Publications

Annual reports

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2020

  1. Seung Jun Shin, Elissa Dodd-Eaton, Gang Peng, Jasmina Bojadzieva, Jingxiao Chen, Christopher Amos, Megan Frone, Payal Khincha, Phuong Mai, Sharon Savage, Mandy Ballinger, David Thomas, Ying Yuan, Louise Strong, and Wenyi Wang (2020). Penetrance of different cancer types in families with Li-Fraumeni syndrome: a validation study using multi-center cohorts. Cancer Research 80:354–60
  2. Mirabello L, Zhu B, Koster R, Karlins E, Dean M, Yeager M, Gianferante M, Spector LG, Morton LM, Karyadi D, Robison LL, Armstrong GT, Bhatia S, Song L, Pankratz N, Pinheiro M, Gastier-Foster JM, Gorlick R, de Toledo SRC, Petrilli AS, Patino-Garcia A, Lecanda F, Gutierrez-Jimeno M, Serra M, Hattinger C, Picci P, Scotlandi K, Flanagan AM, Tirabosco R, Amary MF, Kurucu N, Ilhan IE, Ballinger ML, Thomas DM, Barkauskas DA, Mejia-Baltodano G, Valverde P, Hicks BD, Zhu B, Wang M, Hutchinson AA, Tucker M, Sampson J, Landi MT, Freedman ND, Gapstur S, Carter B, Hoover RN, Chanock SJ, Savage SA. Pathogenic germline variants in cancer-susceptibility genes in osteosarcoma patients. JAMA Oncology 2020 Mar 19. doi: 10.1001/jamaoncol.2020.0197. [Epub ahead of print]
  3. Bartley N, Best M, Jacobs C, Juraskova I, Newson A, Savard J, Meiser B, Ballinger ML, Thomas DM, Biesecker B, Butow P. Cancer patients’ views and understanding of genome sequencing: a qualitative study. J Med Genet 2020 in press.
  4. Butow P, Davies G, Napier C, Bartley N, Juraskova I, Meiser B, Ballinger ML, Schlub T, Thomas DM, Goldstein D, Best MC and members of the PiGeOn Project. Value of Tumor Mutation Profiling to Cancer Patients: An Investigation using the Willingness-To-Pay Technique. JAMA Network Open 2020 in press.
  5. Davies G, Butow P, Napier CE, Bartley, N, Juraskova I, Meiser B, Ballinger ML, Thomas DM, Schlub TE, Best M. 2020. Advanced cancer patient knowledge of and attitudes towards tumor molecular profiling. Translational Oncology. Accepted on 5/5/2020.
  6. Kalachand RD, Stordal B, Madden S, Chandler B, Cunningham J, Goode EL, Ruscito I, Braicu EI, Sehouli J, Ignatov A, Yu H, Katsaros D, Mills GB, Lu KH, Carey MS, Timms KM, Kupryjanczyk J, Rzepecka IK, Podgorska A, McAlpine JN, Swisher EM, Bernards SS, O’Riain C, O’Toole S, O’Leary JJ, Bowtell DD, Thomas DM, Prieske K, Joosse SA, Woelber L, Chaudhry P, Häfner N, Runnebaum IB, Hennessy BT. BRCA1 promoter methylation and clinical outcomes in ovarian cancer: an individual patient data meta-analysis. J Natl Cancer Inst. 2020 May 15:djaa070. doi: 10.1093/jnci/djaa070.
  7. Kovac M, Woolley C, Ribi S, Blattmann C, Roth E, Morini M, Kovacova M, Ameline B, Kulozik A, Bielack S, Hartmann W, Ballinger ML, Thomas DM, Tomlinson I, Nathrath M, Heinimann K, Baumhoer D.J Germline RETvariants underlie a subset of paediatric osteosarcoma. Med Genet. 2020 Mar 16:jmedgenet-2019-106734. doi: 10.1136/jmedgenet-2019-106734. Online ahead of print.
  8. Dancsok AR, Gao D, Lee AF, Steigen SE, Blay JY, Thomas DM, Maki RG, Nielsen TO, Demicco EG.Tumor-associated macrophages and macrophage-related immune checkpoint expression in sarcomas. Oncoimmunology. 2020 Apr 12;9(1):1747340. doi: 10.1080/2162402X.2020.1747340.
  9. Shin SJ, Dodd-Eaton EB, Peng G, Bojadzieva J, Chen J, Amos CI, Frone MN, Khincha PP, Mai PL, Savage SA, Ballinger ML, Thomas DM, Yuan Y, Strong LC, Wang W.Penetrance of Different Cancer Types in Families with Li-Fraumeni Syndrome: A Validation Study Using Multicenter Cohorts. Cancer Res. 2020 Jan 15;80(2):354-360. doi: 10.1158/0008-5472.CAN-19-0728. Epub 2019 Nov 12.
  10. Best MC, Butow P, Jacobs C, Savard J, Biesecker B, Ballinger ML, Bartley N, Davies G, Napier CE, Smit AK, Thomas DM, Newson AJ; Members of the PiGeOn Project.Who should access germline genome sequencing? A mixed methods study of patient views. Clin Genet. 2020 Feb;97(2):329-337. doi: 10.1111/cge.13664. Epub 2019 Nov 26.

