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Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution.

Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF, O'Kane GM, Connor AA, Denroche RE, Grant RC, McLeod J, Wilson JM, Jang GH, Zhang A, Liang SB, Borgida A, Chadwick D, Kalimuthu S, Lungu I, Bartlett JMS, Krzyzanowski PM, Sandhu V, Tiriac H, Froeling FEM, Karasinska JM, Topham JT, Renouf DJ, Schaeffer DF, Jones SJM, Marra MA, Laskin J, Chetty R, Stein LD, Zogopoulos G, Haibe-Kains B, Campbell PJ, Tuveson DA, Knox JJ, Fischer SE, Gallinger S, Notta F.

Nat Genet. 2020 Jan 13. doi: 10.1038/s41588-019-0566-9. [Epub ahead of print]


Re-examining the 1-mm margin and submucosal depth of invasion: a review of 216 malignant colorectal polyps.

Berg KB, Telford JJ, Gentile L, Schaeffer DF.

Virchows Arch. 2020 Jan 8. doi: 10.1007/s00428-019-02711-9. [Epub ahead of print]


Topography, morphology, and etiology of lymphocytic gastritis: a single institution experience.

Yip RHL, Lee LH, Lee LH, Schaeffer DF, Horst BA, Yang HM.

Virchows Arch. 2020 Jan 2. doi: 10.1007/s00428-019-02734-2. [Epub ahead of print]


Should you repeat mismatch repair testing in tumour recurrences? An evaluation of repeat mismatch repair testing by immunohistochemistry in recurrent tumours of the gastrointestinal and gynaecological tracts.

Aird JJ, Steel MJ, Chow C, Ho J, Wolber R, Gilks CB, Hoang LN, Schaeffer DF.

Histopathology. 2019 Nov 2. doi: 10.1111/his.14026. [Epub ahead of print]


Altered Gene Expression along the Glycolysis-Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer.

Karasinska JM, Topham JT, Kalloger SE, Jang GH, Denroche RE, Culibrk L, Williamson LM, Wong HL, Lee MKC, O'Kane GM, Moore RA, Mungall AJ, Moore MJ, Warren C, Metcalfe A, Notta F, Knox JJ, Gallinger S, Laskin J, Marra MA, Jones SJM, Renouf DJ, Schaeffer DF.

Clin Cancer Res. 2020 Jan 1;26(1):135-146. doi: 10.1158/1078-0432.CCR-19-1543. Epub 2019 Sep 3.


Endogenous Hyperinsulinemia Contributes to Pancreatic Cancer Development.

Zhang AMY, Magrill J, de Winter TJJ, Hu X, Skovsø S, Schaeffer DF, Kopp JL, Johnson JD.

Cell Metab. 2019 Sep 3;30(3):403-404. doi: 10.1016/j.cmet.2019.07.003. Epub 2019 Aug 1. No abstract available.


The interaction between SPARC and GRP78 interferes with ER stress signaling and potentiates apoptosis via PERK/eIF2α and IRE1α/XBP-1 in colorectal cancer.

Chern YJ, Wong JCT, Cheng GSW, Yu A, Yin Y, Schaeffer DF, Kennecke HF, Morin G, Tai IT.

Cell Death Dis. 2019 Jun 26;10(7):504. doi: 10.1038/s41419-019-1687-x.


Immunohistochemistry Critical Assay Performance Controls (ICAPC) Reduce Interobserver Variability in the Interpretation of BRAFV600E Immunohistochemistry.

Gale NS, Kalloger SE, Cai E, Abozina A, Derakhshan F, Hickey T, Liu A, Ongaro D, Wolber R, Schaeffer DF.

Appl Immunohistochem Mol Morphol. 2019 Jun 24. doi: 10.1097/PAI.0000000000000784. [Epub ahead of print]


Cytohistological diagnosis of pancreatic serous cystadenoma: a multimodal approach.

Steel M, Rao S, Ho J, Donnellan F, Yang HM, Schaeffer DF.

J Clin Pathol. 2019 Sep;72(9):615-621. doi: 10.1136/jclinpath-2019-205872. Epub 2019 Jun 23.


Off-label use of common predictive biomarkers in gastrointestinal malignancies: a critical appraisal.

Tessier-Cloutier B, Cai E, Schaeffer DF.

Diagn Pathol. 2019 Jun 21;14(1):62. doi: 10.1186/s13000-019-0843-z. Review.


Genomic characterization of a well-differentiated grade 3 pancreatic neuroendocrine tumor.

