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Human-specific RNA analysis shows uncoupled epithelial-mesenchymal plasticity in circulating and disseminated tumour cells from human breast cancer xenografts.

Tachtsidis A, Le AV, Blick T, Gunasinghe D, De Sousa E, Waltham M, Dobrovic A, Thompson EW.

Clin Exp Metastasis. 2019 Jun 12. doi: 10.1007/s10585-019-09977-y. [Epub ahead of print]


A new normalization for Nanostring nCounter gene expression data.

Molania R, Gagnon-Bartsch JA, Dobrovic A, Speed TP.

Nucleic Acids Res. 2019 May 22. pii: gkz433. doi: 10.1093/nar/gkz433. [Epub ahead of print]


BCL-XL and MCL-1 are the key BCL-2 family proteins in melanoma cell survival.

Lee EF, Harris TJ, Tran S, Evangelista M, Arulananda S, John T, Ramnac C, Hobbs C, Zhu H, Gunasingh G, Segal D, Behren A, Cebon J, Dobrovic A, Mariadason JM, Strasser A, Rohrbeck L, Haass NK, Herold MJ, Fairlie WD.

Cell Death Dis. 2019 Apr 24;10(5):342. doi: 10.1038/s41419-019-1568-3.


A reference collection of patient-derived cell line and xenograft models of proneural, classical and mesenchymal glioblastoma.

Stringer BW, Day BW, D'Souza RCJ, Jamieson PR, Ensbey KS, Bruce ZC, Lim YC, Goasdoué K, Offenhäuser C, Akgül S, Allan S, Robertson T, Lucas P, Tollesson G, Campbell S, Winter C, Do H, Dobrovic A, Inglis PL, Jeffree RL, Johns TG, Boyd AW.

Sci Rep. 2019 Mar 20;9(1):4902. doi: 10.1038/s41598-019-41277-z.


Molecular Genomic Profiling of Melanocytic Nevi.

Colebatch AJ, Ferguson P, Newell F, Kazakoff SH, Witkowski T, Dobrovic A, Johansson PA, Saw RPM, Stretch JR, McArthur GA, Long GV, Thompson JF, Pearson JV, Mann GJ, Hayward NK, Waddell N, Scolyer RA, Wilmott JS.

J Invest Dermatol. 2019 Feb 14. pii: S0022-202X(19)30118-6. doi: 10.1016/j.jid.2018.12.033. [Epub ahead of print]


Genomic Analysis of Circulating Tumor DNA Using a Melanoma-Specific UltraSEEK Oncogene Panel.

Gray ES, Witkowski T, Pereira M, Calapre L, Herron K, Irwin D, Chapman B, Khattak MA, Raleigh J, Hatzimihalis A, Cebon J, Sandhu S, McArthur GA, Millward M, Ziman M, Dobrovic A, Wong SQ.

J Mol Diagn. 2019 May;21(3):418-426. doi: 10.1016/j.jmoldx.2018.12.001. Epub 2019 Feb 5.


TERT gene: its function and dysregulation in cancer.

Colebatch AJ, Dobrovic A, Cooper WA.

J Clin Pathol. 2019 Apr;72(4):281-284. doi: 10.1136/jclinpath-2018-205653. Epub 2019 Jan 29. Review.


Fc-gamma receptor polymorphisms, cetuximab therapy, and overall survival in the CCTG CO.20 trial of metastatic colorectal cancer.

Shepshelovich D, Townsend AR, Espin-Garcia O, Latifovic L, O'Callaghan CJ, Jonker DJ, Tu D, Chen E, Morgen E, Price TJ, Shapiro J, Siu LL, Kubo M, Dobrovic A, Ratain MJ, Xu W, Mushiroda T, Liu G.

Cancer Med. 2018 Nov;7(11):5478-5487. doi: 10.1002/cam4.1819. Epub 2018 Oct 14.


Methylation of all BRCA1 copies predicts response to the PARP inhibitor rucaparib in ovarian carcinoma.

