', Gene Expression Patterns, vol. 21, pp. 111 - 118, http://dx.doi.org/10.1016/j.gep.2016.05.002
    Journal articles | 2016
    Dr James Blackburn
    Blackburn J; Roden DL; Ng R; Wu J; Bosman A; Epstein RJ, 2016, 'Damage-inducible intragenic demethylation of the human TP53 tumor suppressor gene is associated with transcription from an alternative intronic promoter', Molecular Carcinogenesis, vol. 55, pp. 1940 - 1951, http://dx.doi.org/10.1002/mc.22441
    Journal articles | 2016
    Dr James Blackburn
    Hardwick SA; Chen WY; Wong T; Deveson IW; Blackburn J; Andersen SB; Nielsen LK; Mattick JS; Mercer TR, 2016, 'Spliced synthetic genes as internal controls in RNA sequencing experiments', Nature Methods, vol. 13, pp. 792 - 798, http://dx.doi.org/10.1038/nmeth.3958
    Journal articles | 2016
    Dr James Blackburn
    Kawasaki M; Kawasaki K; Oommen S; Blackburn J; Watanabe M; Nagai T; Kitamura A; Maeda T; Liu B; Schmidt-Ullrich R; Akiyama T; Inoue JI; Hammond NL; Sharpe PT; Ohazama A, 2016, 'Regional regulation of Filiform tongue papillae development by Ikkα/Irf6', Developmental Dynamics, vol. 245, pp. 937 - 946, http://dx.doi.org/10.1002/dvdy.24427
    Journal articles | 2015
    Dr James Blackburn
    Blackburn J; Kawasaki K; Porntaveetus T; Kawasaki M; Otsuka-Tanaka Y; Miake Y; Ota MS; Watanabe M; Hishinuma M; Nomoto T; Oommen S; Ghafoor S; Harada F; Nozawa-Inoue K; Maeda T; Peterková R; Lesot H; Inoue J; Akiyama T; Schmidt-Ullrich R; Liu B; Hu Y; Page A; Ramírez ; Sharpe PT; Ohazama A, 2015, 'Excess NF-κB induces ectopic odontogenesis in embryonic incisor epithelium', Journal of Dental Research, vol. 94, pp. 121 - 128, http://dx.doi.org/10.1177/0022034514556707
    Journal articles | 2012
    Dr James Blackburn
    Blackburn J; Ohazama A; Kawasaki K; Otsuka-Tanaka Y; Liu B; Honda K; Rountree RB; Hu Y; Kawasaki M; Birchmeier W; Schmidt-Ullrich R; Kinoshita A; Schutte BC; Hammond NL; Dixon MJ; Sharpe PT, 2012, 'The role of Irf6 in tooth epithelial invagination', Developmental Biology, vol. 365, pp. 61 - 70, http://dx.doi.org/10.1016/j.ydbio.2012.02.009
    Journal articles | 2012
    Dr James Blackburn
    Kawasaki K; Porntaveetus T; Oommen S; Ghafoor S; Kawasaki M; Otsuka-Tanaka Y; Blackburn J; Kessler JA; Sharpe PT; Ohazama A, 2012, 'Bmp signalling in filiform tongue papillae development', Archives of Oral Biology, vol. 57, pp. 805 - 813, http://dx.doi.org/10.1016/j.archoralbio.2011.11.014
    Journal articles | 2010
    Dr James Blackburn
    Ohazama A; Blackburn J; Porntaveetus T; Ota MS; Choi HY; Johnson EB; Myers P; Oommen S; Eto K; Kessler JA; Kondo T; Fraser GJ; Streelman JT; Pardiñas UFJ; Tucker AS; Ortiz PE; Charles C; Viriot L; Herz J; Sharpe PT, 2010, 'A role for suppressed incisor cuspal morphogenesis in the evolution of mammalian heterodont dentition', Proceedings of the National Academy of Sciences of the United States of America, vol. 107, pp. 92 - 97, http://dx.doi.org/10.1073/pnas.0907236107
    Journal articles | 2009
    Dr James Blackburn
    Ohazama A; Haycraft CJ; Seppala M; Blackburn J; Ghafoor S; Cobourne M; Martinelli DC; Fan CM; Peterkova R; Lesot H; Yoder BK; Sharpe PT, 2009, 'Primary cilia regulate Shh activity in the control of molar tooth number', Development, vol. 136, pp. 897 - 903, http://dx.doi.org/10.1242/dev.027979
    Journal articles | 2006
    Dr James Blackburn
    Matalová E; š etková J; Míšek I; Blackburn J; Sharpe PT, 2006, 'CD 95 mediated apoptosis in embryogenesis: Implication in tooth development', Orthodontics and Craniofacial Research, vol. 9, pp. 123 - 128, http://dx.doi.org/10.1111/j.1601-6343.2006.00365.x