Williamson LM, Steel M, Grewal JK, Thibodeau ML, Zhao EY, Loree JM, Yang KC, Gorski SM, Mungall AJ, Mungall KL, Moore RA, Marra MA, Laskin J, Renouf DJ, Schaeffer DF, Jones SJM.

Cold Spring Harb Mol Case Stud. 2019 Jun 3;5(3). pii: a003814. doi: 10.1101/mcs.a003814. Print 2019 Jun.


Regulation of pH by Carbonic Anhydrase 9 Mediates Survival of Pancreatic Cancer Cells With Activated KRAS in Response to Hypoxia.

McDonald PC, Chafe SC, Brown WS, Saberi S, Swayampakula M, Venkateswaran G, Nemirovsky O, Gillespie JA, Karasinska JM, Kalloger SE, Supuran CT, Schaeffer DF, Bashashati A, Shah SP, Topham JT, Yapp DT, Li J, Renouf DJ, Stanger BZ, Dedhar S.

Gastroenterology. 2019 Sep;157(3):823-837. doi: 10.1053/j.gastro.2019.05.004. Epub 2019 May 9.


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 Aug 1;25(15):4674-4681. doi: 10.1158/1078-0432.CCR-19-0191. Epub 2019 May 8.


Base excision repair deficiency signatures implicate germline and somatic MUTYH aberrations in pancreatic ductal adenocarcinoma and breast cancer oncogenesis.

Thibodeau ML, Zhao EY, Reisle C, Ch'ng C, Wong HL, Shen Y, Jones MR, Lim HJ, Young S, Cremin C, Pleasance E, Zhang W, Holt R, Eirew P, Karasinska J, Kalloger SE, Taylor G, Majounie E, Bonakdar M, Zong Z, Bleile D, Chiu R, Birol I, Gelmon K, Lohrisch C, Mungall KL, Mungall AJ, Moore R, Ma YP, Fok A, Yip S, Karsan A, Huntsman D, Schaeffer DF, Laskin J, Marra MA, Renouf DJ, Jones SJM, Schrader KA.

Cold Spring Harb Mol Case Stud. 2019 Apr 1;5(2). pii: a003681. doi: 10.1101/mcs.a003681. Print 2019 Apr.


A Novel Multiplex Droplet Digital PCR Assay to Identify and Quantify KRAS Mutations in Clinical Specimens.

Alcaide M, Cheung M, Bushell K, Arthur SE, Wong HL, Karasinska J, Renouf D, Schaeffer DF, McNamara S, Tertre MCD, Batist G, Kennecke HF, Karsan A, Morin RD.

J Mol Diagn. 2019 Mar;21(2):214-227. doi: 10.1016/j.jmoldx.2018.09.007. Epub 2018 Nov 23.


Lymphocytic gastritis induced by pembrolizumab in a patient with metastatic melanoma.

Yip RHL, Lee LH, Schaeffer DF, Horst BA, Yang HM.

Melanoma Res. 2018 Dec;28(6):645-647. doi: 10.1097/CMR.0000000000000502.


Microforceps-assisted diagnosis of a cystic GI stromal tumor lesion.

Sanders D, Ting AYS, Schaeffer DF, Donnellan F.

VideoGIE. 2018 Jul 3;3(9):268-269. doi: 10.1016/j.vgie.2018.06.001. eCollection 2018 Sep. No abstract available.


siRNA Library Screening Identifies a Druggable Immune-Signature Driving Esophageal Adenocarcinoma Cell Growth.

Duggan SP, Garry C, Behan FM, Phipps S, Kudo H, Kirca M, Zaheer A, McGarrigle S, Reynolds JV, Goldin R, Kalloger SE, Schaeffer DF, Long A, Strid J, Kelleher D.

Cell Mol Gastroenterol Hepatol. 2018 Jan 31;5(4):569-590. doi: 10.1016/j.jcmgh.2018.01.012. eCollection 2018.


Outcomes of Surgical and Chemotherapeutic Treatments of Goblet Cell Carcinoid Tumors of the Appendix.

Tsang ES, McConnell YJ, Schaeffer DF, Lee L, Yin Y, Zerhouni S, Schaff K, Speers C, Kennecke HF.

Ann Surg Oncol. 2018 Aug;25(8):2391-2399. doi: 10.1245/s10434-018-6560-0. Epub 2018 Jun 18.


DALM, rest in peace: a pathologist's perspective on dysplasia in inflammatory bowel disease in the post-DALM era.

Chiu K, Riddell RH, Schaeffer DF.