2019

  1. Malkin D, Bond G, Thomas DM, Ballinger ML, World Health Organisation Classification of Tumours – Soft Tissue and Bone 5th edition, 2019. Li Fraumeni Syndrome.
  2. Ballinger ML, Pinese M and Thomas DM (2019). Translating genomic risk into an early detection strategy for sarcoma. Genes Chromosomes Cancer 58: 130-136.
  3. Fortuno C, Cipponi A, Ballinger ML, Tavtigian SV, Olivier M, Ruparel V, Haupt Y, Haupt S, Study ISK, Tucker K, Spurdle AB, Thomas DM and James PA (2019). A quantitative model to predict pathogenicity of missense variants in the TP53 gene. Hum Mutat 40: 788-800.
  4. Heyer EE, Deveson IW, Wooi D, Selinger CI, Lyons RJ, Hayes VM, O’Toole SA, Ballinger ML, Gill D, Thomas DM, Mercer TR and Blackburn J (2019). Diagnosis of fusion genes using targeted RNA sequencing. Nat Commun 10: 1388.
  5. Jones RM, Melton PE, Pinese M, Rea AJ, Ingley E, Ballinger ML, Wood DJ, Thomas DM and Moses EK (2019). Identification of novel sarcoma risk genes using a two-stage genome wide DNA sequencing strategy in cancer cluster families and population case and control cohorts. BMC Med Genet 20: 69.
  6. Lacaze P, Pinese M, Kaplan W, Stone A, Brion MJ, Woods RL, McNamara M, McNeil JJ, Dinger ME and Thomas DM (2019). The Medical Genome Reference Bank: a whole-genome data resource of 4000 healthy elderly individuals. Rationale and cohort design. European Journal of Human Genetics 27: 308-316.
  7. McCabe MJ, Pinese M, Chan CL, Sheriff N, Thompson TJ, Grady J, Wong M, Gauthier MA, Puttick C, Gayevskiy V, Hajdu E, Wong SQ, Barrett W, Earls P, Lukeis R, Cheng YY, Lin RCY, Thomas DM, Watkins DN, Dinger ME, McCormack AI and Cowley MJ (2019). Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases. Cold Spring Harb Mol Case Stud 5: pii: a003764.
  8. Thavaneswaran S, Rath E, Tucker K, Joshua AM, Hess D, Pinese M, Ballinger ML and Thomas DM (2019). Therapeutic implications of germline genetic findings in cancer. Nat Rev Clin Oncol 16: 386-396.
  9. Best MC, Bartley N, Jacobs C, Juraskova I, Goldstien D, Newson AJ, Savard J, Meiser B, Ballinger ML, Napier C, Thomas DM, Biesecker B, Butow P and members of the PiGeOn Project (2019). Patient perspectives on molecular tumour profiling: “Why wouldn’t you?”. BMC Cancer 19:753.
  10. Kansara, M., Thomson, K., Pang, P., Dutour, A., Mirabello, L., Acher, F., Pin, J.P., Demicco, E.G., Yan, J., Teng, M.W.L., Smyth, M.J., Thomas, D.M. (2019). Infiltrating myeloid cells drive osteosarcoma progression via GRM4 regulation of IL23. Cancer Discov, 9: 1511-1519.
  11. Vargas, A.C., Selinger, C., Satgunaseelan, L., Cooper, W.A., Gupta, R., Stalley, P., Brown, W., Soper, J., Schatz, J., Boyle, R., Thomas, D.M., Tattersall, M.H.N., Bhadri, V., Maclean, F., Bonar, S.F., Scolyer, R.A., Karim, R.Z., McCarthy, S.W., Mahar, A., O’Toole, S.A. (2019). FISH analysis of selected soft tissue tumors: Diagnostic experience in a tertiary center. Asia Pac J Clin Oncol, 15: 38-47.
  12. Yanes T, Willis AM, Meiser B, Tucker KM, Best M. (2019). Psychological and behavioural outcomes of genomic testing in cancer: a systematic review. European Journal of Human Genetics; 27 : 28-35.

