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Items: 21

1.

Meta-Analysis of 1,200 Transcriptomic Profiles Identifies a Prognostic Model for Pancreatic Ductal Adenocarcinoma.

Sandhu V, Labori KJ, Borgida A, Lungu I, Bartlett J, Hafezi-Bakhtiari S, Denroche RE, Jang GH, Pasternack D, Mbaabali F, Watson M, Wilson J, Kure EH, Gallinger S, Haibe-Kains B.

JCO Clin Cancer Inform. 2019 May;3:1-16. doi: 10.1200/CCI.18.00102.

2.

NRG1 Gene Fusions Are Recurrent, Clinically Actionable Gene Rearrangements in KRAS Wild-Type Pancreatic Ductal Adenocarcinoma.

Jones MR, Williamson LM, Topham JT, Lee MKC, Goytain A, Ho J, Denroche RE, Jang G, Pleasance E, Shen Y, Karasinska JM, McGhie JP, Gill S, Lim HJ, Moore MJ, Wong HL, Ng T, Yip S, Zhang W, Sadeghi S, Reisle C, Mungall AJ, Mungall KL, Moore RA, Ma Y, Knox JJ, Gallinger S, Laskin J, Marra MA, Schaeffer DF, Jones SJM, Renouf DJ.

Clin Cancer Res. 2019 May 8. doi: 10.1158/1078-0432.CCR-19-0191. [Epub ahead of print]

PMID:
31068372
3.

Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases.

Connor AA, Denroche RE, Jang GH, Lemire M, Zhang A, Chan-Seng-Yue M, Wilson G, Grant RC, Merico D, Lungu I, Bartlett JMS, Chadwick D, Liang SB, Eagles J, Mbabaali F, Miller JK, Krzyzanowski P, Armstrong H, Luo X, Jorgensen LGT, Romero JM, Bavi P, Fischer SE, Serra S, Hafezi-Bakhtiari S, Caglar D, Roehrl MHA, Cleary S, Hollingsworth MA, Petersen GM, Thayer S, Law CHL, Nanji S, Golan T, Smith AL, Borgida A, Dodd A, Hedley D, Wouters BG, O'Kane GM, Wilson JM, Zogopoulos G, Notta F, Knox JJ, Gallinger S.

Cancer Cell. 2019 Feb 11;35(2):267-282.e7. doi: 10.1016/j.ccell.2018.12.010. Epub 2019 Jan 24.

PMID:
30686769
4.

Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer.

Gendoo DMA, Denroche RE, Zhang A, Radulovich N, Jang GH, Lemire M, Fischer S, Chadwick D, Lungu IM, Ibrahimov E, Cao PJ, Stein LD, Wilson JM, Bartlett JMS, Tsao MS, Dhani N, Hedley D, Gallinger S, Haibe-Kains B.

PLoS Comput Biol. 2019 Jan 10;15(1):e1006596. doi: 10.1371/journal.pcbi.1006596. eCollection 2019 Jan.

5.

Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer.

Tiriac H, Belleau P, Engle DD, Plenker D, Deschênes A, Somerville TDD, Froeling FEM, Burkhart RA, Denroche RE, Jang GH, Miyabayashi K, Young CM, Patel H, Ma M, LaComb JF, Palmaira RLD, Javed AA, Huynh JC, Johnson M, Arora K, Robine N, Shah M, Sanghvi R, Goetz AB, Lowder CY, Martello L, Driehuis E, LeComte N, Askan G, Iacobuzio-Donahue CA, Clevers H, Wood LD, Hruban RH, Thompson E, Aguirre AJ, Wolpin BM, Sasson A, Kim J, Wu M, Bucobo JC, Allen P, Sejpal DV, Nealon W, Sullivan JD, Winter JM, Gimotty PA, Grem JL, DiMaio DJ, Buscaglia JM, Grandgenett PM, Brody JR, Hollingsworth MA, O'Kane GM, Notta F, Kim E, Crawford JM, Devoe C, Ocean A, Wolfgang CL, Yu KH, Li E, Vakoc CR, Hubert B, Fischer SE, Wilson JM, Moffitt R, Knox J, Krasnitz A, Gallinger S, Tuveson DA.