    Journal articles | 2005
    Dr James Blackburn
    Courtney JM; Blackburn J; Sharpe PT, 2005, 'The Ectodysplasin and NFκB signalling pathways in odontogenesis', Archives of Oral Biology, vol. 50, pp. 159 - 163, http://dx.doi.org/10.1016/j.archoralbio.2004.11.019
    Journal articles | 2003
    Dr James Blackburn
    Blackburn J; Tarttelin EE; Gregory-Evans CY; Moosajee M; Gregory-Evans K, 2003, 'Transcriptional Regulation and Expression of the Dominant Drusen Gene FBLN3 (EFEMP1) in Mammalian Retina', Investigative Ophthalmology and Visual Science, vol. 44, pp. 4613 - 4621, http://dx.doi.org/10.1167/iovs.03-0112
    Journal articles | 2001
    Dr James Blackburn
    Tarttelin EE; Gregory-Evans CY; Bird AC; Weleber RG; Klein ML; Blackburn J; Gregory-Evans K, 2001, 'Molecular genetic heterogeneity in autosomal dominant drusen', Journal of Medical Genetics, vol. 38, pp. 381 - 384, http://dx.doi.org/10.1136/jmg.38.6.381
    Journal articles |
    Dr James Blackburn
    Whiteley SL; Holleley CE; Wagner S; Blackburn J; Deveson IW; Graves JAM; Georges A, 'Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination', , http://dx.doi.org/10.1101/2021.02.03.429474
  • Conference Papers | 2021
    Dr James Blackburn
    Mueller SA; Gauthier M-EA; Blackburn J; Grady JP; Kratisek S; Dettmer MS; Dahlstrom JE; Lee CS; Luk P; Yu B; Giger R; Kummerfeld S; Clark J; Gupta R; Cowley MJ, 2021, 'Molecular patterns in salivary duct carcinoma identify prognostic subgroups', in ORAL ONCOLOGY, ELSEVIER, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000669389300007&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Conference Abstracts | 2019
    Dr James Blackburn
    Fordham AM; Blackburn J; Heyer EE; Xie J; Mould EV; Gifford AJ; Morgan LT; Wadham C; Fadia M; Fletcher JI; MacKenzie KL; Trahair TN, 2019, 'Abstract 4824: Targeting CD30 as a novel treatment strategy inRANBP2-ALK-rearranged inflammatory myofibroblastic tumor', in Experimental and Molecular Therapeutics, American Association for Cancer Research, presented at Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA, http://dx.doi.org/10.1158/1538-7445.sabcs18-4824
    Conference Abstracts | 2019
    Dr James Blackburn
    Fordham AM; Blackburn J; Heyer EE; Xie J; Mould EV; Gifford AJ; Morgan LT; Wadham C; Fadia M; Fletcher JI; MacKenzie KL; Trahair TN, 2019, 'Targeting CD30 as a novel treatment strategy in RANBP2-ALK-rearranged inflammatory myofibroblastic tumor', in CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, Atlanta, GA, Vol. 79, presented at Annual Meeting of the American-Association-for-Cancer-Research (AACR), Atlanta, GA, 29 March 2019 - 03 April 2019, http://dx.doi.org/10.1158/1538-7445.AM2019-4824

Awards

Grants

Blackburn, J. Improving Fusion Gene Detection and Immune Response Assessment in Sarcoma Patients. ANZSA Research Grant 2020

Blackburn, J. Improving Sarcoma Cancer Diagnostics Through Implementation of a Novel Fusion Gene Test. NFMRI Research Grant, 2020-2021.

Blackburn, J., Heyer, E.E., Trahair, T.N. Accurately Diagnosing Fusion Genes in Paediatric and Adolescent and Young Adult (AYA) Sarcomas. St. Vincent’s Clinic Foundation Research Grant, 2019.

Mercer, T.R., Dinger, M.E., Burnett, L., Blackburn, J. Diagnosis of Inherited Genetic Disorders Using DNA Reference Standards. NHMRC Project Grant, 2018-2020.

Mercer, T.R., Gill, D., Blackburn, J. A Universal Clinical Test for Gene Fusions in Blood Cancer. NHMRC Project Grant, 2016-2018.

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