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Basal biomarkers Nestin and INPP4B predict gemcitabine benefit in metastatic breast cancer: samples from the phase III SBG0102 clinical trial.

Asleh K, Lyck Carstensen S, Tykjaer Jørgensen CL, Burugu S, Gao D, Won JR, Jensen MB, Balslev E, Laenkholm AV, Nielsen DL, Ejlertsen B, Nielsen TO.

Int J Cancer. 2018 Nov 9. doi: 10.1002/ijc.31969. [Epub ahead of print]


TIM-3 expression in breast cancer.

Burugu S, Gao D, Leung S, Chia SK, Nielsen TO.

Oncoimmunology. 2018 Aug 23;7(11):e1502128. doi: 10.1080/2162402X.2018.1502128. eCollection 2018.


The prognostic effects of somatic mutations in ER-positive breast cancer.

Griffith OL, Spies NC, Anurag M, Griffith M, Luo J, Tu D, Yeo B, Kunisaki J, Miller CA, Krysiak K, Hundal J, Ainscough BJ, Skidmore ZL, Campbell K, Kumar R, Fronick C, Cook L, Snider JE, Davies S, Kavuri SM, Chang EC, Magrini V, Larson DE, Fulton RS, Liu S, Leung S, Voduc D, Bose R, Dowsett M, Wilson RK, Nielsen TO, Mardis ER, Ellis MJ.

Nat Commun. 2018 Sep 4;9(1):3476. doi: 10.1038/s41467-018-05914-x.


Ki67 reproducibility using digital image analysis: an inter-platform and inter-operator study.

Acs B, Pelekanou V, Bai Y, Martinez-Morilla S, Toki M, Leung SCY, Nielsen TO, Rimm DL.

Lab Invest. 2018 Sep 4. doi: 10.1038/s41374-018-0123-7. [Epub ahead of print]


An international multicenter study to evaluate reproducibility of automated scoring for assessment of Ki67 in breast cancer.

Rimm DL, Leung SCY, McShane LM, Bai Y, Bane AL, Bartlett JMS, Bayani J, Chang MC, Dean M, Denkert C, Enwere EK, Galderisi C, Gholap A, Hugh JC, Jadhav A, Kornaga EN, Laurinavicius A, Levenson R, Lima J, Miller K, Pantanowitz L, Piper T, Ruan J, Srinivasan M, Virk S, Wu Y, Yang H, Hayes DF, Nielsen TO, Dowsett M.

Mod Pathol. 2018 Aug 24. doi: 10.1038/s41379-018-0109-4. [Epub ahead of print]


The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma.

Banito A, Li X, Laporte AN, Roe JS, Sanchez-Vega F, Huang CH, Dancsok AR, Hatzi K, Chen CC, Tschaharganeh DF, Chandwani R, Tasdemir N, Jones KB, Capecchi MR, Vakoc CR, Schultz N, Ladanyi M, Nielsen TO, Lowe SW.

Cancer Cell. 2018 Aug 13;34(2):346-348. doi: 10.1016/j.ccell.2018.07.006. No abstract available.


The Prosigna gene expression assay and responsiveness to adjuvant cyclophosphamide-based chemotherapy in premenopausal high-risk patients with breast cancer.

Jensen MB, Lænkholm AV, Nielsen TO, Eriksen JO, Wehn P, Hood T, Ram N, Buckingham W, Ferree S, Ejlertsen B.

Breast Cancer Res. 2018 Jul 27;20(1):79. doi: 10.1186/s13058-018-1012-0.


Scoring of tumor-infiltrating lymphocytes: From visual estimation to machine learning.

Klauschen F, Müller KR, Binder A, Bockmayr M, Hägele M, Seegerer P, Wienert S, Pruneri G, de Maria S, Badve S, Michiels S, Nielsen TO, Adams S, Savas P, Symmans F, Willis S, Gruosso T, Park M, Haibe-Kains B, Gallas B, Thompson AM, Cree I, Sotiriou C, Solinas C, Preusser M, Hewitt SM, Rimm D, Viale G, Loi S, Loibl S, Salgado R, Denkert C; International Immuno-Oncology Biomarker Working Group.

Semin Cancer Biol. 2018 Oct;52(Pt 2):151-157. doi: 10.1016/j.semcancer.2018.07.001. Epub 2018 Jul 7. Review.


The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma.

Banito A, Li X, Laporte AN, Roe JS, Sanchez-Vega F, Huang CH, Dancsok AR, Hatzi K, Chen CC, Tschaharganeh DF, Chandwani R, Tasdemir N, Jones KB, Capecchi MR, Vakoc CR, Schultz N, Ladanyi M, Nielsen TO, Lowe SW.

Cancer Cell. 2018 Mar 12;33(3):527-541.e8. doi: 10.1016/j.ccell.2018.01.018. Epub 2018 Mar 1. Erratum in: Cancer Cell. 2018 Aug 13;34(2):346-348.


PAM50 Risk of Recurrence Score Predicts 10-Year Distant Recurrence in a Comprehensive Danish Cohort of Postmenopausal Women Allocated to 5 Years of Endocrine Therapy for Hormone Receptor-Positive Early Breast Cancer.

Lænkholm AV, Jensen MB, Eriksen JO, Rasmussen BB, Knoop AS, Buckingham W, Ferree S, Schaper C, Nielsen TO, Haffner T, Kibøl T, Møller Talman ML, Bak Jylling AM, Tabor TP, Ejlertsen B.

J Clin Oncol. 2018 Mar 10;36(8):735-740. doi: 10.1200/JCO.2017.74.6586. Epub 2018 Jan 25.


The ability of PAM50 risk of recurrence score to predict 10-year distant recurrence in hormone receptor-positive postmenopausal women with special histological subtypes.

Laenkholm AV, Jensen MB, Eriksen JO, Buckingham W, Ferree S, Nielsen TO, Ejlertsen B.

Acta Oncol. 2018 Jan;57(1):44-50. doi: 10.1080/0284186X.2017.1403044. Epub 2017 Dec 4.


Mortality and recurrence rates among systemically untreated high risk breast cancer patients included in the DBCG 77 trials.

Jensen MB, Nielsen TO, Knoop AS, Laenkholm AV, Balslev E, Ejlertsen B.

Acta Oncol. 2018 Jan;57(1):135-140. doi: 10.1080/0284186X.2017.1400181. Epub 2017 Nov 23.


Nestin expression in breast cancer: association with prognosis and subtype on 3641 cases with long-term follow-up.

Asleh K, Won JR, Gao D, Voduc KD, Nielsen TO.

Breast Cancer Res Treat. 2018 Feb;168(1):107-115. doi: 10.1007/s10549-017-4583-z. Epub 2017 Nov 20.


Development and Evaluation of a Pan-Sarcoma Fusion Gene Detection Assay Using the NanoString nCounter Platform.

Chang KTE, Goytain A, Tucker T, Karsan A, Lee CH, Nielsen TO, Ng TL.

J Mol Diagn. 2018 Jan;20(1):63-77. doi: 10.1016/j.jmoldx.2017.09.007. Epub 2017 Nov 20.


LAG-3+ tumor infiltrating lymphocytes in breast cancer: clinical correlates and association with PD-1/PD-L1+ tumors.

Burugu S, Gao D, Leung S, Chia SK, Nielsen TO.

Ann Oncol. 2017 Dec 1;28(12):2977-2984. doi: 10.1093/annonc/mdx557.


The driver landscape of sporadic chordoma.

Tarpey PS, Behjati S, Young MD, Martincorena I, Alexandrov LB, Farndon SJ, Guzzo C, Hardy C, Latimer C, Butler AP, Teague JW, Shlien A, Futreal PA, Shah S, Bashashati A, Jamshidi F, Nielsen TO, Huntsman D, Baumhoer D, Brandner S, Wunder J, Dickson B, Cogswell P, Sommer J, Phillips JJ, Amary MF, Tirabosco R, Pillay N, Yip S, Stratton MR, Flanagan AM, Campbell PJ.