Cancer Discov. 2018 Sep;8(9):1112-1129. doi: 10.1158/2159-8290.CD-18-0349. Epub 2018 May 31.

PMID:
29853643
6.

Recapitulating the clinical scenario of BRCA-associated pancreatic cancer in pre-clinical models.

Golan T, Stossel C, Atias D, Buzhor E, Halperin S, Cohen K, Raitses-Gurevich M, Glick Y, Raskin S, Yehuda D, Feldman A, Schvimer M, Friedman E, Karni R, Wilson JM, Denroche RE, Lungu I, Bartlett JMS, Mbabaali F, Gallinger S, Berger R.

Int J Cancer. 2018 Jul 1;143(1):179-183. doi: 10.1002/ijc.31292. Epub 2018 Feb 23.

PMID:
29396858
7.

Mutations in Mitochondrial DNA From Pancreatic Ductal Adenocarcinomas Associate With Survival Times of Patients and Accumulate as Tumors Progress.

Hopkins JF, Denroche RE, Aguiar JA, Notta F, Connor AA, Wilson JM, Stein LD, Gallinger S, Boutros PC.

Gastroenterology. 2018 May;154(6):1620-1624.e5. doi: 10.1053/j.gastro.2018.01.029. Epub 2018 Mar 29.

PMID:
29378198
8.

Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial.

Aung KL, Fischer SE, Denroche RE, Jang GH, Dodd A, Creighton S, Southwood B, Liang SB, Chadwick D, Zhang A, O'Kane GM, Albaba H, Moura S, Grant RC, Miller JK, Mbabaali F, Pasternack D, Lungu IM, Bartlett JMS, Ghai S, Lemire M, Holter S, Connor AA, Moffitt RA, Yeh JJ, Timms L, Krzyzanowski PM, Dhani N, Hedley D, Notta F, Wilson JM, Moore MJ, Gallinger S, Knox JJ.

Clin Cancer Res. 2018 Mar 15;24(6):1344-1354. doi: 10.1158/1078-0432.CCR-17-2994. Epub 2017 Dec 29.

9.

Exome-Wide Association Study of Pancreatic Cancer Risk.

Grant RC, Denroche RE, Borgida A, Virtanen C, Cook N, Smith AL, Connor AA, Wilson JM, Peterson G, Roberts NJ, Klein AP, Grimmond SM, Biankin A, Cleary S, Moore M, Lemire M, Zogopoulos G, Stein L, Gallinger S.

Gastroenterology. 2018 Feb;154(3):719-722.e3. doi: 10.1053/j.gastro.2017.10.015. Epub 2017 Oct 24.

10.

Pancreatic cancer ascites xenograft-an expeditious model mirroring advanced therapeutic resistant disease.

Golan T, Stossel C, Schvimer M, Atias D, Halperin S, Buzhor E, Raitses-Gurevich M, Cohen K, Pri-Chen S, Wilson J, Denroche RE, Lungu I, Bartlett JMS, Mbabaali F, Yarden Y, Nataraj NB, Gallinger S, Berger R.

Oncotarget. 2017 Jun 20;8(25):40778-40790. doi: 10.18632/oncotarget.17253.

11.

Genomic hallmarks of localized, non-indolent prostate cancer.

Fraser M, Sabelnykova VY, Yamaguchi TN, Heisler LE, Livingstone J, Huang V, Shiah YJ, Yousif F, Lin X, Masella AP, Fox NS, Xie M, Prokopec SD, Berlin A, Lalonde E, Ahmed M, Trudel D, Luo X, Beck TA, Meng A, Zhang J, D'Costa A, Denroche RE, Kong H, Espiritu SM, Chua ML, Wong A, Chong T, Sam M, Johns J, Timms L, Buchner NB, Orain M, Picard V, Hovington H, Murison A, Kron K, Harding NJ, P'ng C, Houlahan KE, Chu KC, Lo B, Nguyen F, Li CH, Sun RX, de Borja R, Cooper CI, Hopkins JF, Govind SK, Fung C, Waggott D, Green J, Haider S, Chan-Seng-Yue MA, Jung E, Wang Z, Bergeron A, Dal Pra A, Lacombe L, Collins CC, Sahinalp C, Lupien M, Fleshner NE, He HH, Fradet Y, Tetu B, van der Kwast T, McPherson JD, Bristow RG, Boutros PC.