Kondrashova O, Topp M, Nesic K, Lieschke E, Ho GY, Harrell MI, Zapparoli GV, Hadley A, Holian R, Boehm E, Heong V, Sanij E, Pearson RB, Krais JJ, Johnson N, McNally O, Ananda S, Alsop K, Hutt KJ, Kaufmann SH, Lin KK, Harding TC, Traficante N; Australian Ovarian Cancer Study (AOCS), deFazio A, McNeish IA, Bowtell DD, Swisher EM, Dobrovic A, Wakefield MJ, Scott CL.

Nat Commun. 2018 Sep 28;9(1):3970. doi: 10.1038/s41467-018-05564-z.


DNA Methylation Profiling of Breast Cancer Cell Lines along the Epithelial Mesenchymal Spectrum-Implications for the Choice of Circulating Tumour DNA Methylation Markers.

Le AV, Szaumkessel M, Tan TZ, Thiery JP, Thompson EW, Dobrovic A.

Int J Mol Sci. 2018 Aug 28;19(9). pii: E2553. doi: 10.3390/ijms19092553.


Mismatch Repair Protein Defects and Microsatellite Instability in Malignant Pleural Mesothelioma.

Arulananda S, Thapa B, Walkiewicz M, Zapparoli GV, Williams DS, Dobrovic A, John T.

J Thorac Oncol. 2018 Oct;13(10):1588-1594. doi: 10.1016/j.jtho.2018.07.015. Epub 2018 Jul 26.


Adapting an Established Clinical Chemistry Quality Control Measure for Droplet Generation Performance in Digital PCR.

Goh SK, Wong BKL, Muralidharan V, Christophi C, Do H, Dobrovic A.

Clin Chem. 2018 Aug;64(8):1255-1257. doi: 10.1373/clinchem.2018.291120. Epub 2018 Jun 11. No abstract available.


Somatic GNAQ mutation in the forme fruste of Sturge-Weber syndrome.

Hildebrand MS, Harvey AS, Malone S, Damiano JA, Do H, Ye Z, McQuillan L, Maixner W, Kalnins R, Nolan B, Wood M, Ozturk E, Jones NC, Gillies G, Pope K, Lockhart PJ, Dobrovic A, Leventer RJ, Scheffer IE, Berkovic SF.

Neurol Genet. 2018 May 1;4(3):e236. doi: 10.1212/NXG.0000000000000236. eCollection 2018 Jun.


Fresh Frozen Plasma Transfusion Can Confound the Analysis of Circulating Cell-Free DNA.

Goh SK, Muralidharan V, Christophi C, Dobrovic A.

Clin Chem. 2018 Apr;64(4):749-751. doi: 10.1373/clinchem.2017.285684. Epub 2018 Feb 13. No abstract available.


In Reply to Leone.

Do H, Arulananda S, John T, Dobrovic A.

J Thorac Oncol. 2018 Feb;13(2):e22-e23. doi: 10.1016/j.jtho.2017.11.119. No abstract available.


Optimizing Amplification of the GC-Rich TERT Promoter Region Using 7-Deaza-dGTP for Droplet Digital PCR Quantification of TERT Promoter Mutations.

Colebatch AJ, Witkowski T, Waring PM, McArthur GA, Wong SQ, Dobrovic A.

Clin Chem. 2018 Apr;64(4):745-747. doi: 10.1373/clinchem.2017.284257. Epub 2018 Jan 30. No abstract available.


White Blood Cell BRCA1 Promoter Methylation Status and Ovarian Cancer Risk: A Perspective.

Dobrovic A.

Ann Intern Med. 2018 Mar 6;168(5):365-366. doi: 10.7326/M17-3340. Epub 2018 Jan 16. No abstract available.


Sensitive quantitative detection of somatic mosaic mutation in "double cortex" syndrome.

Damiano JA, Do H, Ozturk E, Burgess R, Kalnins R, Jones NC, Dobrovic A, Berkovic SF, Hildebrand MS.

Epileptic Disord. 2017 Dec 1;19(4):450-455. doi: 10.1684/epd.2017.0944.


LRH-1 expression patterns in breast cancer tissues are associated with tumour aggressiveness.

Pang JB, Molania R, Chand A, Knower K, Takano EA, Byrne DJ, Mikeska T, Millar EKA, Lee CS, O'Toole SA, Clyne C, Gorringe KL, Dobrovic A, Fox SB.

Oncotarget. 2017 Jul 28;8(48):83626-83636. doi: 10.18632/oncotarget.18886. eCollection 2017 Oct 13.


GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.

Cameron DL, Schröder J, Penington JS, Do H, Molania R, Dobrovic A, Speed TP, Papenfuss AT.

Genome Res. 2017 Dec;27(12):2050-2060. doi: 10.1101/gr.222109.117. Epub 2017 Nov 2.


Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer.

Garsed DW, Alsop K, Fereday S, Emmanuel C, Kennedy CJ, Etemadmoghadam D, Gao B, Gebski V, Garès V, Christie EL, Wouters MCA, Milne K, George J, Patch AM, Li J, Arnau GM, Semple T, Gadipally SR, Chiew YE, Hendley J, Mikeska T, Zapparoli GV, Amarasinghe K, Grimmond SM, Pearson JV, Waddell N, Hung J, Stewart CJR, Sharma R, Allan PE, Rambau PF, McNally O, Mileshkin L, Hamilton A, Ananda S, Grossi M, Cohen PA, Leung YC, Rome RM, Beale P, Blomfield P, Friedlander M, Brand A, Dobrovic A, Köbel M, Harnett P, Nelson BH, Bowtell DDL, deFazio A; Nadia Traficante, for the Australian Ovarian Cancer Study Group.

Clin Cancer Res. 2018 Feb 1;24(3):569-580. doi: 10.1158/1078-0432.CCR-17-1621. Epub 2017 Oct 23.


TERT structural rearrangements in metastatic pheochromocytomas.

Dwight T, Flynn A, Amarasinghe K, Benn DE, Lupat R, Li J, Cameron DL, Hogg A, Balachander S, Candiloro ILM, Wong SQ, Robinson BG, Papenfuss AT, Gill AJ, Dobrovic A, Hicks RJ, Clifton-Bligh RJ, Tothill RW.

Endocr Relat Cancer. 2018 Jan;25(1):1-9. doi: 10.1530/ERC-17-0306. Epub 2017 Oct 3.


DNA Breathing Enables Closed-Tube Mutant Allele Enrichment for Circulating Tumor DNA Analysis.

Dobrovic A.

Clin Chem. 2017 Oct;63(10):e1-e3. doi: 10.1373/clinchem.2017.276493. Epub 2017 Sep 13. No abstract available.


BRCA2 carriers with male breast cancer show elevated tumour methylation.

Deb S, Gorringe KL, Pang JB, Byrne DJ, Takano EA, Investigators K, Dobrovic A, Fox SB.

BMC Cancer. 2017 Sep 11;17(1):641. doi: 10.1186/s12885-017-3632-7.


De novo activating epidermal growth factor mutations (EGFR) in small-cell lung cancer.

Thai A, Chia PL, Russell PA, Do H, Dobrovic A, Mitchell P, John T.

Intern Med J. 2017 Sep;47(9):1071-1074. doi: 10.1111/imj.13531.


EGFR and KRAS mutations do not enrich for the activation of IL-6, JAK1 or phosphorylated STAT3 in resected lung adenocarcinoma.

Clay TD, Russell PA, Do H, Sundararajan V, Conron M, Wright GM, Solomon B, Dobrovic A, McLachlan SA, Moore MM.

Med Oncol. 2017 Sep 6;34(10):175. doi: 10.1007/s12032-017-1031-1.


Combination Osimertinib and Gefitinib in C797S and T790M EGFR-Mutated Non-Small Cell Lung Cancer.

Arulananda S, Do H, Musafer A, Mitchell P, Dobrovic A, John T.

J Thorac Oncol. 2017 Nov;12(11):1728-1732. doi: 10.1016/j.jtho.2017.08.006. Epub 2017 Aug 24.


Reducing Artifactual EGFR T790M Mutations in DNA from Formalin-Fixed Paraffin-Embedded Tissue by Use of Thymine-DNA Glycosylase.

Do H, Molania R, Mitchell PL, Vaiskunaite R, Murdoch JD, Dobrovic A.

Clin Chem. 2017 Sep;63(9):1506-1514. doi: 10.1373/clinchem.2017.271932. Epub 2017 Jul 18.


Assessing alternative base substitutions at primer CpG sites to optimise unbiased PCR amplification of methylated sequences.

