By Mr John Grady

Book Chapters

Lin FP; Tran M; Thavaneswaran S; Grady JP; Kansara M; Chan J; Ballinger ML; Simes J; Thomas DM, 2025, 'Automating Precision Oncology Literature Curation: A Decision Tree Approach Using Large Language Models', in , pp. 248 - 252, http://dx.doi.org/10.3233/SHTI250839

Journal articles

Nagrial A; Carlino MS; Gunjur A; Brown MP; Harris S; Underhill C; Zielinski R; Kee D; Lam WS; Chan H; Harrup R; So J; Collins IM; Michael M; Chionh F; Uy C; Mariadason J; Torres J; Ballinger ML; Grady JP; Tavancheh E; Palmer J; Thomas DM; Wilkie K; Cebon J; Klein O, 2026, 'Nivolumab and Ipilimumab Combination Treatment in Patients with Advanced Intrahepatic Cholangiocarcinoma and Gallbladder Cancer: Results from the Phase II MoST-CIRCUIT Trial', Clinical Cancer Research an Official Journal of the American Association for Cancer Research, 32, pp. 3203 - 3212, http://dx.doi.org/10.1158/1078-0432.CCR-25-4009

Kong BY; Lin FP-Y; Espinoza D; Aberoumand M; Thavaneswaran S; Meniawy T; Desai J; Harrup R; Nayagam SS; Charakidis M; Cuff K; Sebastian L; Lee CK; Wheeler P; Kansara M; Grady JP; Thomas DM; Ballinger ML; Simes J; Goldstein D, 2026, 'Tucatinib and trastuzumab in advanced cancers with HER2 mutations or amplifications: a molecular screening and therapeutics (MoST) program substudy', npj Precision Oncology, http://dx.doi.org/10.1038/s41698-026-01590-z

Cote GM; Aberoumand M; Choy E; Sebastian L; Mazzola E; Grimison P; Merriam P; Ballinger M; Thavaneswaran S; Lin F; Grady JP; Millward M; Brown MP; Harrup R; Espinoza D; Demetri G; Littlefield BA; Simes RJ; George S; Thomas D, 2026, 'A Phase 2 Study of Eribulin in Patients with Metastatic Angiosarcoma and Epithelioid Hemangioendothelioma', Clinical Cancer Research, 32, pp. 2206 - 2213, http://dx.doi.org/10.1158/1078-0432.CCR-25-3362

Lin FP; Thavaneswaran S; Grady JP; Napier CE; Kansara M; Sebastian L; Kee D; Desai J; Zaheed M; Chinchen S; Oakes SR; Blackburn J; Scott HS; Glover A; Fox SB; Goldstein D; Leo P; Amanuel B; Mersiades A; Millward M; Brown MP; Charakidis M; Pokorny AMJ; Craft P; Espinoza D; Grimison P; Harrup R; Joshua AM; O'byrne K; Lee CK; Cowley MJ; Ballinger ML; Simes J; Thomas DM, 2026, 'Genomic Therapy Matching in Rare and Refractory Cancers', JAMA Oncology, 12, pp. 458 - 467, http://dx.doi.org/10.1001/jamaoncol.2026.0127

Koh B; Thavaneswaran S; Lin F; Grady J; Maddula M; Haghighi KS; Kansara M; Huang ML; Ballinger ML; Simes J; Thomas DM; Goldstein D, 2026, 'Exceptional Response to Durvalumab and Tremelimumab in Pancreatic Acinar Cell Carcinoma With Ultramutated Phenotype Associated With a DNA Polymerase-ε Mutation', JCO Precision Oncology, 10, http://dx.doi.org/10.1200/PO-25-01003