Mod Pathol. 2018 Aug;31(8):1180-1190. doi: 10.1038/s41379-018-0068-9. Epub 2018 May 22. Review.


Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice.

Prentice LM, Miller RR, Knaggs J, Mazloomian A, Aguirre Hernandez R, Franchini P, Parsa K, Tessier-Cloutier B, Lapuk A, Huntsman D, Schaeffer DF, Sheffield BS.

PLoS One. 2018 Apr 26;13(4):e0196434. doi: 10.1371/journal.pone.0196434. eCollection 2018.


CDKN2A founder mutation in pancreatic ductal adenocarcinoma patients without cutaneous features of Familial Atypical Multiple Mole Melanoma (FAMMM) syndrome.

Cremin C, Howard S, Le L, Karsan A, Schaeffer DF, Renouf D, Schrader KA.

Hered Cancer Clin Pract. 2018 Mar 7;16:7. doi: 10.1186/s13053-018-0088-y. eCollection 2018.


Molecular characterization of ERBB2-amplified colorectal cancer identifies potential mechanisms of resistance to targeted therapies: a report of two instructive cases.

Owen DR, Wong HL, Bonakdar M, Jones M, Hughes CS, Morin GB, Jones SJM, Renouf DJ, Lim H, Laskin J, Marra M, Yip S, Schaeffer DF.

Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2). pii: a002535. doi: 10.1101/mcs.a002535. Print 2018 Apr.


Tumor budding as a standardized parameter in gastrointestinal carcinomas: more than just the colon.

Berg KB, Schaeffer DF.

Mod Pathol. 2018 Jun;31(6):862-872. doi: 10.1038/s41379-018-0028-4. Epub 2018 Feb 6. Review.


Cell of origin affects tumour development and phenotype in pancreatic ductal adenocarcinoma.

Lee AYL, Dubois CL, Sarai K, Zarei S, Schaeffer DF, Sander M, Kopp JL.

Gut. 2018 Jan 23. pii: gutjnl-2017-314426. doi: 10.1136/gutjnl-2017-314426. [Epub ahead of print]


Prognostic Factors for Locoregional Recurrence in Neuroendocrine Tumors of the Rectum.

Tsang ES, McConnell YJ, Schaeffer DF, Yin Y, Speers CH, Kennecke HF.

Dis Colon Rectum. 2018 Feb;61(2):187-192. doi: 10.1097/DCR.0000000000000996.


Loss of Pten and Activation of Kras Synergistically Induce Formation of Intraductal Papillary Mucinous Neoplasia From Pancreatic Ductal Cells in Mice.

Kopp JL, Dubois CL, Schaeffer DF, Samani A, Taghizadeh F, Cowan RW, Rhim AD, Stiles BL, Valasek M, Sander M.

Gastroenterology. 2018 Apr;154(5):1509-1523.e5. doi: 10.1053/j.gastro.2017.12.007. Epub 2017 Dec 19.


Molecular characterization of metastatic pancreatic neuroendocrine tumors (PNETs) using whole-genome and transcriptome sequencing.

Wong HL, Yang KC, Shen Y, Zhao EY, Loree JM, Kennecke HF, Kalloger SE, Karasinska JM, Lim HJ, Mungall AJ, Feng X, Davies JM, Schrader K, Zhou C, Karsan A, Jones SJM, Laskin J, Marra MA, Schaeffer DF, Gorski SM, Renouf DJ.

Cold Spring Harb Mol Case Stud. 2018 Feb 1;4(1). pii: a002329. doi: 10.1101/mcs.a002329. Print 2018 Feb.


SATB2 as an Immunohistochemical Marker for Colorectal Adenocarcinoma: A Concise Review of Benefits and Pitfalls.

Berg KB, Schaeffer DF.

Arch Pathol Lab Med. 2017 Oct;141(10):1428-1433. doi: 10.5858/arpa.2016-0243-RS. Review.


Successful targeting of the NRG1 pathway indicates novel treatment strategy for metastatic cancer.

Jones MR, Lim H, Shen Y, Pleasance E, Ch'ng C, Reisle C, Leelakumari S, Zhao C, Yip S, Ho J, Zhong E, Ng T, Ionescu D, Schaeffer DF, Mungall AJ, Mungall KL, Zhao Y, Moore RA, Ma Y, Chia S, Ho C, Renouf DJ, Gelmon K, Jones SJM, Marra MA, Laskin J.

Ann Oncol. 2017 Dec 1;28(12):3092-3097. doi: 10.1093/annonc/mdx523.