Candiloro ILM, Mikeska T, Dobrovic A.

Clin Epigenetics. 2017 Apr 4;9:31. doi: 10.1186/s13148-017-0328-4. eCollection 2017.


Breast ductal carcinoma in situ carry mutational driver events representative of invasive breast cancer.

Pang JB, Savas P, Fellowes AP, Mir Arnau G, Kader T, Vedururu R, Hewitt C, Takano EA, Byrne DJ, Choong DY, Millar EK, Lee CS, O'Toole SA, Lakhani SR, Cummings MC, Mann GB, Campbell IG, Dobrovic A, Loi S, Gorringe KL, Fox SB.

Mod Pathol. 2017 Jul;30(7):952-963. doi: 10.1038/modpathol.2017.21. Epub 2017 Mar 24.


Evaluation of Different Oligonucleotide Base Substitutions at CpG Binding sites in Multiplex Bisulfite-PCR sequencing.

Lu J, Ru K, Candiloro I, Dobrovic A, Korbie D, Trau M.

Sci Rep. 2017 Mar 22;7:45096. doi: 10.1038/srep45096.


Erratum: An optimised direct lysis method for gene expression studies on low cell numbers.

Le AV, Huang D, Blick T, Thompson EW, Dobrovic A.

Sci Rep. 2017 Mar 9;7:43075. doi: 10.1038/srep43075. No abstract available.


Probe-Free Digital PCR Quantitative Methodology to Measure Donor-Specific Cell-Free DNA after Solid-Organ Transplantation.

Goh SK, Muralidharan V, Christophi C, Do H, Dobrovic A.

Clin Chem. 2017 Mar;63(3):742-750. doi: 10.1373/clinchem.2016.264838. Epub 2017 Jan 18.


Reduced abundance of the E3 ubiquitin ligase E6AP contributes to decreased expression of the INK4/ARF locus in non-small cell lung cancer.

Gamell C, Gulati T, Levav-Cohen Y, Young RJ, Do H, Pilling P, Takano E, Watkins N, Fox SB, Russell P, Ginsberg D, Monahan BJ, Wright G, Dobrovic A, Haupt S, Solomon B, Haupt Y.

Sci Signal. 2017 Jan 10;10(461). pii: eaaf8223. doi: 10.1126/scisignal.aaf8223.


Germline polymorphisms as biomarkers of tumor response in colorectal cancer patients treated with anti-EGFR monoclonal antibodies: a systematic review and meta-analysis.

Morgen EK, Lenz HJ, Jonker DJ, Tu D, Milano G, Graziano F, Zalcberg J, Karapetis CS, Dobrovic A, O'Callaghan CJ, Liu G.

Pharmacogenomics J. 2017 Dec;17(6):535-542. doi: 10.1038/tpj.2016.56. Epub 2016 Nov 29. Review.


Digital PCR of Genomic Rearrangements for Monitoring Circulating Tumour DNA.

Do H, Cameron D, Molania R, Thapa B, Rivalland G, Mitchell PL, Murone C, John T, Papenfuss A, Dobrovic A.

Adv Exp Med Biol. 2016;924:139-146.


Clustered somatic mutations are frequent in transcription factor binding motifs within proximal promoter regions in melanoma and other cutaneous malignancies.

Colebatch AJ, Di Stefano L, Wong SQ, Hannan RD, Waring PM, Dobrovic A, McArthur GA, Papenfuss AT.

Oncotarget. 2016 Oct 11;7(41):66569-66585. doi: 10.18632/oncotarget.11892.


Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas.

Lim AM, Wong NC, Pidsley R, Zotenko E, Corry J, Dobrovic A, Clark SJ, Rischin D, Solomon B.

Clin Epigenetics. 2016 Jul 18;8:74. doi: 10.1186/s13148-016-0235-0. eCollection 2016.


Temporal changes of EGFR mutations and T790M levels in tumour and plasma DNA following AZD9291 treatment.

Chia PL, Do H, Morey A, Mitchell P, Dobrovic A, John T.

Lung Cancer. 2016 Aug;98:29-32. doi: 10.1016/j.lungcan.2016.05.003. Epub 2016 May 11.


Comparison of 3 Methodologies for Genotyping of Small Deletion and Insertion Polymorphisms.