Carlino MS; Gao B; Michael M; Marshall H; Gunjur A; Chan H; Zielinski R; So J; Harris SJ; Kee D; Collins IM; Lam WS; Lyle M; Underhill C; Brown MP; Harrup R; Wong SF; Grady J; Ballinger M; Tavancheh E; Thomas DM; Palmer J; Wilkie K; Cebon J; Klein O, 2026, 'Nivolumab and Ipilimumab in Advanced Mismatch Repair–Deficient/Microsatellite Instability–High Noncolorectal Cancers: A Nonrandomized Clinical Trial', JAMA Oncology, 12, pp. 39 - 47, http://dx.doi.org/10.1001/jamaoncol.2025.4721

Southi N; Sim H-W; Grady J; Ballinger M; Thomas D; Thavaneswaran S, 2026, '145P Characterising homologous recombination deficiencies in gliomas', ESMO Open, 11, pp. 106288 - 106288, http://dx.doi.org/10.1016/j.esmoop.2026.106288

Jung MS; Poltavets V; Skhinas JN; Tax G; Kamili A; Xie J; Ghamrawi S; Graber P; Mao J; Wong-Erasmus M; Cui L; Kimpton K; Venkat P; Mayoh C; Lin A; Fleuren EDG; Fordham AM; Barger Z; Grady J; Thomas DM; Du EY; Graf NS; Cowley MJ; Gifford AJ; Fletcher JI; Lau LMS; Dolman MEM; Gooding JJ; Kavallaris M; Dolman E, 2025, 'High-throughput 3D engineered paediatric tumour models for precision medicine', Molecular Systems Biology, 21, pp. 1748 - 1777, http://dx.doi.org/10.1038/s44320-025-00152-y

Thavaneswaran S; Lin F; Espinoza D; Grady J; Kok PS; Chinchen S; Pavlakis N; Andelkovic V; Charakidis M; Craft P; Brown M; Desai J; Lau P; Kansara M; Simes J; Thomas D, 2025, 'A signal-seeking phase 2 study of tremelimumab in advanced cancers with high tumour mutational burden', Npj Precision Oncology, 9, http://dx.doi.org/10.1038/s41698-025-01156-5

Gao B; Carlino MS; Michael M; Underhill C; Marshall H; Gunjur A; So J; Kee D; Antill Y; Lam WS; Chan H; Harrup R; Hamilton A; Grady J; Ballinger M; Tavancheh E; Yoon WH; Palmer J; Thomas D; Wilkie K; Cebon J; Klein O, 2025, 'Nivolumab and Ipilimumab Combination Treatment in Advanced Ovarian and Endometrial Clear Cell Cancers: A Nonrandomized Clinical Trial', JAMA Oncology, 11, pp. 982 - 989, http://dx.doi.org/10.1001/jamaoncol.2025.1916

Thavaneswaran S; Sim HW; Grady J; Espinoza D; Huang ML; Lin F; McGrath M; Desai J; Charakidis M; Brown M; Kansara M; Simes J; Thomas D, 2025, 'A phase II trial of larotrectinib in tumors with NTRK fusions or extremes of NTRK mRNA overexpression identified by comprehensive genomic profiling', Oncologist, 30, http://dx.doi.org/10.1093/oncolo/oyae339

Zhu Y; Lin FP-Y; So JY; Oh EW; Philipsen S; Thomas DM; Grady JP; Lawrence BJ; Wilson MK, 2025, 'Actionability of genomic alterations in the Molecular Screening and Therapeutics (MoST) program in New Zealand (NZ) depending on residence in NZ or Australia.', JOURNAL OF CLINICAL ONCOLOGY, 43, pp. E13763 - E13763, http://dx.doi.org/10.1200/JCO.2025.43.16_suppl.e13763

Lin FP-Y; Goldstein D; Grady JP; Napier C; Thavaneswaran S; Pitiyarachchi O; Kansara M; Chantrill LA; Sjoquist K; Thornton K; Raina A; Magenau A; Simes J; Ballinger ML; Sharbeen G; Timpson P; Pajic M; Phillips P; Thomas DM, 2025, 'Genomic and outcome analysis of recurrent versus de novo metastatic pancreatic ductal adenocarcinoma (PDAC) receiving systemic therapy: Results from the Australian MoST and CaSP screening programs.', JOURNAL OF CLINICAL ONCOLOGY, 43, pp. 4120 - 4120, http://dx.doi.org/10.1200/JCO.2025.43.16_suppl.4120

