Publications

  1. Chen M, Andreozzi M, Pockaj B, Barrett MT, Ocal IT, McCullough AE, Linnaus ME, Chang JM, Yearley JH, Annamalai L, Anderson KS. Development and validation of a novel clinical fluorescence in situ hybridization assay to detect JAK2 and PD-L1 amplification: a fluorescence in situ hybridization assay for JAK2 and PD-L1 amplification. Mod Pathol. 2017 Nov; 30 (11):1516-1526 Epub 2017 July 28
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  2. Barrett MT, Deiotte R, Lenkiewicz E, Malasi S, Holley T, Evers L, Posner RG, Jones T, Han H, Sausen M, Velculescu VE, Drebin J, O'Dwyer P, Jameson G, Ramanathan RK, Von Hoff DD. Clinical study of genomic drivers in pancreatic ductal adenocarcinoma. Br J Cancer. 2017 Aug 08; 117 (4):572-582 Epub 2017 July 18
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  3. Bryce AH, Borad MJ, Egan JB, Condjella RM, Liang WS, Fonseca R, McCullough AE, Hunt KS, Ritacca NR, Barrett MT, Patel MD, Young SW, Silva AC, Ho TH, Halfdanarson TR, Stanton ML, Cheville J, Swanson S, Schneider DE, McWilliams RR, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Cuyugan L, McDonald J, Adkins J, Mastrian SD, Von Hoff DD, Craig DW, Stewart AK, Carpten JD. Comprehensive Genomic Analysis of Metastatic Mucinous Urethral Adenocarcinoma Guides Precision Oncology Treatment: Targetable EGFR Amplification Leading to Successful Treatment With Erlotinib. Clin Genitourin Cancer. 2017 Aug; 15 (4):e727-e734 Epub 2016 Dec 01
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  4. Goncalves PH, Heilbrun LK, Barrett MT, Kummar S, Hansen AR, Siu LL, Piekarz RL, Sukari AW, Chao J, Pilat MJ, Smith DW, Casetta L, Boerner SA, Chen A, Lenkiewicz E, Malasi S, LoRusso PM. A phase 2 study of vorinostat in locally advanced, recurrent, or metastatic adenoid cystic carcinoma. Oncotarget. 2017 May 16; 8: (20)32918-32929.
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  5. Whatcott CJ, Ng S, Barrett MT, Hostetter G, Von Hoff DD, Han H. Inhibition of ROCK1 kinase modulates both tumor cells and stromal fibroblasts in pancreatic cancer. PLoS One. 2017; 12 (8):e0183871 Epub 2017 Aug 25
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  6. Borad MJ, Egan JB, Condjella RM, Liang WS, Fonseca R, Ritacca NR, McCullough AE, Barrett MT, Hunt KS, Champion MD, Patel MD, Young SW, Silva AC, Ho TH, Halfdanarson TR, McWilliams RR, Lazaridis KN, Ramanathan RK, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Cuyugan L, McDonald J, Adkins J, Mastrian SD, Valdez R, Jaroszewski DE, Von Hoff DD, Craig DW, Stewart AK, Carpten JD, Bryce AH. Clinical Implementation of Integrated Genomic Profiling in Patients with Advanced Cancers. Sci Rep. 2016 Dec 23; 6: (1)25.
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  7. Wang Y, Ding X, Wang S, Moser CD, Shaleh HM, Mohamed EA, Chaiteerakij R, Allotey LK, Chen G, Miyabe K, McNulty MS, Ndzengue A, Barr Fritcher EG, Knudson RA, Greipp PT, Clark KJ, Torbenson MS, Kipp BR, Zhou J, Barrett MT, Gustafson MP, Alberts SR, Borad MJ, Roberts LR. Antitumor effect of FGFR inhibitors on a novel cholangiocarcinoma patient derived xenograft mouse model endogenously expressing an FGFR2-CCDC6 fusion protein. Cancer Lett. 2016 Sep 28; 380 (1):163-73 Epub 2016 May 20
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  8. Barrett MT, Anderson KS, Lenkiewicz E, Andreozzi M, Cunliffe HE, Klassen CL, Dueck AC, McCullough AE, Reddy SK, Ramanathan RK, Northfelt DW, Pockaj BA. Genomic amplification of 9p24.1 targeting JAK2, PD-L1, and PD-L2 is enriched in high-risk triple negative breast cancer. Oncotarget. 2015 Sep 22; 6: (28)26483-93.
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  9. Sausen M, Phallen J, Adleff V, Jones S, Leary RJ, Barrett MT, Anagnostou V, Parpart-Li S, Murphy D, Kay Li Q, Hruban CA, Scharpf R, White JR, O'Dwyer PJ, Allen PJ, Eshleman JR, Thompson CB, Klimstra DS, Linehan DC, Maitra A, Hruban RH, Diaz LA Jr, Von Hoff DD, Johansen JS, Drebin JA, Velculescu VE. Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients. Nat Commun. 2015 Jul 07; 6:7686.
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  10. Xu J, Margol AS, Shukla A, Ren X, Finlay JL, Krieger MD, Gilles FH, Couch FJ, Aziz M, Fung ET, Asgharzadeh S, Barrett MT, Erdreich-Epstein A. Disseminated Medulloblastoma in a Child with Germline BRCA2 6174delT Mutation and without Fanconi Anemia. Front Oncol. 2015; 5:191.
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  11. Ramos P, Karnezis AN, Craig DW, Sekulic A, Russell ML, Hendricks WP, Corneveaux JJ, Barrett MT, Shumansky K, Yang Y, Shah SP, Prentice LM, Marra MA, Kiefer J, Zismann VL, McEachron TA, Salhia B, Prat J, D'Angelo E, Clarke BA, Pressey JG, Farley JH, Anthony SP, Roden RB, Cunliffe HE, Huntsman DG, Trent JM. Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4. Nat Genet. 2014 May; 46: (5)427-9.
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  12. McGhan LJ, McCullough AE, Protheroe CA, Dueck AC, Lee JJ, Nunez-Nateras R, Castle EP, Gray RJ, Wasif N, Goetz MP, Hawse JR, Henry TJ, Barrett MT, Cunliffe HE, Pockaj BA. Androgen receptor-positive triple negative breast cancer: a unique breast cancer subtype. Ann Surg Oncol. 2014 Feb; 21: (2)361-7.
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  13. Borad MJ, Champion MD, Egan JB, Liang WS, Fonseca R, Bryce AH, McCullough AE, Barrett MT, Hunt K, Patel MD, Young SW, Collins JM, Silva AC, Condjella RM, Block M, McWilliams RR, Lazaridis KN, Klee EW, Bible KC, Harris P, Oliver GR, Bhavsar JD, Nair AA, Middha S, Asmann Y, Kocher JP, Schahl K, Kipp BR, Barr Fritcher EG, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Phillips L, McDonald J, Adkins J, Mastrian SD, Placek P, Watanabe AT, Lobello J, Han H, Von Hoff D, Craig DW, Stewart AK, Carpten JD. Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma. PLoS Genet. 2014 Feb; 10: (2)e1004135.
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  14. Stieber D, Golebiewska A, Evers L, Lenkiewicz E, Brons NH, Nicot N, Oudin A, Bougnaud S, Hertel F, Bjerkvig R, Vallar L, Barrett MT, Niclou SP. Glioblastomas are composed of genetically divergent clones with distinct tumourigenic potential and variable stem cell-associated phenotypes. Acta Neuropathol. 2014 Feb; 127(2):203-19. Epub 2013 Oct 24.
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  15. Egan JB, Barrett MT, Champion MD, Middha S, Lenkiewicz E, Evers L, Francis P, Schmidt J, Shi CX, Van Wier S, Badar S, Ahmann G, Kortuem KM, Boczek NJ, Fonseca R, Craig DW, Carpten JD, Borad MJ, Stewart AK. Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements. PLoS One. 2014; 9: (2)e87113.
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  16. Evers L, Perez-Mancera PA, Lenkiewicz E, Tang N, Aust D, Knosel T, Rummele P, Holley T, Kassner M, Aziz M, Ramanathan RK, Von Hoff DD, Yin H, Pilarsky C, Barrett MT. STAG2 is a clinically relevant tumor suppressor in pancreatic ductal adenocarcinoma. Genome Med. 2014; 6(1):9. Epub 2014 Jan 31.
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  17. Przybytkowski E, Lenkiewicz E, Barrett M, Klein K, Nabavi S, Greenwood C, Basik M. Chromosome-breakage genomic instability and chromothripsis in breast cancer. BMC Genomics. 2014; 15:579. Epub 2014 Jul 9
  18. Kurywchak P, Kiefer J, Lenkiewicz E, Evers L, Holley T, Barrett M, Weiss GJ. Elucidating potentially significant genomic regions involved in the initiation and progression of undifferentiated pleomorphic sarcoma. Rare Tumors. 2013 Feb 11; 5(1):e14. Epub 2013 Mar 25.
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  19. Barrett MT, Lenkiewicz E, Evers L, Holley T, Ruiz C, Bubendorf L, Sekulic A, Ramanathan RK, Von Hoff DD. Clonal evolution and therapeutic resistance in solid tumors. Front Pharmacol. 2013; 4:2. Epub 2013 Jan 28.
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  20. Liu SV, Lenkiewicz E, Evers L, Holley T, Kiefer J, Ruiz C, Glatz K, Bubendorf L, Demeure MJ, Eng C, Ramanathan RK, Von Hoff DD, Barrett MT. Genomic analysis and selected molecular pathways in rare cancers. Phys Biol. 2012 Dec; 9(6):065004. Epub 2012 Nov 29.
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  21. Keats JJ, Chesi M, Egan JB, Garbitt VM, Palmer SE, Braggio E, Van Wier S, Blackburn PR, Baker AS, Dispenzieri A, Kumar S, Rajkumar SV, Carpten JD, Barrett M, Fonseca R, Stewart AK, Bergsagel PL. Clonal competition with alternating dominance in multiple myeloma. Blood. 2012 Aug 2; 120: (5)1067-76.
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  22. Braggio E, Dogan A, Keats JJ, Chng WJ, Huang G, Matthews JM, Maurer MJ, Law ME, Bosler DS, Barrett M, Lossos IS, Witzig TE, Fonseca R. Genomic analysis of marginal zone and lymphoplasmacytic lymphomas identified common and disease-specific abnormalities. Mod Pathol. 2012 May; 25: (5)651-60.
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  23. Liang WS, Craig DW, Carpten J, Borad MJ, Demeure MJ, Weiss GJ, Izatt T, Sinari S, Christoforides A, Aldrich J, Kurdoglu A, Barrett M, Phillips L, Benson H, Tembe W, Braggio E, Kiefer JA, Legendre C, Posner R, Hostetter GH, Baker A, Egan JB, Han H, Lake D, Stites EC, Ramanathan RK, Fonseca R, Stewart AK, Von Hoff. Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing. PLoS One. 2012; 7(10):e43192. Epub 2012 Oct 10.
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  24. Holley T, Lenkiewicz E, Evers L, Tembe W, Ruiz C, Gsponer JR, Rentsch CA, Bubendorf L, Stapleton M, Amorese D, Legendre C, Cunliffe HE, McCullough AE, Pockaj B, Craig D, Carpten J, Von Hoff D, Iacobuzio-Donahue C, Barrett MT. Deep clonal profiling of formalin fixed paraffin embedded clinical samples. PLoS ONE. 2012; 7(11):e50586.
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  25. Arora S, Korn RL, Lenkiewicz E, Cherni I, Beach TG, Hostetter G, Barrett MT, Weiss GJ. Clonal evolution of a case of treatment refractory maxillary sinus carcinoma. PLoS One. 2012; 7(9):e45614. Epub 2012 Sep 28.
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  26. Ruiz C, Lenkiewicz E, Evers L, Holley T, Robeson A, Kiefer J, Demeure MJ, Hollingsworth MA, Shen M, Prunkard D, Rabinovitch PS, Zellweger T, Mousses S, Trent JM, Carpten JD, Bubendorf L, Von Hoff D, Barrett MT. Advancing a clinically relevant perspective of the clonal nature of cancer. Proc Natl Acad Sci U S A. 2011 Jul 19; 108(29):12054-9. Epub 2011 Jul 05.
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  27. Baehner FL, Lee M, Demeure MJ, Bussey KJ, Kiefer JA, Barrett MT. Genomic signatures of cancer: basis for individualized risk assessment, selective staging and therapy. J Surg Oncol. 2011 May 1; 103(6):563-73.
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  28. Ruiz C, Holz DR, Oeggerli M, Schneider S, Gonzales IM, Kiefer JM, Zellweger T, Bachmann A, Koivisto PA, Helin HJ, Mousses S, Barrett MT, Azorsa DO, Bubendorf L. Amplification and overexpression of vinculin are associated with increased tumour cell proliferation and progression in advanced prostate cancer. J Pathol. 2011 Mar; 223(4):543-52. Epub 2011 Jan 05.
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  29. Pandita A, Bayani J, Paderova J, Marrano P, Graham C, Barrett M, Prasad M, Zielenska M, Squire JA. Integrated cytogenetic and high-resolution array CGH analysis of genomic alterations associated with MYCN amplification. Cytogenet Genome Res. 2011; 134(1):27-39. Epub 2011 Apr 18.
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  30. Robbins CM, Tembe WA, Baker A, Sinari S, Moses TY, Beckstrom-Sternberg S, Beckstrom-Sternberg J, Barrett M, Long J, Chinnaiyan A, Lowey J, Suh E, Pearson JV, Craig DW, Agus DB, Pienta KJ, Carpten JD. Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors. Genome Res. 2011 Jan; 21(1):47-55. Epub 2010 Dec 8
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  31. Garrido-Laguna I, Tan AC, Uson M, Angenendt M, Ma WW, Villaroel MC, Zhao M, Rajeshkumar NV, Jimeno A, Donehower R, Iacobuzio-Donahue C, Barrett M, Rudek MA, Rubio-Viqueira B, Laheru D, Hidalgo M. Integrated preclinical and clinical development of mTOR inhibitors in pancreatic cancer. Br J Cancer. 2010 Aug 24; 103(5):649-55. Epub 2010 Jul 27.
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  32. Lai LA, Kostadinov R, Barrett MT, Peiffer DA, Pokholok D, Odze R, Sanchez CA, Maley CC, Reid BJ, Gunderson KL, Rabinovitch PS. Deletion at fragile sites is a common and early event in Barrett's esophagus. Mol Cancer Res. 2010 Aug; 8(8):1084-94. Epub 2010 Jul 20.
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  33. Sekulic A, Miller A, Barrett M, Ejadi S, Mengos A, Pockaj B, Markovic S. Identification of targetable cellular subsets within melanoma tumors. J Clin Oncol. 2009 May 20; 27: (15_suppl)9082.
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  34. Braggio E, Keats JJ, Leleu X, Van Wier S, Jimenez-Zepeda VH, Valdez R, Schop RF, Price-Troska T, Henderson K, Sacco A, Azab F, Greipp P, Gertz M, Hayman S, Rajkumar SV, Carpten J, Chesi M, Barrett M, Stewart AK, Dogan A, Bergsagel PL, Ghobrial IM, Fonseca R. Identification of copy number abnormalities and inactivating mutations in two negative regulators of nuclear factor-kappaB signaling pathways in Waldenstrom's macroglobulinemia. Cancer Res. 2009 Apr 15; 69: (8)3579-88.
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  35. Braggio E, Keats JJ, Leleu X, Wier SV, Jimenez-Zepeda VH, Schop RF, Chesi M, Barrett M, Stewart AK, Dogan A, Bergsagel PL, Ghobrial IM, Fonseca R. High-resolution genomic analysis in Waldenstrom's macroglobulinemia identifies disease-specific and common abnormalities with marginal zone lymphomas. Clin Lymphoma Myeloma. 2009 Mar; 9: (1)39-42.
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  36. Basu GD, Azorsa DO, Kiefer JA, Rojas AM, Tuzmen S, Barrett MT, Trent JM, Kallioniemi O, Mousses S. Functional evidence implicating S100P in prostate cancer progression. Int J Cancer. 2008 Jul 15; 123(2):330-9.
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  37. Prasad M, Bernardini M, Tsalenko A, Marrano P, Paderova J, Lee CH, Ben-Dor A, Barrett MT, Squire JA. High definition cytogenetics and oligonucleotide aCGH analyses of cisplatin-resistant ovarian cancer cells. Genes Chromosomes Cancer. 2008 May; 47(5):427-36.
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  38. Keats JJ, Fonseca R, Chesi M, Schop R, Baker A, Chng WJ, Van Wier S, Tiedemann R, Shi CX, Sebag M, Braggio E, Henry T, Zhu YX, Fogle H, Price-Troska T, Ahmann G, Mancini C, Brents LA, Kumar S, Greipp P, Dispenzieri A, Bryant B, Mulligan G, Bruhn L, Barrett M, Valdez R, Trent J, Stewart AK, Carpten J, Bergsagel PL. Promiscuous mutations activate the noncanonical NF-kappaB pathway in multiple myeloma. Cancer Cell. 2007 Aug; 12: (2)131-44.
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  39. Barrett MT. Stacking the chips for biological discovery. Nat Genet. 2005 Jun; 37 Suppl:S1.
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  40. Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS, Yakhini Z, Bruhn L, Laderman S. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A. 2004 Dec 21; 101(51):17765-70. Epub 2004 Dec 10.
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  41. Barrett MT, Pritchard D, