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Systematic evaluation of PAXgene tissue fixation for the histopathological and molecular study of lung cancer.

Southwood M, Krenz T, Cant N, Maurya M, Gazdova J, Maxwell P, McGready C, Moseley E, Hughes S, Salto-Tellez M, Groelz D, Rassl D; STRATfix Consortium.

J Pathol Clin Res. 2019 Sep 30. doi: 10.1002/cjp2.145. [Epub ahead of print]


Defining the molecular evolution of extrauterine high grade serous carcinoma.

Beirne JP, McArt DG, Roddy A, McDermott C, Ferris J, Buckley NE, Coulter P, McCabe N, Eddie SL, Dunne PD, O'Reilly P, Gilmore A, Feeney L, Ewing DL, Drapkin RI, Salto-Tellez M, Kennedy RD, Harley IJG, McCluggage WG, Mullan PB.

Gynecol Oncol. 2019 Sep 4. pii: S0090-8258(19)31481-7. doi: 10.1016/j.ygyno.2019.08.029. [Epub ahead of print]


NUQA: Estimating cancer spatial and temporal heterogeneity and evolution through alignment-free methods.

Roddy AC, Jurek A, Souza J, Gilmore A, O'Reilly PG, Stupnikov A, de Castro DG, Prise KM, Salto-Tellez M, McArt DG.

Mol Biol Evol. 2019 Aug 19. pii: msz182. doi: 10.1093/molbev/msz182. [Epub ahead of print]


Cancer taxonomy: pathology beyond pathology.

Salto-Tellez M, Cree IA.

Eur J Cancer. 2019 Jul;115:57-60. doi: 10.1016/j.ejca.2019.03.026. Epub 2019 May 17.


A Machine Learning Platform to Optimize the Translation of Personalized Network Models to the Clinic.

Salvucci M, Rahman A, Resler AJ, Udupi GM, McNamara DA, Kay EW, Laurent-Puig P, Longley DB, Johnston PG, Lawler M, Wilson R, Salto-Tellez M, Van Schaeybroeck S, Rafferty M, Gallagher WM, Rehm M, Prehn JHM.

JCO Clin Cancer Inform. 2019 Apr;3:1-17. doi: 10.1200/CCI.18.00056.


Recommendations for determining HPV status in patients with oropharyngeal cancers under TNM8 guidelines: a two-tier approach.

Craig SG, Anderson LA, Schache AG, Moran M, Graham L, Currie K, Rooney K, Robinson M, Upile NS, Brooker R, Mesri M, Bingham V, McQuaid S, Jones T, McCance DJ, Salto-Tellez M, McDade SS, James JA.

Br J Cancer. 2019 Apr;120(8):827-833. doi: 10.1038/s41416-019-0414-9. Epub 2019 Mar 20.


Invited review-next-generation sequencing: a modern tool in cytopathology.

Roy-Chowdhuri S, Pisapia P, Salto-Tellez M, Savic S, Nacchio M, de Biase D, Tallini G, Troncone G, Schmitt F.

Virchows Arch. 2019 Jul;475(1):3-11. doi: 10.1007/s00428-019-02559-z. Epub 2019 Mar 15. Review.


Immune activation by DNA damage predicts response to chemotherapy and survival in oesophageal adenocarcinoma.

Turkington RC, Knight LA, Blayney JK, Secrier M, Douglas R, Parkes EE, Sutton EK, Stevenson L, McManus D, Halliday S, McCavigan AM, Logan GE, Walker SM, Steele CJ, Perner J, Bornschein J, MacRae S, Miremadi A, McCarron E, McQuaid S, Arthur K, James JA, Eatock MM, O'Neill R, Noble F, Underwood TJ, Harkin DP, Salto-Tellez M, Fitzgerald RC, Kennedy RD; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Study Group.

Gut. 2019 Nov;68(11):1918-1927. doi: 10.1136/gutjnl-2018-317624. Epub 2019 Mar 9.


Training and accreditation standards for pathologists undertaking clinical trial work.

Rees G, Salto-Tellez M, Lee JL, Oien K, Verrill C, Freeman A, Mirabile I, West NP; National Cancer Research Institute (NCRI) Cellular-Molecular Pathology (CM-Path) clinical trials working group.

J Pathol Clin Res. 2019 Apr;5(2):100-107. doi: 10.1002/cjp2.124. Epub 2019 Feb 27.


Automated Tumour Recognition and Digital Pathology Scoring Unravels New Role for PD-L1 in Predicting Good Outcome in ER-/HER2+ Breast Cancer.

Humphries MP, Hynes S, Bingham V, Cougot D, James J, Patel-Socha F, Parkes EE, Blayney JK, O'Rorke MA, Irwin GW, McArt DG, Kennedy RD, Mullan PB, McQuaid S, Salto-Tellez M, Buckley NE.

J Oncol. 2018 Dec 17;2018:2937012. doi: 10.1155/2018/2937012. eCollection 2018.


Sex hormone receptor expression and survival in esophageal adenocarcinoma: a prospective cohort study.

McMenamin ÚC, Trainor J, Coleman HG, McManus DT, McQuaid S, Bingham V, James J, Salto-Tellez M, Johnston BT, Turkington RC.

Oncotarget. 2018 Oct 19;9(82):35300-35312. doi: 10.18632/oncotarget.26236. eCollection 2018 Oct 19.


High PTGS2 expression in post-neoadjuvant chemotherapy-treated oesophageal adenocarcinoma is associated with improved survival: a population-based cohort study.

Spence AD, Trainor J, McMenamin Ú, Turkington RC, McQuaid S, Bingham V, James J, Salto-Tellez M, McManus DT, Johnston BT, Cardwell CR, Coleman HG.

Histopathology. 2019 Mar;74(4):587-596. doi: 10.1111/his.13786. Epub 2019 Jan 25.


Vitamin D receptor as a marker of prognosis in oesophageal adenocarcinoma: a prospective cohort study.

McCain S, Trainor J, McManus DT, McMenamin ÚC, McQuaid S, Bingham V, James JA, Salto-Tellez M, Turkington RC, Coleman HG.

Oncotarget. 2018 Sep 28;9(76):34347-34356. doi: 10.18632/oncotarget.26151. eCollection 2018 Sep 28.


Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression.

Stupnikov A, O'Reilly PG, McInerney CE, Roddy AC, Dunne PD, Gilmore A, Ellis HP, Flannery T, Healy E, McIntosh SA, Savage K, Kurian KM, Emmert-Streib F, Prise KM, Salto-Tellez M, McArt DG.

JCO Precis Oncol. 2018 Sep 13;2. doi: 10.1200/PO.18.00014.


Critical Appraisal of Programmed Death Ligand 1 Reflex Diagnostic Testing: Current Standards and Future Opportunities.

Humphries MP, McQuaid S, Craig SG, Bingham V, Maxwell P, Maurya M, McLean F, Sampson J, Higgins P, Greene C, James J, Salto-Tellez M.

J Thorac Oncol. 2019 Jan;14(1):45-53. doi: 10.1016/j.jtho.2018.09.025. Epub 2018 Oct 6.


Artificial intelligence-the third revolution in pathology.

Salto-Tellez M, Maxwell P, Hamilton P.

Histopathology. 2019 Feb;74(3):372-376. doi: 10.1111/his.13760. No abstract available.


Glucose transporter 1 expression as a marker of prognosis in oesophageal adenocarcinoma.

Blayney JK, Cairns L, Li G, McCabe N, Stevenson L, Peters CJ, Reid NB, Spence VJ, Chisambo C, McManus D, James J, McQuaid S, Craig S, Arthur K, McArt D, Ong CJ, Lao-Sirieix P, Hamilton P, Salto-Tellez M, Eatock M, Coleman HG, Fitzgerald RC, Kennedy RD, Turkington RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Study Group.

Oncotarget. 2018 Apr 6;9(26):18518-18528. doi: 10.18632/oncotarget.24906. eCollection 2018 Apr 6.


A gene signature associated with PTEN activation defines good prognosis intermediate risk prostate cancer cases.

Ong CW, Maxwell P, Alvi MA, McQuaid S, Waugh D, Mills I, Salto-Tellez M.

J Pathol Clin Res. 2018 Apr;4(2):103-113. doi: 10.1002/cjp2.94. Epub 2018 Feb 28.


Validation of the systematic scoring of immunohistochemically stained tumour tissue microarrays using QuPath digital image analysis.

Loughrey MB, Bankhead P, Coleman HG, Hagan RS, Craig S, McCorry AMB, Gray RT, McQuaid S, Dunne PD, Hamilton PW, James JA, Salto-Tellez M.

Histopathology. 2018 Aug;73(2):327-338. doi: 10.1111/his.13516. Epub 2018 May 21.


More Than a Decade of Molecular Diagnostic Cytopathology Leading Diagnostic and Therapeutic Decision-Making.

Salto-Tellez M.

Arch Pathol Lab Med. 2018 Apr;142(4):443-445. doi: 10.5858/apra.2017-0258-ED. No abstract available.


HER2 testing of gastro-oesophageal adenocarcinoma: a commentary and guidance document from the Association of Clinical Pathologists Molecular Pathology and Diagnostics Committee.

Wong NACS, Amary F, Butler R, Byers R, Gonzalez D, Haynes HR, Ilyas M, Salto-Tellez M, Taniere P.

J Clin Pathol. 2018 May;71(5):388-394. doi: 10.1136/jclinpath-2017-204943. Epub 2018 Feb 8. Review.


Practical guide for the comparison of two next-generation sequencing systems for solid tumour analysis in a universal healthcare system.

Maxwell P, Hynes SO, Fuchs M, Craig S, McGready C, McLean F, McQuaid S, James J, Salto-Tellez M.

J Clin Pathol. 2019 Mar;72(3):225-231. doi: 10.1136/jclinpath-2017-204917. Epub 2018 Jan 31.


Targeting c-MET in gastrointestinal tumours: rationale, opportunities and challenges.

Bradley CA, Salto-Tellez M, Laurent-Puig P, Bardelli A, Rolfo C, Tabernero J, Khawaja HA, Lawler M, Johnston PG, Van Schaeybroeck S; MErCuRIC consortium.

Nat Rev Clin Oncol. 2018 Jan 23;15(3):150. doi: 10.1038/nrclinonc.2018.13. [Epub ahead of print]


More Than a Decade of Molecular Diagnostic Cytopathology Leading Diagnostic and Therapeutic Decision-Making.

Salto-Tellez M.

Arch Pathol Lab Med. 2018 Jan 12. doi: 10.5858/arpa.2017-0258-ED. [Epub ahead of print] No abstract available.


Integrated tumor identification and automated scoring minimizes pathologist involvement and provides new insights to key biomarkers in breast cancer.

Bankhead P, Fernández JA, McArt DG, Boyle DP, Li G, Loughrey MB, Irwin GW, Harkin DP, James JA, McQuaid S, Salto-Tellez M, Hamilton PW.

Lab Invest. 2018 Jan;98(1):15-26. doi: 10.1038/labinvest.2017.131. Epub 2017 Dec 18.


RNAscope in situ hybridization confirms mRNA integrity in formalin-fixed, paraffin-embedded cancer tissue samples.

Bingham V, McIlreavey L, Greene C, O'Doherty E, Clarke R, Craig S, Salto-Tellez M, McQuaid S, Lewis C, James J.

Oncotarget. 2017 Oct 16;8(55):93392-93403. doi: 10.18632/oncotarget.21851. eCollection 2017 Nov 7.


QuPath: Open source software for digital pathology image analysis.

Bankhead P, Loughrey MB, Fernández JA, Dombrowski Y, McArt DG, Dunne PD, McQuaid S, Gray RT, Murray LJ, Coleman HG, James JA, Salto-Tellez M, Hamilton PW.

Sci Rep. 2017 Dec 4;7(1):16878. doi: 10.1038/s41598-017-17204-5.


Training in molecular cytopathology testing.

Maxwell P, Salto-Tellez M.

Cytopathology. 2018 Feb;29(1):5-9. doi: 10.1111/cyt.12495. Epub 2017 Nov 17. Review.


Morphomolecular pathology: setting the framework for a new generation of pathologists.

Jones JL, Oien KA, Lee JL, Salto-Tellez M.

Br J Cancer. 2017 Nov 21;117(11):1581-1582. doi: 10.1038/bjc.2017.340. Epub 2017 Nov 9. No abstract available.


Time for change: a new training programme for morpho-molecular pathologists?

Moore DA, Young CA, Morris HT, Oien KA, Lee JL, Jones JL, Salto-Tellez M.

J Clin Pathol. 2018 Apr;71(4):285-290. doi: 10.1136/jclinpath-2017-204821. Epub 2017 Nov 7. Review.


Rare cancers: the greatest inequality in cancer research and oncology treatment.

Alvi MA, Wilson RH, Salto-Tellez M.

Br J Cancer. 2017 Oct 24;117(9):1255-1257. doi: 10.1038/bjc.2017.321. Epub 2017 Sep 21. No abstract available.


Diagnostic accuracy of haptoglobin within ovarian cyst fluid as a potential point-of-care test for epithelial ovarian cancer: an observational study.

Mahyuddin AP, Liu L, Zhao C, Kothandaraman N, Salto-Tellez M, Pang B, Lim D, Annalamai L, Chan J, Lim T, Biswas A, Rice G, Razvi K, Choolani M.

BJOG. 2018 Mar;125(4):421-431. doi: 10.1111/1471-0528.14835. Epub 2017 Sep 4.