Lin FP-Y; Huang ML; Grady JP; Thavaneswaran S; Kansara M; Napier C; Ballinger ML; Simes J; Thomas DM, 2025, 'Machine learning-based classification of cancer types using genomic profiling data from the Australian Molecular Screening and Therapeutics (MoST) program.', JOURNAL OF CLINICAL ONCOLOGY, 43, pp. e13683 - e13683, http://dx.doi.org/10.1200/JCO.2025.43.16_suppl.e13683

Novis E; Glover A; Grady JP; Silvestri A; Thavaneswaran S; Lin F; Ballinger ML; Thomas DM, 2025, 'Oncogenic mutations in the TP53 and PI-3 kinase/AKT pathway are independent predictors of survival for advanced thyroid cancer: Analysis from the Molecular Screening and Therapeutics (MoST) program', Surgery United States, 177, http://dx.doi.org/10.1016/j.surg.2024.05.058

Kansara M; Thavaneswaran S; Lin FP; Kok P-S; Grady J; Thomas H; Corpuz T; Mundra P; Lu J; Ballinger M; Desai J; Harrup RA; Craft P; Charakidis M; O'Byrne KJ; Selva-Nayagam S; Millwar M; Grimiso P; Simes J; Thomas D, 2025, 'A phase II trial of palbociclib and avelumab in advanced solid tumours with CDK4/6 pathway alterations', ANNALS OF ONCOLOGY, 36, http://dx.doi.org/10.1016/j.annonc.2025.08.2175

Gaughran G; Zaheed M; Harris SJ; Napier C; Yap M; Bellinger M; Grady J; Kee D; Caillet V; Davies A; Thavaneswaran S; Thomas DM, 2025, 'HIF2α pathway aberrations across tumour types: A rare but actionable entity with high germline conversion', ANNALS OF ONCOLOGY, 36, http://dx.doi.org/10.1016/j.annonc.2025.10.1192

Pavlakis N; Lee CK; Ballinger ML; Brown CSB; Grady JP; Lin F; Thavaneswaran S; Mersiades AJ; Di-Xin Zhou D; Lee J; John T; Napier CE; Cummins MM; Collignon E; Sebastian L; Turnbull OMH; Simes J; Thomas DM; Solomon BJ, 2025, 'P2.06.61 ASPiRATION. Australian Nationwide Cohort Study to Assess Impact of Comprehensive Genomic Profiling in Metastatic Lung Cancer', Journal of Thoracic Oncology, 20, pp. S318 - S319, http://dx.doi.org/10.1016/j.jtho.2025.09.595

Gaughran G; Mamrot J; Fitzgerald S; Kee D; Napier C; Harris SJ; Thavaneswaran S; Grady J; Davies A; Bellinger M; Thomas DM, 2025, 'Real-world experience of liquid biopsy (LBx) vs tissue-based comprehensive genomic profiling (tCGP)', ANNALS OF ONCOLOGY, 36, http://dx.doi.org/10.1016/j.annonc.2025.10.1211

Thavaneswaran S; Lin F; Grady JP; Espinoza D; Huang ML; Chinchen S; Sebastian L; Kansara M; Mersiades T; Lee CK; Desai J; Grimison P; Brown M; Millward M; Harrup R; O’Byrne K; Nagrial A; Craft P; Simes J; Joshua AM; Thomas DM, 2024, 'A signal-seeking phase 2 study of Trastuzumab emtansine in tumours harbouring HER2 amplification or mutation', Npj Precision Oncology, 8, http://dx.doi.org/10.1038/s41698-024-00698-4

Sharaf R; Jin DX; Grady J; Napier C; Ebot E; Frampton GM; Albacker LA; Thomas DM; Montesion M, 2023, 'A pan-sarcoma landscape of telomeric content shows that alterations in RAD51B and GID4 are associated with higher telomeric content', Npj Genomic Medicine, 8, http://dx.doi.org/10.1038/s41525-023-00369-6