2018

  1. Lacaze, P., Pinese, M., Kaplan, W., Stone, A., Brion, M.J., Woods, R.L., McNamara, M., McNeil, J.J., Dinger, M.E., Thomas, D.M. 2018 The Medical Genome Reference Bank: a whole-genome data resource of 4000 healthy elderly individuals. Rationale and cohort design. Eur J Hum Genet, doi: 10.1038/s41431- 41018-40279-z.
  2. Best, M., Newson, A.J., Meiser, B., Juraskova, I., Goldstein, D., Tucker, K., Ballinger, M.L., Hess, D., Schlub, T.E., Biesecker, B., Vines, R., Vines, K., Thomas, D., Young, M.A., Savard, J., Jacobs, C., Butow, P. 2018 The PiGeOn project: protocol for a longitudinal study examining psychosocial, behavioural and ethical issues and outcomes in cancer tumour genomic profiling. BMC Cancer, 18: 389.
  3. Best, M., Newson, A.J., Meiser, B., Juraskova, I., Goldstein, D., Tucker, K., Ballinger, M.L., Hess, D., Schlub, T.E., Biesecker, B., Vines, R., Vines, K., Thomas, D., Young, M.A., Savard, J., Jacobs, C., Butow, P. 2018 The PiGeOn project: protocol of a longitudinal study examining psychosocial and ethical issues and outcomes in germline genomic sequencing for cancer. BMC Cancer, 18: 454.
  4. Chou, A., Froio, D., Nagrial, A.M., Parkin, A., Murphy, K.J., Chin, V.T., Wohl, D., Steinmann, A., Stark, R., Drury, A., Walters, S.N., Vennin, C., Burgess, A., Pinese, M., Chantrill, L.A., Cowley, M.J., Molloy, T.J., Waddell, N., Johns, A., Grimmond, S.M., Chang, D.K., Biankin, A.V., Sansom, O.J., Morton, J.P., Grey, S.T., Cox, T.R., Turchini, J., Samra, J., Clarke, S.J., Timpson, P., Gill, A.J., Pajic, M. 2018 Tailored first-line and second-line CDK4-targeting treatment combinations in mouse models of pancreatic cancer. Gut, 67: 2142-2155.
  5. Gounder, M.M., Thomas, D.M., Tap, W.D. 2018 Locally aggressive connective tissue tumors. J Clin Oncol, 36: 202-209.
  6. Koster, R., Panagiotou, O.A., Wheeler, W.A., Karlins, E., Gastier-Foster, J.M., Caminada de Toledo, S.R., Petrilli, A.S., Flanagan, A.M., Tirabosco, R., Andrulis, I.L., Wunder, J.S., Gokgoz, N., Patino-Garcia, A., Lecanda, F., Serra, M., Hattinger, C., Picci, P., Scotlandi, K., Thomas, D.M., Ballinger, M.L., Gorlick, R., Barkauskas, D.A., Spector, L.G., Tucker, M., Belynda, D.H., Yeager, M., Hoover, R.N., Wacholder, S., Chanock, S.J., Savage, S.A., Mirabello, L. 2018 Genome-wide association study identifies the GLDC/IL33 locus associated with survival of osteosarcoma patients. Int J Cancer, 142: 1594-1601.
  7. Rasmussen, V., Forrest, L.E., Rogasik, M., Girodet, M., Meeus, P., Sunyach, M.P., Blay, J.Y., Bally, O., Brahmi, M., Ballinger, M.L., Niedermayr, E., Thomas, D.M., Halliday, J., James, P., Ray-Coquard, I., Young, M.A., International Sarcoma Kindred, S. 2018 A comparison of Australian and French families affected by sarcoma: perceptions of genetics and incidental findings. Per Med, 15: 13-24.
  8. Thavaneswaran, S., Sebastian, L., Ballinger, M., Best, M., Hess, D., Lee, C.K., Sjoquist, K.M., Hague, W.E., Butow, P.N., Simes, R.J., Thomas, D. 2018 Cancer Molecular Screening and Therapeutics (MoST): a framework for multiple, parallel signal-seeking studies of targeted therapies for rare and neglected cancers. Med J Aust, 209: 354-355.
  9. Walczak, A., Patterson, P., Thomas, D. 2018 Trials and tribulations: improving outcomes for adolescents and young adults with rare and low survival cancers. Med J Aust, 209: 330-332.
  10. Woodcock, F., Doble, B., Cancer 2015 Consortium*. 2018 Mapping the EORTC-QLQ-C30 to the EQ- 5D-3L: An Assessment of Existing and Newly Developed Algorithms. Med Decis Making, 38: 954-967. (*D Thomas Chief Investigator)
  11. Zilberg, C., Lee, M.W., Yu, B., Ashford, B., Kraitsek, S., Ranson, M., Shannon, K., Cowley, M., Iyer, N.G., Palme, C.E., Ch’ng, S., Low, T.H., O’Toole, S., Clark, J.R., Gupta, R. 2018 Analysis of clinically relevant somatic mutations in high-risk head and neck cutaneous squamous cell carcinoma. Mod Pathol, 31: 275-287.