Goh SK, Musafer A, Witkowski T, Muralidharan V, Christophi C, Do H, Dobrovic A.

Clin Chem. 2016 Jul;62(7):1012-9. doi: 10.1373/clinchem.2016.256388.


Fc-γ Receptor Polymorphisms, Cetuximab Therapy, and Survival in the NCIC CTG CO.17 Trial of Colorectal Cancer.

Liu G, Tu D, Lewis M, Cheng D, Sullivan LA, Chen Z, Morgen E, Simes J, Price TJ, Tebbutt NC, Shapiro JD, Jeffery GM, Mellor JD, Mikeska T, Virk S, Shepherd LE, Jonker DJ, O'Callaghan CJ, Zalcberg JR, Karapetis CS, Dobrovic A.

Clin Cancer Res. 2016 May 15;22(10):2435-44. doi: 10.1158/1078-0432.CCR-15-0414.


Associations between the IASLC/ATS/ERS lung adenocarcinoma classification and EGFR and KRAS mutations.

Clay TD, Russell PA, Do H, Sundararajan V, Conron M, Wright GM, Dobrovic A, Moore MM, McLachlan SA.

Pathology. 2016 Jan;48(1):17-24. doi: 10.1016/j.pathol.2015.11.002. Epub 2015 Dec 12.


MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing.

Wong NC, Pope BJ, Candiloro IL, Korbie D, Trau M, Wong SQ, Mikeska T, Zhang X, Pitman M, Eggers S, Doyle SR, Dobrovic A.

BMC Bioinformatics. 2016 Feb 24;17:98. doi: 10.1186/s12859-016-0950-8.


Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat.

Wong NC, Pope BJ, Candiloro I, Korbie D, Trau M, Wong SQ, Mikeska T, van Denderen BJ, Thompson EW, Eggers S, Doyle SR, Dobrovic A.

Gigascience. 2015 Nov 26;4:55. doi: 10.1186/s13742-015-0098-x. eCollection 2015.


"Cancer 2015": A Prospective, Population-Based Cancer Cohort-Phase 1: Feasibility of Genomics-Guided Precision Medicine in the Clinic.

Parisot JP, Thorne H, Fellowes A, Doig K, Lucas M, McNeil JJ, Doble B, Dobrovic A, John T, James PA, Lipton L, Ashley D, Hayes T, McMurrick P, Richardson G, Lorgelly P, Fox SB, Thomas DM.

J Pers Med. 2015 Oct 29;5(4):354-69. doi: 10.3390/jpm5040354.


Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour.

Huang KT, Mikeska T, Li J, Takano EA, Millar EK, Graham PH, Boyle SE, Campbell IG, Speed TP, Dobrovic A, Fox SB.

BMC Cancer. 2015 Oct 9;15:669. doi: 10.1186/s12885-015-1676-0.


Copy number analysis of ductal carcinoma in situ with and without recurrence.

Gorringe KL, Hunter SM, Pang JM, Opeskin K, Hill P, Rowley SM, Choong DY, Thompson ER, Dobrovic A, Fox SB, Mann GB, Campbell IG.

Mod Pathol. 2015 Sep;28(9):1174-84. doi: 10.1038/modpathol.2015.75. Epub 2015 Jun 19.


An optimised direct lysis method for gene expression studies on low cell numbers.

Le AV, Huang D, Blick T, Thompson EW, Dobrovic A.

Sci Rep. 2015 Aug 5;5:12859. doi: 10.1038/srep12859. Erratum in: Sci Rep. 2017 Mar 09;7:43075.


Monitoring response to therapy in melanoma by quantifying circulating tumour DNA with droplet digital PCR for BRAF and NRAS mutations.

Tsao SC, Weiss J, Hudson C, Christophi C, Cebon J, Behren A, Dobrovic A.

Sci Rep. 2015 Jun 22;5:11198. doi: 10.1038/srep11198.


Appraisal of the technologies and review of the genomic landscape of ductal carcinoma in situ of the breast.

Pang JM, Gorringe KL, Wong SQ, Dobrovic A, Campbell IG, Fox SB.

Breast Cancer Res. 2015 Jun 16;17:80. doi: 10.1186/s13058-015-0586-z. Review.

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