Thavaneswaran S; Kansara M; Lin F; Espinoza D; Grady JP; Lee CK; Ballinger ML; Sebastian L; Corpuz T; Qiu MR; Mundra P; Bailey CG; Schmitz U; Simes J; Joshua AM; Thomas DM, 2023, 'A signal-seeking Phase 2 study of olaparib and durvalumab in advanced solid cancers with homologous recombination repair gene alterations', British Journal of Cancer, 129, pp. 475 - 485, http://dx.doi.org/10.1038/s41416-023-02311-0

Kansara M; Lin FP-Y; Thavaneswaran S; Napier CE; Grady JP; Ballinger ML; Simes J; Thomas DM, 2023, 'Genomic alterations associated with response to immune checkpoint inhibitors in rare cancers: A biomarker exploration study from the Australian Molecular Screening and Therapeutics (MoST) Program.', Journal of Clinical Oncology, 41, pp. 2594 - 2594, http://dx.doi.org/10.1200/jco.2023.41.16_suppl.2594

Thavaneswaran S; Lin FP-Y; Napier CE; Grady JP; Ballinger ML; Kansara M; Grimison PS; Pavlakis N; Wong MK; Sjoquist KM; Goldstein D; Chantrill LA; Simes J; Thomas DM, 2023, 'Genomic targetability and survival outcomes of biliary tract cancers (BTC): A retrospective cohort study of the Australian Molecular Screening and Therapeutics (MoST) program', JOURNAL OF CLINICAL ONCOLOGY, 41, http://dx.doi.org/10.1200/JCO.2023.41.16_suppl.4093

Lin FP-Y; Thavaneswaran S; Napier CE; Grady JP; Kansara M; Sebastian L; Kee D; Zaheed M; Millward M; Brown MP; Charakidis M; Craft PS; Grimison PS; Harrup RA; O'Byrne KJ; Desai J; Lee CK; Ballinger ML; Simes J; Thomas DM, 2023, 'Genomic therapy matching in rare and refractory cancers: Updated results from a retrospective cohort study in the Molecular Screening and Therapeutic (MoST) program', JOURNAL OF CLINICAL ONCOLOGY, 41, http://dx.doi.org/10.1200/JCO.2023.41.16_suppl.1540

Thavaneswaran S; Mersiades A; Lin FP-Y; Espinoza D; Grady JP; Lee CK; Desai J; Brown MP; Grimison PS; O'Byrne KJ; Harrup RA; Nagrial A; Sebastian L; Chinchen S; Kansara M; Craft PS; Millward M; Simes J; Joshua AM; Thomas DM, 2023, 'Trastuzumab emtansine (T-DM1) in advanced cancers with HER2 mutations or amplification: Results from the Molecular Screening and Therapeutics (MoST) Program substudy', JOURNAL OF CLINICAL ONCOLOGY, 41, http://dx.doi.org/10.1200/JCO.2023.41.16_suppl.3127

Sharaf R; Jin DX; Grady J; Frampton GM; Albacker LA; Thomas D; Montesion M, 2022, '1487MO A pan-sarcoma investigation of genetic alterations associated with high telomeric content', Annals of Oncology, 33, pp. S1226 - S1227, http://dx.doi.org/10.1016/j.annonc.2022.07.1590

Thavaneswaran S; Chan WY; Asghari R; Grady JP; Deegan M; Jansen VM; Thomas DM, 2022, 'Clinical Response to Seribantumab, an Anti-Human Epidermal Growth Factor Receptor-3 Immunoglobulin 2 Monoclonal Antibody, in a Patient With Metastatic Pancreatic Ductal Adenocarcinoma Harboring an NRG1 Fusion', JCO PRECISION ONCOLOGY, 6, http://dx.doi.org/10.1200/PO.22.00263