2017

  1. Ballinger, M.L., Best, A., Mai, P.L., Khincha, P.P., Loud, J.T., Peters, J.A., Achatz, M.I., Chojniak, R., Balieiro da Costa, A., Santiago, K.M., Garber, J., O’Neill, A.F., Eeles, R.A., Evans, D.G., Bleiker, E., Sonke, G.S., Ruijs, M., Loo, C., Schiffman, J., Naumer, A., Kohlmann, W., Strong, L.C., Bojadzieva, J., Malkin, D., Rednam, S.P., Stoffel, E.M., Koeppe, E., Weitzel, J.N., Slavin, T.P., Nehoray, B., Robson, M., Walsh, M., Manelli, L., Villani, A., Thomas, D.M., Savage, S.A. 2017 Baseline surveillance in Li-Fraumeni syndrome using whole-body magnetic resonance imaging: a meta-analysis. JAMA Oncol, 3: 1634-1639.
  2. Ballinger, M.L., Ferris, N.J., Moodie, K., Mitchell, G., Shanley, S., James, P.A., Thomas, D.M. 2017 Surveillance in germline TP53 mutation carriers utilizing whole-body magnetic resonance imaging. JAMA Oncol, 3: 1735-1736.
  3. Cho, D., Roncolato, F.T., Man. J., Simes, J., Lord, S.J., Links, M.J., Lee, C.K. 2017 Clinical equipoise for trials of novel biological therapies, therapeutic success rates and predictors of success: a meta-analysis. JCO Prec Oncol 1:1-12
  4. Doble, B., John, T., Thomas, D., Fellowes, A., Fox, S., Lorgelly, P. 2017 Cost-effectiveness of precision medicine in the fourth-line treatment of metastatic lung adenocarcinoma: An early decision analytic model of multiplex targeted sequencing. Lung Cancer, 107: 22-35.
  5. Fleuren, E.D.G., Vlenterie, M., van der Graaf, W., Hillebrandt-Roeffen, M.H.S., Blackburn, J., Ma, X., Chan, H., Magias, M.C., van Erp, A., van Houdt, L., Cebeci, S., van de Ven, A., Flucke, U.E., Heyer, E.E., Thomas, D.M., Lord, C.J., Marini, K.D., Vaghjiani, V., Mercer, T., Cain, J.E., Wu, J., Versleijen-Jonkers, Y.M.H., Daly, R.J. 2017 Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes. Cancer Res, 77: 4279-4292.
  6. Khoo, T.K., Yu, B., Smith, J.A., Clarke, A.J., Luk, P.P., Selinger, C.I., Mahon, K.L., Kraitsek, S., Palme, C., Boyer, M.J., Dinger, M.E., Cowley, M.J., O’Toole, S.A., Clark, J.R., Gupta, R. 2017 Somatic mutations in salivary duct carcinoma and potential therapeutic targets. Oncotarget, 8: 75893-75903.