Nat Commun. 2017 Oct 12;8(1):890. doi: 10.1038/s41467-017-01026-0.


Cell Cycle-Dependent Tumor Engraftment and Migration Are Enabled by Aurora-A.

Chu TLH, Connell M, Zhou L, He Z, Won J, Chen H, Rahavi SMR, Mohan P, Nemirovsky O, Fotovati A, Pujana MA, Reid GSD, Nielsen TO, Pante N, Maxwell CA.

Mol Cancer Res. 2018 Jan;16(1):16-31. doi: 10.1158/1541-7786.MCR-17-0417. Epub 2017 Oct 9.


Emerging targets in cancer immunotherapy.

Burugu S, Dancsok AR, Nielsen TO.

Semin Cancer Biol. 2018 Oct;52(Pt 2):39-52. doi: 10.1016/j.semcancer.2017.10.001. Epub 2017 Oct 5. Review.


Death by HDAC Inhibition in Synovial Sarcoma Cells.

Laporte AN, Poulin NM, Barrott JJ, Wang XQ, Lorzadeh A, Vander Werff R, Jones KB, Underhill TM, Nielsen TO.

Mol Cancer Ther. 2017 Dec;16(12):2656-2667. doi: 10.1158/1535-7163.MCT-17-0397. Epub 2017 Sep 6.


Role of Cytotoxic Tumor-Infiltrating Lymphocytes in Predicting Outcomes in Metastatic HER2-Positive Breast Cancer: A Secondary Analysis of a Randomized Clinical Trial.

Liu S, Chen B, Burugu S, Leung S, Gao D, Virk S, Kos Z, Parulekar WR, Shepherd L, Gelmon KA, Nielsen TO.

JAMA Oncol. 2017 Nov 9;3(11):e172085. doi: 10.1001/jamaoncol.2017.2085. Epub 2017 Nov 9.


High-Throughput Screening of Myxoid Liposarcoma Cell Lines: Survivin Is Essential for Tumor Growth.

de Graaff MA, Malu S, Guardiola I, Kruisselbrink AB, de Jong Y, Corver WE, Gelderblom H, Hwu P, Nielsen TO, Lazar AJ, Somaiah N, Bovée JVMG.

Transl Oncol. 2017 Aug;10(4):546-554. doi: 10.1016/j.tranon.2017.05.007. Epub 2017 Jun 24.


Competing Risks of Mortality by PAM50 Intrinsic Subtype of British Columbia Tamoxifen-Treated Cohort of Postmenopausal Patients With Breast Cancer.

Chapman JW, Liu S, Leung S, Nielsen TO.

Clin Breast Cancer. 2017 Jul;17(4):e215-e224. doi: 10.1016/j.clbc.2017.01.002. Epub 2017 Jan 20.


HDAC and Proteasome Inhibitors Synergize to Activate Pro-Apoptotic Factors in Synovial Sarcoma.

Laporte AN, Barrott JJ, Yao RJ, Poulin NM, Brodin BA, Jones KB, Underhill TM, Nielsen TO.

PLoS One. 2017 Jan 5;12(1):e0169407. doi: 10.1371/journal.pone.0169407. eCollection 2017.


An mRNA Gene Expression-Based Signature to Identify FGFR1-Amplified Estrogen Receptor-Positive Breast Tumors.

Luo J, Liu S, Leung S, Gru AA, Tao Y, Hoog J, Ho J, Davies SR, Allred DC, Salavaggione AL, Snider J, Mardis ER, Nielsen TO, Ellis MJ.

J Mol Diagn. 2017 Jan;19(1):147-161. doi: 10.1016/j.jmoldx.2016.09.007.


Advances in sarcoma diagnostics and treatment.

Dancsok AR, Asleh-Aburaya K, Nielsen TO.

Oncotarget. 2017 Jan 24;8(4):7068-7093. doi: 10.18632/oncotarget.12548. Review.