Programmed cell death ligand 1 cut-point is associated with reduced disease specific survival in resected pancreatic ductal adenocarcinoma.

Tessier-Cloutier B, Kalloger SE, Al-Kandari M, Milne K, Gao D, Nelson BH, Renouf DJ, Sheffield BS, Schaeffer DF.

BMC Cancer. 2017 Sep 5;17(1):618. doi: 10.1186/s12885-017-3634-5.


A predictive analysis of the SP120 and 10D7G2 antibodies for human equilibrative nucleoside transporter 1 (hENT1) in pancreatic ductal adenocarcinoma treated with adjuvant gemcitabine.

Kalloger SE, Riazy M, Tessier-Cloutier B, Karasinska JM, Gao D, Peixoto RD, Samimi S, Chow C, Wong HL, Mackey JR, Renouf DJ, Schaeffer DF.

J Pathol Clin Res. 2017 Jul 19;3(3):179-190. doi: 10.1002/cjp2.75. eCollection 2017 Jul.


Inactivation of the Kinase Domain of CDK10 Prevents Tumor Growth in a Preclinical Model of Colorectal Cancer, and Is Accompanied by Downregulation of Bcl-2.

Weiswald LB, Hasan MR, Wong JCT, Pasiliao CC, Rahman M, Ren J, Yin Y, Gusscott S, Vacher S, Weng AP, Kennecke HF, Bièche I, Schaeffer DF, Yapp DT, Tai IT.

Mol Cancer Ther. 2017 Oct;16(10):2292-2303. doi: 10.1158/1535-7163.MCT-16-0666. Epub 2017 Jun 29.


Cytologic features and clinical implications of undifferentiated carcinoma with osteoclastic giant cells of the pancreas: An analysis of 15 cases.

Reid MD, Muraki T, HooKim K, Memis B, Graham RP, Allende D, Shi J, Schaeffer DF, Singh R, Basturk O, Adsay V.

Cancer Cytopathol. 2017 Jul;125(7):563-575. doi: 10.1002/cncy.21859. Epub 2017 Apr 3.


Personalized oncogenomics in the management of gastrointestinal carcinomas-early experiences from a pilot study.

Sheffield BS, Tessier-Cloutier B, Li-Chang H, Shen Y, Pleasance E, Kasaian K, Li Y, Jones SJ, Lim HJ, Renouf DJ, Huntsman DG, Yip S, Laskin J, Marra M, Schaeffer DF.

Curr Oncol. 2016 Dec;23(6):e571-e575. doi: 10.3747/co.23.3165. Epub 2016 Dec 21.


IgG4-related disease and lymphocyte-variant hypereosinophilic syndrome: A comparative case series.

Carruthers MN, Park S, Slack GW, Dalal BI, Skinnider BF, Schaeffer DF, Dutz JP, Law JK, Donnellan F, Marquez V, Seidman M, Wong PC, Mattman A, Chen LY.

Eur J Haematol. 2017 Apr;98(4):378-387. doi: 10.1111/ejh.12842. Epub 2017 Jan 20.


Identification of recurrent mutational events in anorectal melanoma.

Yang HM, Hsiao SJ, Schaeffer DF, Lai C, Remotti HE, Horst D, Mansukhani MM, Horst BA.

Mod Pathol. 2017 Feb;30(2):286-296. doi: 10.1038/modpathol.2016.179. Epub 2016 Oct 14.


In-depth mutational analyses of colorectal neuroendocrine carcinomas with adenoma or adenocarcinoma components.

Woischke C, Schaaf CW, Yang HM, Vieth M, Veits L, Geddert H, Märkl B, Stömmer P, Schaeffer DF, Frölich M, Blum H, Vosberg S, Greif PA, Jung A, Kirchner T, Horst D.

Mod Pathol. 2017 Jan;30(1):95-103. doi: 10.1038/modpathol.2016.150. Epub 2016 Sep 2.


Ileal "carcinoid" tumors-small size belies deadly intent: high rate of nodal metastasis in tumors ≤1 cm in size.

Walsh JC, Schaeffer DF, Kirsch R, Pollett A, Manzoni M, Riddell RH, Albarello L.

Hum Pathol. 2016 Oct;56:123-7. doi: 10.1016/j.humpath.2016.05.023. Epub 2016 Jun 18.


Intraepithelial lymphocytosis is a frequent finding in biopsies from ileal pouch-anal anastomoses.

Schaeffer DF, Walsh JC, Tyler AD, Ben-Bassat O, Silverberg MS, Riddell RH, Kirsch R.

Hum Pathol. 2016 Aug;54:31-6. doi: 10.1016/j.humpath.2016.03.007. Epub 2016 Apr 8.


Primary hepatic perivascular epithelioid tumor (PEComa).

Schaeffer DF, Poulin MP.

Ann Hepatol. 2016 May-Jun;15(3):436-7. doi: 10.5604/16652681.1198822. No abstract available.


Sensitivities of Biopsy Sites in the Endoscopic Evaluation of Graft-Versus-Host Disease: Retrospective Review from a Tertiary Center.

Ip S, Marquez V, Schaeffer DF, Donnellan F.

Dig Dis Sci. 2016 Aug;61(8):2351-2356. doi: 10.1007/s10620-016-4142-1. Epub 2016 Mar 30.


Versican: a novel modulator of hepatic fibrosis.

Bukong TN, Maurice SB, Chahal B, Schaeffer DF, Winwood PJ.

Lab Invest. 2016 Mar;96(3):361-74. doi: 10.1038/labinvest.2015.152. Epub 2016 Jan 11.


Unusual case of drug-induced cholestasis due to glucosamine and chondroitin sulfate.

Ip S, Jeong R, Schaeffer DF, Yoshida EM.

World J Hepatol. 2015 Oct 28;7(24):2559-62. doi: 10.4254/wjh.v7.i24.2559.


Ductal pancreatic cancer modeling and drug screening using human pluripotent stem cell- and patient-derived tumor organoids.

Huang L, Holtzinger A, Jagan I, BeGora M, Lohse I, Ngai N, Nostro C, Wang R, Muthuswamy LB, Crawford HC, Arrowsmith C, Kalloger SE, Renouf DJ, Connor AA, Cleary S, Schaeffer DF, Roehrl M, Tsao MS, Gallinger S, Keller G, Muthuswamy SK.

Nat Med. 2015 Nov;21(11):1364-71. doi: 10.1038/nm.3973. Epub 2015 Oct 26.


Immunophenotyping of ampullary carcinomata allows for stratification of treatment specific subgroups.

Leo JM, Kalloger SE, Peixoto RD, Gale NS, Webber DL, Owen DA, Renouf D, Schaeffer DF.

J Clin Pathol. 2016 May;69(5):431-9. doi: 10.1136/jclinpath-2015-203337. Epub 2015 Oct 23.


Simplified 2-tier histologic grading system accurately predicts outcomes in goblet cell carcinoid of the appendix.

Lee LH, McConnell YJ, Tsang E, Zerhouni S, Speers C, Kennecke H, Schaeffer DF.

Hum Pathol. 2015 Dec;46(12):1881-9. doi: 10.1016/j.humpath.2015.08.005. Epub 2015 Aug 22.


Prognostic role and implications of mutation status of tumor suppressor gene ARID1A in cancer: a systematic review and meta-analysis.

Luchini C, Veronese N, Solmi M, Cho H, Kim JH, Chou A, Gill AJ, Faraj SF, Chaux A, Netto GJ, Nakayama K, Kyo S, Lee SY, Kim DW, Yousef GM, Scorilas A, Nelson GS, Köbel M, Kalloger SE, Schaeffer DF, Yan HB, Liu F, Yokoyama Y, Zhang X, Pang D, Lichner Z, Sergi G, Manzato E, Capelli P, Wood LD, Scarpa A, Correll CU.

Oncotarget. 2015 Nov 17;6(36):39088-97. doi: 10.18632/oncotarget.5142. Review.


Gastrointestinal Endoscopic Ultrasound-Guided Fine-Needle Aspiration Biopsy Specimens: Adequate Diagnostic Yield and Accuracy Can Be Achieved without On-Site Evaluation.

O'Connor K, Cheriyan DG, Li-Chang HH, Kalloger SE, Garrett J, Byrne MF, Weiss AA, Donnellan F, Schaeffer DF.

Acta Cytol. 2015;59(4):305-10. doi: 10.1159/000439398. Epub 2015 Sep 5.


Mismatch repair status may predict response to adjuvant chemotherapy in resectable pancreatic ductal adenocarcinoma.

Riazy M, Kalloger SE, Sheffield BS, Peixoto RD, Li-Chang HH, Scudamore CH, Renouf DJ, Schaeffer DF.

Mod Pathol. 2015 Oct;28(10):1383-9. doi: 10.1038/modpathol.2015.89. Epub 2015 Jul 31.

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