  7. Leroy, B., Ballinger, M.L., Baran-Marszak, F., Bond, G.L., Braithwaite, A., Concin, N., Donehower, L.A., El-Deiry, W.S., Fenaux, P., Gaidano, G., Langerod, A., Hellstrom-Lindberg, E., Iggo, R., Lehmann-Che, J., Mai, P.L., Malkin, D., Moll, U.M., Myers, J.N., Nichols, K.E., Pospisilova, S., Ashton-Prolla, P., Rossi, D., Savage, S.A., Strong, L.C., Tonin, P.N., Zeillinger, R., Zenz, T., Fraumeni, J.F., Jr., Taschner, P.E., Hainaut, P., Soussi, T. 2017 Recommended guidelines for validation, quality control, and reporting of TP53 variants in clinical practice. Cancer Res, 77: 1250-1260.
  8. Lorgelly, P.K., Doble, B., Rowen, D., Brazier, J., Cancer 2015 Investigators*. 2017 Condition-specific or generic preference-based measures in oncology? A comparison of the EORTC-8D and the EQ-5D-3L. Qual Life Res, 26: 1163-1176. (*D Thomas Chief Investigator)
  9. McBride, K.A., Ballinger, M.L., Schlub, T.E., Young, M.A., Tattersall, M.H., Kirk, J., Eeles, R., Killick, E., Walker, L.G., Shanley, S., Thomas, D.M., Mitchell, G. 2017 Psychosocial morbidity in TP53 mutation carriers: is whole-body cancer screening beneficial? Fam Cancer, 16: 423-432.
  10. Peng, G., Bojadzieva, J., Ballinger, M.L., Li, J., Blackford, A.L., Mai, P.L., Savage, S.A., Thomas, D.M., Strong, L.C., Wang, W. 2017 Estimating TP53 mutation carrier probability in families with Li-Fraumeni syndrome using LFSPRO. Cancer Epidemiol Biomarkers Prev, 26: 837-844.
  11. Takeda, K., Nakayama, M., Hayakawa, Y., Kojima, Y., Ikeda, H., Imai, N., Ogasawara, K., Okumura, K., Thomas, D.M., Smyth, M.J. 2017 IFN-gamma is required for cytotoxic T cell-dependent cancer genome immunoediting. Nat Commun, 8: 14607.
  12. Thomas, D.M. 2017 Is Li-Fraumeni syndrome really much more common? Hum Mutat, 38: 1619.
  13. Thomas, D.M., Whelan, J. in Cancer in Adolescents and Young Adults. Pediatric Oncology (eds. Bleyer, A., Barr, R., Ries, L., Whelan, J. & Ferrari, A.) 417-427 (Springer International Publishing, 2017).
  14. Warton, K., Yuwono, N.L., Cowley, M.J., McCabe, M.J., So, A., Ford, C.E. 2017 Evaluation of Streck BCT and PAXgene stabilised blood collection tubes for cell-free circulating DNA studies in plasma. Mol Diagn Ther, 21: 563-570.
  15. Willis, A.M., Smith, S.K., Meiser, B., Ballinger, M.L., Thomas, D.M., Young, M.A. 2017 Sociodemographic, psychosocial and clinical factors associated with uptake of genetic counseling for hereditary cancer: a systematic review. Clin Genet, 92: 121-133.