Australian Pancreatic Genome Initiative Lab

Selected Publications

DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association.

Lakis V, Lawlor RT, Newell F, Patch AM, Mafficini A, Sadanandam A, Koufariotis LT, Johnston RL, Leonard C, Wood S, Rusev B, Corbo V, Luchini C, Cingarlini S, Landoni L, Salvia R, Milella M, Chang D, Bailey P, Jamieson NB, Duthie F, Gingras MC, Muzny DM, Wheeler DA, Gibbs RA, Milione M; APGI; ARC-Net, Pederzoli P, Samra JS, Gill AJ, Johns AL, Pearson JV, Biankin AV, Grimmond SM, Waddell N, Nones K, Scarpa A.

Commun Biol. 2021 Feb 3;4(1):155. doi: 10.1038/s42003-020-01469-0.

Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer.

Dreyer SB, Upstill-Goddard R, Paulus-Hock V, Paris C, Lampraki EM, Dray E, Serrels B, Caligiuri G, Rebus S, Plenker D, Galluzzo Z, Brunton H, Cunningham R, Tesson M, Nourse C, Bailey UM, Jones M, Moran-Jones K, Wright DW, Duthie F, Oien K, Evers L, McKay CJ, McGregor GA, Gulati A, Brough R, Bajrami I, Pettitt S, Dziubinski ML, Candido J, Balkwill F, Barry ST, Grützmann R, Rahib L; Glasgow Precision Oncology Laboratory; Australian Pancreatic Cancer Genome Initiative, Johns A, Pajic M, Froeling FEM, Beer P, Musgrove EA, Petersen GM, Ashworth A, Frame MC, Crawford HC, Simeone DM, Lord C, Mukhopadhyay D, Pilarsky C, Tuveson DA, Cooke SL, Jamieson NB, Morton JP, Sansom OJ, Bailey PJ, Biankin AV, Chang DK.

Gastroenterology. 2020 Oct 8:S0016-5085(20)35229-X. doi: 10.1053/j.gastro.2020.09.043.

Precision Oncology in Surgery: Patient Selection for Operable Pancreatic Cancer.

Dreyer SB, Pinese M, Jamieson NB, Scarlett CJ, Colvin EK, Pajic M, Johns AL, Humphris JL, Wu J, Cowley MJ, Chou A, Nagrial AM, Chantrill L, Chin VT, Jones MD, Moran-Jones K, Carter CR, Dickson EJ, Samra JS, Merrett ND, Gill AJ, Kench JG, Duthie F, Miller DK, Cooke S, Aust D, Knösel T, Rümmele P, Grützmann R, Pilarsky C, Nguyen NQ, Musgrove EA, Bailey PJ, McKay CJ, Biankin AV, Chang DK; Australian Pancreatic Cancer Genome Initiative; Glasgow Precision Oncology Laboratory.

Ann Sug. 2020 Aug;272(2):366-376. doi: 10.1097/SLA.0000000000003143.

 

HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer.

Brunton H, Caligiuri G, Cunningham R, Upstill-Goddard R, Bailey UM, Garner IM, Nourse C, Dreyer S, Jones M, Moran-Jones K, Wright DW, Paulus-Hock V, Nixon C, Thomson G, Jamieson NB, McGregor GA, Evers L, McKay CJ, Gulati A, Brough R, Bajrami I, Pettitt SJ, Dziubinski ML, Barry ST, Grützmann R, Brown R, Curry E; Glasgow Precision Oncology Laboratory; Australian Pancreatic Cancer Genome Initiative, Pajic M, Musgrove EA, Petersen GM, Shanks E, Ashworth A, Crawford HC, Simeone DM, Froeling FEM, Lord CJ, Mukhopadhyay D, Pilarsky C, Grimmond SE, Morton JP, Sansom OJ, Chang DK, Bailey PJ, Biankin AV.

Cell Rep 2020 May 12;31(6):107625. doi: 10.1016/j.celrep.2020.107625.

 

Pan-cancer analysis of whole genomes.

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.

Nature 2020 Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6.

 

Targeting the undruggable in pancreatic cancer using nano-based gene silencing drugs.