αB-crystallin Expression in Breast Cancer is Associated with Brain Metastasis.

Voduc KD, Nielsen TO, Perou CM, Harrell JC, Fan C, Kennecke H, Minn AJ, Cryns VL, Cheang MCU.

NPJ Breast Cancer. 2015 Oct 21;1. pii: 15014. doi: 10.1038/npjbcancer.2015.14.


High-Risk Premenopausal Luminal A Breast Cancer Patients Derive no Benefit from Adjuvant Cyclophosphamide-based Chemotherapy: Results from the DBCG77B Clinical Trial.

Nielsen TO, Jensen MB, Burugu S, Gao D, Jørgensen CL, Balslev E, Ejlertsen B.

Clin Cancer Res. 2017 Feb 15;23(4):946-953. doi: 10.1158/1078-0432.CCR-16-1278. Epub 2016 Sep 6.


Basal biomarkers nestin and INPP4b identify intrinsic subtypes accurately in breast cancers that are weakly positive for oestrogen receptor.

Asleh-Aburaya K, Sheffield BS, Kos Z, Won JR, Wang XQ, Gao D, Wolber R, Gilks CB, Bernard PS, Chia SK, Nielsen TO.

Histopathology. 2017 Jan;70(2):185-194. doi: 10.1111/his.13038. Epub 2016 Sep 29.


Establishment and characterization of a new human myxoid liposarcoma cell line (DL-221) with the FUS-DDIT3 translocation.

de Graaff MA, Yu JS, Beird HC, Ingram DR, Nguyen T, Juehui Liu J, Bolshakov S, Szuhai K, Åman P, Torres KE, Lev D, Nielsen TO, Bovée JV, Lazar AJ, Somaiah N.

Lab Invest. 2016 Aug;96(8):885-94. doi: 10.1038/labinvest.2016.64. Epub 2016 Jun 6.


Analytical validation of a standardized scoring protocol for Ki67: phase 3 of an international multicenter collaboration.

Leung SCY, Nielsen TO, Zabaglo L, Arun I, Badve SS, Bane AL, Bartlett JMS, Borgquist S, Chang MC, Dodson A, Enos RA, Fineberg S, Focke CM, Gao D, Gown AM, Grabau D, Gutierrez C, Hugh JC, Kos Z, Lænkholm AV, Lin MG, Mastropasqua MG, Moriya T, Nofech-Mozes S, Osborne CK, Penault-Llorca FM, Piper T, Sakatani T, Salgado R, Starczynski J, Viale G, Hayes DF, McShane LM, Dowsett M.

NPJ Breast Cancer. 2016 May 18;2:16014. doi: 10.1038/npjbcancer.2016.14. eCollection 2016.


Immune infiltrates in the breast cancer microenvironment: detection, characterization and clinical implication.

Burugu S, Asleh-Aburaya K, Nielsen TO.

Breast Cancer. 2017 Jan;24(1):3-15. doi: 10.1007/s12282-016-0698-z. Epub 2016 May 2. Review.


Identification of cytotoxic agents disrupting synovial sarcoma oncoprotein interactions by proximity ligation assay.

Laporte AN, Ji JX, Ma L, Nielsen TO, Brodin BA.

Oncotarget. 2016 Jun 7;7(23):34384-94. doi: 10.18632/oncotarget.8882.


Molecular subtype profiling of invasive breast cancers weakly positive for estrogen receptor.

Sheffield BS, Kos Z, Asleh-Aburaya K, Wang XQ, Leung S, Gao D, Won J, Chow C, Rachamadugu R, Stijleman I, Wolber R, Gilks CB, Myles N, Thomson T, Hayes MM, Bernard PS, Nielsen TO, Chia SK.

Breast Cancer Res Treat. 2016 Feb;155(3):483-90. doi: 10.1007/s10549-016-3689-z. Epub 2016 Feb 4.


PAM50 gene signatures and breast cancer prognosis with adjuvant anthracycline- and taxane-based chemotherapy: correlative analysis of C9741 (Alliance).

Liu MC, Pitcher BN, Mardis ER, Davies SR, Friedman PN, Snider JE, Vickery TL, Reed JP, DeSchryver K, Singh B, Gradishar WJ, Perez EA, Martino S, Citron ML, Norton L, Winer EP, Hudis CA, Carey LA, Bernard PS, Nielsen TO, Perou CM, Ellis MJ, Barry WT.

NPJ Breast Cancer. 2016;2. pii: 15023. doi: 10.1038/npjbcancer.2015.23. Epub 2016 Jan 6.


Targeting Human Cancer by a Glycosaminoglycan Binding Malaria Protein.

Salanti A, Clausen TM, Agerbæk MØ, Al Nakouzi N, Dahlbäck M, Oo HZ, Lee S, Gustavsson T, Rich JR, Hedberg BJ, Mao Y, Barington L, Pereira MA, LoBello J, Endo M, Fazli L, Soden J, Wang CK, Sander AF, Dagil R, Thrane S, Holst PJ, Meng L, Favero F, Weiss GJ, Nielsen MA, Freeth J, Nielsen TO, Zaia J, Tran NL, Trent J, Babcook JS, Theander TG, Sorensen PH, Daugaard M.

Cancer Cell. 2015 Oct 12;28(4):500-514. doi: 10.1016/j.ccell.2015.09.003.


The genomic landscape of epithelioid sarcoma cell lines and tumours.

Jamshidi F, Bashashati A, Shumansky K, Dickson B, Gokgoz N, Wunder JS, Andrulis IL, Lazar AJ, Shah SP, Huntsman DG, Nielsen TO.

J Pathol. 2016 Jan;238(1):63-73. doi: 10.1002/path.4636. Epub 2015 Oct 19.


Dual loss of the SWI/SNF complex ATPases SMARCA4/BRG1 and SMARCA2/BRM is highly sensitive and specific for small cell carcinoma of the ovary, hypercalcaemic type.

Karnezis AN, Wang Y, Ramos P, Hendricks WP, Oliva E, D'Angelo E, Prat J, Nucci MR, Nielsen TO, Chow C, Leung S, Kommoss F, Kommoss S, Silva A, Ronnett BM, Rabban JT, Bowtell DD, Weissman BE, Trent JM, Gilks CB, Huntsman DG.

J Pathol. 2016 Feb;238(3):389-400. doi: 10.1002/path.4633. Epub 2015 Dec 21.


New Strategies in Sarcoma: Linking Genomic and Immunotherapy Approaches to Molecular Subtype.

Lim J, Poulin NM, Nielsen TO.

Clin Cancer Res. 2015 Nov 1;21(21):4753-9. doi: 10.1158/1078-0432.CCR-15-0831. Epub 2015 Sep 1. Review.


TLE3 is not a predictive biomarker for taxane sensitivity in the NCIC CTG MA.21 clinical trial.

Bartlett JM, Nielsen TO, Gao D, Gelmon KA, Quintayo MA, Starczynski J, Han L, Burnell MJ, Levine MN, Chen BE, Shepherd LE, Chapman JW; NCIC CTG.

Br J Cancer. 2015 Sep 1;113(5):722-8. doi: 10.1038/bjc.2015.271. Epub 2015 Aug 18.


Adverse local tissue reactions in metal-on-polyethylene total hip arthroplasty due to trunnion corrosion: the risk of misdiagnosis.

Whitehouse MR, Endo M, Zachara S, Nielsen TO, Greidanus NV, Masri BA, Garbuz DS, Duncan CP.

Bone Joint J. 2015 Aug;97-B(8):1024-30. doi: 10.1302/0301-620X.97B8.34682. Erratum in: Bone Joint J. 2015 Dec;97-B(12):1732.


Identification of a Low-Risk Luminal A Breast Cancer Cohort That May Not Benefit From Breast Radiotherapy.