Natural killer-like signature observed post therapy in locally advanced rectal cancer is a determinant of pathological response and improved survival.

Alderdice M, Dunne PD, Cole AJ, O'Reilly PG, McArt DG, Bingham V, Fuchs MA, McQuaid S, Loughrey MB, Murray GI, Samuel LM, Lawler M, Wilson RH, Salto-Tellez M, Coyle VM.

Mod Pathol. 2017 Sep;30(9):1287-1298. doi: 10.1038/modpathol.2017.47. Epub 2017 Jun 16.


Molecular profiling of signet ring cell colorectal cancer provides a strong rationale for genomic targeted and immune checkpoint inhibitor therapies.

Alvi MA, Loughrey MB, Dunne P, McQuaid S, Turkington R, Fuchs MA, McGready C, Bingham V, Pang B, Moore W, Maxwell P, Lawler M, James JA, Murray GI, Wilson RH, Salto-Tellez M.

Br J Cancer. 2017 Jul 11;117(2):203-209. doi: 10.1038/bjc.2017.168. Epub 2017 Jun 8.


Standardising RNA profiling based biomarker application in cancer-The need for robust control of technical variables.

Stewart JP, Richman S, Maughan T, Lawler M, Dunne PD, Salto-Tellez M.

Biochim Biophys Acta Rev Cancer. 2017 Aug;1868(1):258-272. doi: 10.1016/j.bbcan.2017.05.005. Epub 2017 May 23. Review.


Statin use, candidate mevalonate pathway biomarkers, and colon cancer survival in a population-based cohort study.

Gray RT, Loughrey MB, Bankhead P, Cardwell CR, McQuaid S, O'Neill RF, Arthur K, Bingham V, McGready C, Gavin AT, James JA, Hamilton PW, Salto-Tellez M, Murray LJ, Coleman HG.

Br J Cancer. 2017 Jun 6;116(12):1652-1659. doi: 10.1038/bjc.2017.139. Epub 2017 May 18.


Consistency and reproducibility of next-generation sequencing and other multigene mutational assays: A worldwide ring trial study on quantitative cytological molecular reference specimens.

Malapelle U, Mayo-de-Las-Casas C, Molina-Vila MA, Rosell R, Savic S, Bihl M, Bubendorf L, Salto-Tellez M, de Biase D, Tallini G, Hwang DH, Sholl LM, Luthra R, Weynand B, Vander Borght S, Missiaglia E, Bongiovanni M, Stieber D, Vielh P, Schmitt F, Rappa A, Barberis M, Pepe F, Pisapia P, Serra N, Vigliar E, Bellevicine C, Fassan M, Rugge M, de Andrea CE, Lozano MD, Basolo F, Fontanini G, Nikiforov YE, Kamel-Reid S, da Cunha Santos G, Nikiforova MN, Roy-Chowdhuri S, Troncone G; Molecular Cytopathology Meeting Group.

Cancer Cytopathol. 2017 Aug;125(8):615-626. doi: 10.1002/cncy.21868. Epub 2017 May 5.


Evaluation of PTGS2 Expression, PIK3CA Mutation, Aspirin Use and Colon Cancer Survival in a Population-Based Cohort Study.

Gray RT, Cantwell MM, Coleman HG, Loughrey MB, Bankhead P, McQuaid S, O'Neill RF, Arthur K, Bingham V, McGready C, Gavin AT, Cardwell CR, Johnston BT, James JA, Hamilton PW, Salto-Tellez M, Murray LJ.

Clin Transl Gastroenterol. 2017 Apr 27;8(4):e91. doi: 10.1038/ctg.2017.18.


Targeting c-MET in gastrointestinal tumours: rationale, opportunities and challenges.

Bradley CA, Salto-Tellez M, Laurent-Puig P, Bardelli A, Rolfo C, Tabernero J, Khawaja HA, Lawler M, Johnston PG, Van Schaeybroeck S; MErCuRIC consortium.

Nat Rev Clin Oncol. 2017 Sep;14(9):562-576. doi: 10.1038/nrclinonc.2017.40. Epub 2017 Apr 4. Review. Erratum in: Nat Rev Clin Oncol. 2018 Jan 23;:.


Erratum to: JMJD6 is a driver of cellular proliferation and motility and a marker of poor prognosis in breast cancer.

Lee YF, Miller LD, Chan XB, Black MA, Pang B, Ong CW, Salto-Tellez M, Liu ET, Desai KV.

Breast Cancer Res. 2017 Mar 28;19(1):42. doi: 10.1186/s13058-017-0830-9. No abstract available.


Response to Park et al. reply to 'Back to the future: routine morphological assessment of the tumour microenvironment is prognostic in stage II/III colon cancer in a large population-based study'.

Hynes SO, Coleman HG, Kelly PJ, Dunne PD, Salto-Tellez M, Loughrey MB.

Histopathology. 2017 Aug;71(2):327-329. doi: 10.1111/his.13221. Epub 2017 May 19. No abstract available.


Back to the future: routine morphological assessment of the tumour microenvironment is prognostic in stage II/III colon cancer in a large population-based study.

Hynes SO, Coleman HG, Kelly PJ, Irwin S, O'Neill RF, Gray RT, McGready C, Dunne PD, McQuaid S, James JA, Salto-Tellez M, Loughrey MB.

Histopathology. 2017 Jul;71(1):12-26. doi: 10.1111/his.13181. Epub 2017 Apr 3.


RUNX3 is oncogenic in natural killer/T-cell lymphoma and is transcriptionally regulated by MYC.

Selvarajan V, Osato M, Nah GSS, Yan J, Chung TH, Voon DC, Ito Y, Ham MF, Salto-Tellez M, Shimizu N, Choo SN, Fan S, Chng WJ, Ng SB.

Leukemia. 2017 Oct;31(10):2219-2227. doi: 10.1038/leu.2017.40. Epub 2017 Jan 25.


Tissue-based next generation sequencing: application in a universal healthcare system.

Hynes SO, Pang B, James JA, Maxwell P, Salto-Tellez M.

Br J Cancer. 2017 Feb 28;116(5):553-560. doi: 10.1038/bjc.2016.452. Epub 2017 Jan 19. Review.


samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files.

Stupnikov A, Tripathi S, de Matos Simoes R, McArt D, Salto-Tellez M, Glazko G, Dehmer M, Emmert-Streib F.

Bioinformatics. 2016 Nov 1;32(21):3345-3347. Epub 2016 Jul 10.


Activation of STING-Dependent Innate Immune Signaling By S-Phase-Specific DNA Damage in Breast Cancer.

Parkes EE, Walker SM, Taggart LE, McCabe N, Knight LA, Wilkinson R, McCloskey KD, Buckley NE, Savage KI, Salto-Tellez M, McQuaid S, Harte MT, Mullan PB, Harkin DP, Kennedy RD.

J Natl Cancer Inst. 2016 Oct 5;109(1). doi: 10.1093/jnci/djw199. Print 2017 Jan.


Building a 'Repository of Science': The importance of integrating biobanks within molecular pathology programmes.

Lewis C, McQuaid S, Hamilton PW, Salto-Tellez M, McArt D, James JA.

Eur J Cancer. 2016 Nov;67:191-199. doi: 10.1016/j.ejca.2016.08.009. Epub 2016 Sep 24. Review.


BCL-2 system analysis identifies high-risk colorectal cancer patients.

Lindner AU, Salvucci M, Morgan C, Monsefi N, Resler AJ, Cremona M, Curry S, Toomey S, O'Byrne R, Bacon O, Stühler M, Flanagan L, Wilson R, Johnston PG, Salto-Tellez M, Camilleri-Broët S, McNamara DA, Kay EW, Hennessy BT, Laurent-Puig P, Van Schaeybroeck S, Prehn JHM.

Gut. 2017 Dec;66(12):2141-2148. doi: 10.1136/gutjnl-2016-312287. Epub 2016 Sep 23.


A Stepwise Integrated Approach to Personalized Risk Predictions in Stage III Colorectal Cancer.

Salvucci M, Würstle ML, Morgan C, Curry S, Cremona M, Lindner AU, Bacon O, Resler AJ, Murphy ÁC, O'Byrne R, Flanagan L, Dasgupta S, Rice N, Pilati C, Zink E, Schöller LM, Toomey S, Lawler M, Johnston PG, Wilson R, Camilleri-Broët S, Salto-Tellez M, McNamara DA, Kay EW, Laurent-Puig P, Van Schaeybroeck S, Hennessy BT, Longley DB, Rehm M, Prehn JH.

Clin Cancer Res. 2017 Mar 1;23(5):1200-1212. doi: 10.1158/1078-0432.CCR-16-1084. Epub 2016 Sep 20.


Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned.

Li G, Bankhead P, Dunne PD, O'Reilly PG, James JA, Salto-Tellez M, Hamilton PW, McArt DG.

Brief Bioinform. 2017 Jul 1;18(4):634-646. doi: 10.1093/bib/bbw044.

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