Kokkinos J, Ignacio RMC, Sharbeen G, Boyer C, Gonzales-Aloy E, Goldstein D; Australian Pancreatic Cancer Genome Initiative (APGI).

Biomaterials. 2020 Jan 8;240:119742. doi: 10.1016/j.biomaterials.2019.119742.

 

International validation and update of the Amsterdam model for prediction of survival after pancreatoduodenectomy for pancreatic cancer.

van Roessel S, Strijker M, Steyerberg EW, Groen JV, Mieog JS, Groot VP, He J, De Pastena M, Marchegiani G, Bassi C, Suhool A, Jang JY, Busch OR, Halimi A, Zarantonello L, Groot Koerkamp B, Samra JS, Mittal A, Gill AJ, Bolm L, van Eijck CH, Abu Hilal M, Del Chiaro M, Keck T, Alseidi A, Wolfgang CL, Malleo G, Besselink MG.

Eur J Surg Oncol. 2019 Dec 28. pii: S0748-7983(19)31519-7. doi: doi: 1 10.1016/j.ejso.2019.12.023.

 

MCL-1 antagonism enhances the anti-invasive effects of dasatinib in pancreatic adenocarcinoma.

Castillo L, Young AIJ, Mawson A, Schafranek P, Steinmann AM, Nessem D, Parkin A, Johns A, Chou A, Law AMK, Lucas MC, Murphy KJ, Deng N, Gallego-Ortega D, Caldon CE, APGI, Timpson P, Pajic M, Ormandy CJ, Oakes SR.

Oncogene. 2019 Nov 18. doi: 10.1038/s41388-019-1091-0.

 

Development and validation of a targeted gene sequencing panel for application to disparate cancers.

McCabe MJ, Gauthier MA, Chan CL, Thompson TJ, De Sousa SMC, Puttick C, Grady JP, Gayevskiy V, Tao J, Ying K, Cipponi A, Deng N, Swarbrick A, Thomas ML, Lord RV, Johns AL, Kohonen-Corish M, O'Toole SA, Clark J, Mueller SA, Gupta R, McCormack AI, Dinger ME, Cowley MJ; kConFab.

Sci Rep. 2019 Nov 19;9(1):17052. doi: 10.1038/s41598-019-52000-3.

 

Genetic counselling and personalised risk assessment in the Australian pancreatic cancer screening program.

Dwarte T, McKay S, Johns A, Tucker K, Spigelman AD, Williams D, Stoita A.

Hered Cancer Clin Pract. 2019 Oct 23;17:30. doi: 10.1186/s13053-019-0129-1.

 

CAF hierarchy driven by pancreatic cancer cell p53-status creates a pro-metastatic and chemoresistant environment via perlecan.

Vennin C, Mélénec P, Rouet R, Nobis M, Cazet AS, Murphy KJ, Herrmann D, Reed DA, Lucas MC, Warren SC, Elgundi Z, Pinese M, Kalna G, Roden D, Samuel M, Zaratzian A, Grey ST, Da Silva A, Leung W; Australian Pancreatic Genome Initiative (APGI), Mathivanan S, Wang Y, Braithwaite AW, Christ D, Benda A, Parkin A, Phillips PA, Whitelock JM, Gill AJ, Sansom OJ, Croucher DR, Parker BL, Pajic M, Morton JP, Cox TR, Timpson P.

Nat Commun. 2019 Aug 12;10(1):3637. doi: 10.1038/s41467-019-10968-6.

 

ROBO2 is a stroma suppressor gene in the pancreas and acts via TGF-β signalling.

Pinho AV, Van Bulck M, Chantrill L, Arshi M, Sklyarova T, Herrmann D, Vennin C, Gallego-Ortega D, Mawson A, Giry-Laterriere M, Magenau A, Leuckx G, Baeyens L, Gill AJ, Phillips P, Timpson P, Biankin AV, Wu J, Rooman I.

Nat Commun. 2018 Nov 30;9(1):5083. doi: 10.1038/s41467-018-07497-z.

 

Precision Oncology in Surgery: Patient Selection for operable Pancreatic Cancer.

Dreyer SB, Pinese M, Jamieson NB, Scarlett CJ, Colvin EK, Pajic M, Johns AL, Humphris JL, Wu J, Cowley MJ, Chou A, Nagrial AM, Chantrill L, Chin VT, Jones MD, Moran-Jones K, Carter CR, Dickson EJ, Samra JS, Merrett ND, Gill AJ, Kench JG, Duthie F, Miller DK, Cooke S, Aust D, Knösel T, Rümmele P, Grützmann R, Pilarsky C, Nguyen NQ, Musgrove EA, Bailey PJ, McKay CJ, Biankin AV, Chang DK; Australian Pancreatic Cancer Genome Initiative; Glasgow Precision Oncology Laboratory.

Ann Surgery. 2018 Nov.doi: 1097/SLA.0000000000003143.

 

Provenance and risk in transfer of biological materials.

Nielsen J, Bubela T, Chalmers DRC, Johns A, Kahl L, Kamens J, Lawson C, Liddicoat J, McWhirter R, Monotti A, Scheibner J, Whitton T, Nicol D.

PLoS Biol. 2018 Aug 13;16 (8):e2006031. doi: 10.1371/journal.pbio.2006031.

 

The Path to reducing duplication of Human Research Ethics review in Australia.

Amber L. Johns, Dianne Nicol, Nik Zeps and Don Chalmers.

Medicine and Law. Number 1 March 2017 Vol 36.

 

Lost in translation: returning germline genetic results in genome-scale cancer research.

Johns AL, McKay SH, Humphris JL, Pinese M, Chantrill LA, Mead RS, Tucker K, Andrews L, Goodwin A, Leonard C, High HA, Nones K, Patch AM, Merrett ND, Pavlakis N, Kassahn KS, Samra JS, Miller DK, Chang DK, Pajic M, Australian Pancreatic Cancer Genome Initiative, Pearson JV, Grimmond SM, Waddell N, Zeps N, Gill AJ, Biankin AV.

Genome Med. 2017 Apr 28; 8(41). doi: 1186/s13073-017-0430-4.

 

SerpinB2 regulates stromal remodelling and local invasion in pancreatic cancer.

Harris NL, Vennin C, Conway JR, Vine KL, Pinese M, Cowley MJ, Shearer RF, Lucas MC, Herrmann D, Allam AH, Pajic M, Morton JP; Australian Pancreatic Cancer Genome Initiative, Biankin AV, Ranson M, Timpson P, Saunders DN.

Oncogene. 2017 Mar 27. doi: 10.1038/onc.2017.63. [Epub ahead of print].

 

Transient tissue priming via ROCK inhibition uncouples pancreatic cancer progression, sensitivity to chemotherapy, and metastasis.

Vennin C, Chin VT, Warren SC, Lucas MC, Herrmann D, Magenau A, Melenec P, Walters SN, Del Monte-Nieto G, Conway JR, Nobis M, Allam AH, McCloy RA, Currey N, Pinese M, Boulghourjian A, Zaratzian A, Adam AA, Heu C, Nagrial AM, Chou A, Steinmann A, Drury A, Froio D, Giry-Laterriere M, Harris NL, Phan T, Jain R, Weninger W, McGhee EJ, Whan R, Johns AL, Samra JS, Chantrill L, Gill AJ, Kohonen-Corish M, Harvey RP, Biankin AV; Australian Pancreatic Cancer Genome Initiative (APGI), Evans TR, Anderson KI, Grey ST, Ormandy CJ, Gallego-Ortega D, Wang Y, Samuel MS, Sansom OJ, Burgess A, Cox TR, Morton JP, Pajic M, Timpson P.

Sci Transl Med. 2017 Apr 5;9(384). pii: eaai8504. doi: 10.1126/scitranslmed.aai8504.

 

Whole-genome landscape of pancreatic neuroendocrine tumours.

Scarpa A, Chang DK, Nones K, Corbo V, Patch AM, Bailey P, Lawlor RT, Johns AL, Miller DK, Mafficini A, Rusev B, Scardoni M, Antonello D, Barbi S, Sikora KO, Cingarlini S, Vicentini C, McKay S, Quinn MC, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, McLean S, Nourse C, Nourbakhsh E, Wilson PJ, Anderson MJ, Fink JL, Newell F, Waddell N, Holmes O, Kazakoff SH, Leonard C, Wood S, Xu Q, Nagaraj SH, Amato E, Dalai I, Bersani S, Cataldo I, Dei Tos AP, Capelli P, Davì MV, Landoni L, Malpaga A, Miotto M, Whitehall VL, Leggett BA, Harris JL, Harris J, Jones MD, Humphris J, Chantrill LA, Chin V, Nagrial AM, Pajic M, Scarlett CJ, Pinho A, Rooman I, Toon C, Wu J, Pinese M, Cowley M, Barbour A, Mawson A, Humphrey ES, Colvin EK, Chou A, Lovell JA, Jamieson NB, Duthie F, Gingras MC, Fisher WE, Dagg RA, Lau LM, Lee M, Pickett HA, Reddel RR, Samra JS, Kench JG, Merrett ND, Epari K, Nguyen NQ, Zeps N, Falconi M, Simbolo M, Butturini G, Van Buren G, Partelli S, Fassan M; Australian Pancreatic Cancer Genome Initiative, Khanna KK, Gill AJ, Wheeler DA, Gibbs RA, Musgrove EA, Bassi C, Tortora G, Pederzoli P, Pearson JV, Waddell N, Biankin AV, Grimmond S.

Nature 2017 Mar 02; 543(?):65–71. doi:10.1038/nature21063.

 

Mitochondrial mutations and metabolic adaptation in pancreatic cancer.

Hardie RA, van Dam E, Cowley M, Han TL, Balaban S, Pajic M, Pinese M, Iconomou M, Shearer RF, McKenna J, Miller D, Waddell N, Pearson JV, Grimmond SM; Australian Pancreatic Cancer Genome Initiative, Sazanov L, Biankin AV, Villas-Boas S, Hoy AJ, Turner N, Saunders DN. Cancer Metab. 2017 Jan 30; 5(9) doi:1186/s40170-017-0164-1.

 

Hypermutation in pancreatic cancer.

Humphris JL, Patch A, Nones K, Bailey PJ, Johns AL, McKay S, Chang DK, Miller DK, Pajic M, Kassahn KS, Quinn MC, Bruxner JC, Christ AN, Harliwong I, drisoglu S, Manning S, Nourse C, Nourbakhsh E, Stone A, Wilson PJ, Anderson M, Fink JL, Holmes O, Kazakoff S, Leonard C, Newell F, Waddell N, Wood S, Mead RS, Xu Q, Wu J, Pinese M, Cowley MJ, Jones MD, Nagrial AM, Chin VT, Chantrill LA, Mawson A, Chou A, Scarlett CJ, Pinho AV, Rooman I, Giry-Laterriere M, Samra JS, Kench JG, Merrett ND, Toon CW, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, McKay CJ, Carter CR, Dickson EJ, Graham JS, Duthie F, Oien K, Hair J, Morton JP, Sansom OJ, Grützmann R, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL, Morgan RA, Lawlor RT, Rusev B, Corbo V, Salvia R, Cataldo I, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Hofmann O, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Gill AJ, Pearson JV, Grimmond SM, Waddell N, Biankin AV.

Gastroenterology 2017 Jan;152(1):68-74.e2. doi: 10.1053/j.gastro.2016.09.060.

 

Diagnosis and Management of Hereditary Pancreatic Cancer.

Humphris JL, Biankin AV;

Recent Results Cancer Res. 2016; 205:61-83. Doi: 10.1007/978-3-319-29998-3 5.

 

Genomic analyses identify molecular subtypes of pancreatic cancer.

Bailey P, Chang DK, Nones K, Johns AL, Patch AM, Gingras MC, Miller DK, Christ AN, Bruxner TJ, Quinn MC, Nourse C, etal., Biankin AV, Grimmond SM.

Nature 2016 March 3;531(7592):47-52.

 

Ampullary Cancers Harbor ELF3 Tumor Suppressor Gene Mutations and Exhibit Frequent WNT Dysregulation.

Gingras MC, Covington KR, Chang DK, Donehower LA, Gill AJ, Ittmann MM, Creighton CJ, Johns AL, Shinbrot E, Dewal N, Fisher WE, APGI, Pilarsky C, et al Gibbs RA.

Cell Rep. 2016 Feb 2;14(4):907-19.

 

 


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