Liu FF, Shi W, Done SJ, Miller N, Pintilie M, Voduc D, Nielsen TO, Nofech-Mozes S, Chang MC, Whelan TJ, Weir LM, Olivotto IA, McCready DR, Fyles AW.

J Clin Oncol. 2015 Jun 20;33(18):2035-40. doi: 10.1200/JCO.2014.57.7999. Epub 2015 May 11.


Defining breast cancer intrinsic subtypes by quantitative receptor expression.

Cheang MC, Martin M, Nielsen TO, Prat A, Voduc D, Rodriguez-Lescure A, Ruiz A, Chia S, Shepherd L, Ruiz-Borrego M, Calvo L, Alba E, Carrasco E, Caballero R, Tu D, Pritchard KI, Levine MN, Bramwell VH, Parker J, Bernard PS, Ellis MJ, Perou CM, Di Leo A, Carey LA.

Oncologist. 2015 May;20(5):474-82. doi: 10.1634/theoncologist.2014-0372. Epub 2015 Apr 23.


CCR 20th Anniversary Commentary: The Development of Breast Cancer Molecular Subtyping.

Nielsen TO, Perou CM.

Clin Cancer Res. 2015 Apr 15;21(8):1779-81. doi: 10.1158/1078-0432.CCR-14-2552.


An international study to increase concordance in Ki67 scoring.

Polley MY, Leung SC, Gao D, Mastropasqua MG, Zabaglo LA, Bartlett JM, McShane LM, Enos RA, Badve SS, Bane AL, Borgquist S, Fineberg S, Lin MG, Gown AM, Grabau D, Gutierrez C, Hugh JC, Moriya T, Ohi Y, Osborne CK, Penault-Llorca FM, Piper T, Porter PL, Sakatani T, Salgado R, Starczynski J, Lænkholm AV, Viale G, Dowsett M, Hayes DF, Nielsen TO.

Mod Pathol. 2015 Jun;28(6):778-86. doi: 10.1038/modpathol.2015.38. Epub 2015 Feb 20.


Cancer genomics: why rare is valuable.

Jamshidi F, Nielsen TO, Huntsman DG.

J Mol Med (Berl). 2015 Apr;93(4):369-81. doi: 10.1007/s00109-015-1260-8. Epub 2015 Feb 14. Review.


A phase II study of SB939, a novel pan-histone deacetylase inhibitor, in patients with translocation-associated recurrent/metastatic sarcomas-NCIC-CTG IND 200†.

Chu QS, Nielsen TO, Alcindor T, Gupta A, Endo M, Goytain A, Xu H, Verma S, Tozer R, Knowling M, Bramwell VB, Powers J, Seymour LK, Eisenhauer EA.

Ann Oncol. 2015 May;26(5):973-81. doi: 10.1093/annonc/mdv033. Epub 2015 Jan 28.


Synovial sarcoma: recent discoveries as a roadmap to new avenues for therapy.

Nielsen TO, Poulin NM, Ladanyi M.

Cancer Discov. 2015 Feb;5(2):124-34. doi: 10.1158/2159-8290.CD-14-1246. Epub 2015 Jan 22. Review.


Prognostic and predictive investigation of PAM50 intrinsic subtypes in the NCIC CTG MA.21 phase III chemotherapy trial.

Liu S, Chapman JA, Burnell MJ, Levine MN, Pritchard KI, Whelan TJ, Rugo HS, Albain KS, Perez EA, Virk S, Barry G, Gao D, O'Brien P, Shepherd LE, Nielsen TO, Gelmon KA.

Breast Cancer Res Treat. 2015 Jan;149(2):439-48. doi: 10.1007/s10549-014-3259-1. Epub 2015 Jan 1.


NY-ESO-1 (CTAG1B) expression in mesenchymal tumors.

Endo M, de Graaff MA, Ingram DR, Lim S, Lev DC, Briaire-de Bruijn IH, Somaiah N, Bovée JV, Lazar AJ, Nielsen TO.

Mod Pathol. 2015 Apr;28(4):587-95. doi: 10.1038/modpathol.2014.155. Epub 2014 Nov 21.


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