Lin FP; Thavaneswaran S; Grady JP; Ballinger M; Kansara M; Oakes SR; Desai J; Lee CK; Simes J; Thomas DM, 2021, 'Criteria-based curation of a therapy-focused compendium to support treatment recommendations in precision oncology', Npj Precision Oncology, 5, pp. 58, http://dx.doi.org/10.1038/s41698-021-00194-z

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, 33, pp. 1896 - 1909, http://dx.doi.org/10.1038/s41379-020-0576-2

Joshua AM; Prawira A; Thavaneswaran S; Cosman R; Lee CK; Sjoquist KM; Simes J; Thomas DM; Espinoza D; Sebastian L; Ballinger ML; Hague W; Chinchen S; Collignon E; Kansara M; Palacios T; Grady J; Barker H; Thornton K, 2020, 'A signal-seeking trial of olaparib and durvalumab in homologous repair-deficient tumors: A sub-study of the cancer molecular screening and therapeutics (MoST) program.', Journal of Clinical Oncology, 38, pp. 3073 - 3073, http://dx.doi.org/10.1200/jco.2020.38.15_suppl.3073

Shukla A; Nguyen THM; Moka SB; Ellis JJ; Grady JP; Oey H; Cristino AS; Khanna KK; Kroese DP; Krause L; Dray E; Fink JL; Duijf PHG, 2020, 'Chromosome arm aneuploidies shape tumour evolution and drug response', Nature Communications, 11, pp. 449 - 449, http://dx.doi.org/10.1038/s41467-020-14286-0

Smith AM; Zhang CRC; Cristino AS; Grady JP; Fink JL; Moore AS, 2020, 'Erratum: PTEN deletion drives acute myeloid leukemia resistance to MEK inhibitors.', Oncotarget, 11, pp. 305, http://dx.doi.org/10.18632/oncotarget.27402

McCabe M; Gauthier M-E; Chan C-L; Thompson T; De Sousa S; Puttick C; Grady J; Gayevskiy V; Tao J; Ying K; Cipponi A; Deng N; Swarbrick A; Thomas M; kConFab ; Lord R; Johns A; Kohonen-Corish M; O'Toole S; Clark J; Mueller S; Gupta R; McCormack A; Dinger M; Cowley M; Bastick P; Friedlander M; Colley A; Andrews L; Young M-A; Tucker K; Williams R; Aghmesheh M, 2019, 'Development and validation of a targeted gene sequencing panel for application to disparate cancers', Scientific Reports, 9, pp. 17052, http://dx.doi.org/10.1038/s41598-019-52000-3

Smith AM; Zhang CRC; Cristino AS; Grady JP; Fink JL; Moore AS, 2019, 'PTEN deletion drives acute myeloid leukemia resistance to MEK inhibitors.', Oncotarget, 10, pp. 5755 - 5767, http://dx.doi.org/10.18632/oncotarget.27206

McCabe MJ; Pinese M; Chan CL; Sheriff N; Thompson TJ; Grady J; Wong M; Gauthier MEA; 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; Cowley MJ; Wong-Erasmus M, 2019, 'Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases', Cold Spring Harbor Molecular Case Studies, 5, pp. a003764, http://dx.doi.org/10.1101/mcs.a003764

Hayhurst H; Anagnostou M-E; Bogle HJ; Grady JP; Taylor RW; Bindoff LA; McFarland R; Turnbull DM; Lax NZ, 2019, 'Dissecting the neuronal vulnerability underpinning Alpers' syndrome: a clinical and neuropathological study.', Brain Pathol, 29, pp. 97 - 113, http://dx.doi.org/10.1111/bpa.12640

Dutta AK; Fink JL; Grady JP; Morgan GJ; Mullighan CG; To LB; Hewett DR; Zannettino ACW, 2019, 'Subclonal evolution in disease progression from MGUS/SMM to multiple myeloma is characterised by clonal stability.', Leukemia, 33, pp. 457 - 468, http://dx.doi.org/10.1038/s41375-018-0206-x

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, 51, pp. S83 - S83, http://dx.doi.org/10.1016/j.pathol.2018.12.210

Parrish RR; Grady J; Codadu NK; Trevelyan AJ; Racca C, 2018, 'Simultaneous profiling of activity patterns in multiple neuronal subclasses.', J Neurosci Methods, 303, pp. 16 - 29, http://dx.doi.org/10.1016/j.jneumeth.2018.03.012

Sithamparanathan S; Rocha MC; Parikh JD; Rygiel KA; Falkous G; Grady J; Hollingsworth KG; Trenell MI; Taylor RW; Turnbull DM; Gorman GS; Corris P, 2018, 'Skeletal Muscle Mitochondrial Oxidative Phosphorylation Function in Idiopathic Pulmonary Arterial Hypertension – in Vivo and in Vitro Study', American Journal of Respiratory and Critical Care Medicine, 197, pp. a2443 - a2443, http://dx.doi.org/10.1164/ajrccm-conference.2018.197.1_meetingabstracts.a2443

Reeve AK; Grady JP; Cosgrave EM; Bennison E; Chen C; Hepplewhite PD; Morris CM, 2018, 'Mitochondrial dysfunction within the synapses of substantia nigra neurons in Parkinson's disease', NPJ PARKINSONS DISEASE, 4, http://dx.doi.org/10.1038/s41531-018-0044-6

Lin C-Y; Shukla A; Grady JP; Fink JL; Dray E; Duijf PHG, 2018, 'Translocation Breakpoints Preferentially Occur in Euchromatin and Acrocentric Chromosomes.', Cancers (Basel), 10, http://dx.doi.org/10.3390/cancers10010013

Parrish RR; Grady J; Codadu NK; Racca C; Trevelyan AJ, 2018, 'Graphical user interface for simultaneous profiling of activity patterns in multiple neuronal subclasses.', Data Brief, 20, pp. 226 - 233, http://dx.doi.org/10.1016/j.dib.2018.07.069

Su T; Grady JP; Afshar S; McDonald SA; Taylor RW; Turnbull DM; Greaves LC, 2018, 'Inherited pathogenic mitochondrial DNA mutations and gastrointestinal stem cell populations.', J Pathol, 246, pp. 427 - 432, http://dx.doi.org/10.1002/path.5156

Grady JP; Pickett SJ; Ng YS; Alston CL; Blakely EL; Hardy SA; Feeney CL; Bright AA; Schaefer AM; Gorman GS; McNally RJ; Taylor RW; Turnbull DM; McFarland R, 2018, 'mtDNA heteroplasmy level and copy number indicate disease burden in m.3243A>G mitochondrial disease.', EMBO Mol Med, 10, http://dx.doi.org/10.15252/emmm.201708262

Rocha MC; Rosa HS; Grady JP; Blakely EL; He L; Romain N; Haller RG; Newman J; McFarland R; Ng YS; Gorman GS; Schaefer AM; Tuppen HA; Taylor RW; Turnbull DM, 2018, 'Pathological mechanisms underlying single large-scale mitochondrial DNA deletions.', Ann Neurol, 83, pp. 115 - 130, http://dx.doi.org/10.1002/ana.25127

Pickett SJ; Grady JP; Ng YS; Gorman GS; Schaefer AM; Wilson IJ; Cordell HJ; Turnbull DM; Taylor RW; McFarland R, 2018, 'Phenotypic heterogeneity in m.3243A>G mitochondrial disease: The role of nuclear factors.', Ann Clin Transl Neurol, 5, pp. 333 - 345, http://dx.doi.org/10.1002/acn3.532

Sithamparanathan S; Rocha MC; Parikh JD; Rygiel KA; Falkous G; Grady JP; Hollingsworth KG; Trenell MI; Taylor RW; Turnbull DM; Gorman GS; Corris PA, 2018, 'Skeletal muscle mitochondrial oxidative phosphorylation function in idiopathic pulmonary arterial hypertension: in vivo and in vitro study.', Pulm Circ, 8, pp. 2045894018768290, http://dx.doi.org/10.1177/2045894018768290

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