Nature. 2017 Jan 19;541(7637):359-364. doi: 10.1038/nature20788. Epub 2017 Jan 9.

PMID:
28068672
12.

Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns.

Notta F, Chan-Seng-Yue M, Lemire M, Li Y, Wilson GW, Connor AA, Denroche RE, Liang SB, Brown AM, Kim JC, Wang T, Simpson JT, Beck T, Borgida A, Buchner N, Chadwick D, Hafezi-Bakhtiari S, Dick JE, Heisler L, Hollingsworth MA, Ibrahimov E, Jang GH, Johns J, Jorgensen LG, Law C, Ludkovski O, Lungu I, Ng K, Pasternack D, Petersen GM, Shlush LI, Timms L, Tsao MS, Wilson JM, Yung CK, Zogopoulos G, Bartlett JM, Alexandrov LB, Real FX, Cleary SP, Roehrl MH, McPherson JD, Stein LD, Hudson TJ, Campbell PJ, Gallinger S.

Nature. 2017 Feb 2;542(7639):124. doi: 10.1038/nature20164. Epub 2016 Nov 16. No abstract available.

PMID:
27851734
13.

Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma.

Connor AA, Denroche RE, Jang GH, Timms L, Kalimuthu SN, Selander I, McPherson T, Wilson GW, Chan-Seng-Yue MA, Borozan I, Ferretti V, Grant RC, Lungu IM, Costello E, Greenhalf W, Palmer D, Ghaneh P, Neoptolemos JP, Buchler M, Petersen G, Thayer S, Hollingsworth MA, Sherker A, Durocher D, Dhani N, Hedley D, Serra S, Pollett A, Roehrl MHA, Bavi P, Bartlett JMS, Cleary S, Wilson JM, Alexandrov LB, Moore M, Wouters BG, McPherson JD, Notta F, Stein LD, Gallinger S.

JAMA Oncol. 2017 Jun 1;3(6):774-783. doi: 10.1001/jamaoncol.2016.3916.

14.

A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns.

Notta F, Chan-Seng-Yue M, Lemire M, Li Y, Wilson GW, Connor AA, Denroche RE, Liang SB, Brown AM, Kim JC, Wang T, Simpson JT, Beck T, Borgida A, Buchner N, Chadwick D, Hafezi-Bakhtiari S, Dick JE, Heisler L, Hollingsworth MA, Ibrahimov E, Jang GH, Johns J, Jorgensen LG, Law C, Ludkovski O, Lungu I, Ng K, Pasternack D, Petersen GM, Shlush LI, Timms L, Tsao MS, Wilson JM, Yung CK, Zogopoulos G, Bartlett JM, Alexandrov LB, Real FX, Cleary SP, Roehrl MH, McPherson JD, Stein LD, Hudson TJ, Campbell PJ, Gallinger S.

Nature. 2016 Oct 20;538(7625):378-382. doi: 10.1038/nature19823. Epub 2016 Oct 12. Erratum in: Nature. 2017 Feb 2;542(7639):124.

15.

A cancer cell-line titration series for evaluating somatic classification.

Denroche RE, Mullen L, Timms L, Beck T, Yung CK, Stein L, McPherson JD, Brown AM.

BMC Res Notes. 2015 Dec 26;8:823. doi: 10.1186/s13104-015-1803-7.

16.

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DT, Gut IG.

Nat Commun. 2015 Dec 9;6:10001. doi: 10.1038/ncomms10001.

17.

Fine mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci.

Kachuri L, Amos CI, McKay JD, Johansson M, Vineis P, Bueno-de-Mesquita HB, Boutron-Ruault MC, Johansson M, Quirós JR, Sieri S, Travis RC, Weiderpass E, Le Marchand L, Henderson BE, Wilkens L, Goodman GE, Chen C, Doherty JA, Christiani DC, Wei Y, Su L, Tworoger S, Zhang X, Kraft P, Zaridze D, Field JK, Marcus MW, Davies MPA, Hyde R, Caporaso NE, Landi MT, Severi G, Giles GG, Liu G, McLaughlin JR, Li Y, Xiao X, Fehringer G, Zong X, Denroche RE, Zuzarte PC, McPherson JD, Brennan P, Hung RJ.

Carcinogenesis. 2016 Jan;37(1):96-105. doi: 10.1093/carcin/bgv165. Epub 2015 Nov 20.

18.

Spatial genomic heterogeneity within localized, multifocal prostate cancer.

Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, Lalonde E, Meng A, Hennings-Yeomans PH, McPherson A, Sabelnykova VY, Zia A, Fox NS, Livingstone J, Shiah YJ, Wang J, Beck TA, Have CL, Chong T, Sam M, Johns J, Timms L, Buchner N, Wong A, Watson JD, Simmons TT, P'ng C, Zafarana G, Nguyen F, Luo X, Chu KC, Prokopec SD, Sykes J, Dal Pra A, Berlin A, Brown A, Chan-Seng-Yue MA, Yousif F, Denroche RE, Chong LC, Chen GM, Jung E, Fung C, Starmans MH, Chen H, Govind SK, Hawley J, D'Costa A, Pintilie M, Waggott D, Hach F, Lambin P, Muthuswamy LB, Cooper C, Eeles R, Neal D, Tetu B, Sahinalp C, Stein LD, Fleshner N, Shah SP, Collins CC, Hudson TJ, McPherson JD, van der Kwast T, Bristow RG.

Nat Genet. 2015 Jul;47(7):736-45. doi: 10.1038/ng.3315. Epub 2015 May 25.

PMID:
26005866
19.

SeqControl: process control for DNA sequencing.

Chong LC, Albuquerque MA, Harding NJ, Caloian C, Chan-Seng-Yue M, de Borja R, Fraser M, Denroche RE, Beck TA, van der Kwast T, Bristow RG, McPherson JD, Boutros PC.

Nat Methods. 2014 Oct;11(10):1071-5. doi: 10.1038/nmeth.3094. Epub 2014 Aug 31.

PMID:
25173705
20.

A two-dimensional pooling strategy for rare variant detection on next-generation sequencing platforms.

Zuzarte PC, Denroche RE, Fehringer G, Katzov-Eckert H, Hung RJ, McPherson JD.

PLoS One. 2014 Apr 11;9(4):e93455. doi: 10.1371/journal.pone.0093455. eCollection 2014.

21.

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

Biankin AV, Waddell N, Kassahn KS, Gingras MC, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch AM, Wu J, Chang DK, Cowley MJ, Gardiner BB, Song S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Gongora M, Pajic M, Scarlett CJ, Gill AJ, Pinho AV, Rooman I, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Nones K, Fink JL, Christ A, Bruxner T, Cloonan N, Kolle G, Newell F, Pinese M, Mead RS, Humphris JL, Kaplan W, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chou A, Chin VT, Chantrill LA, Mawson A, Samra JS, Kench JG, Lovell JA, Daly RJ, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N; Australian Pancreatic Cancer Genome Initiative, Kakkar N, Zhao F, Wu YQ, Wang M, Muzny DM, Fisher WE, Brunicardi FC, Hodges SE, Reid JG, Drummond J, Chang K, Han Y, Lewis LR, Dinh H, Buhay CJ, Beck T, Timms L, Sam M, Begley K, Brown A, Pai D, Panchal A, Buchner N, De Borja R, Denroche RE, Yung CK, Serra S, Onetto N, Mukhopadhyay D, Tsao MS, Shaw PA, Petersen GM, Gallinger S, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL, Morgan RA, Lawlor RT, Capelli P, Corbo V, Scardoni M, Tortora G, Tempero MA, Mann KM, Jenkins NA, Perez-Mancera PA, Adams DJ, Largaespada DA, Wessels LF, Rust AG, Stein LD, Tuveson DA, Copeland NG, Musgrove EA, Scarpa A, Eshleman JR, Hudson TJ, Sutherland RL, Wheeler DA, Pearson JV, McPherson JD, Gibbs RA, Grimmond SM.

Nature. 2012 Nov 15;491(7424):399-405. doi: 10.1038/nature11547. Epub 2012 Oct 24.

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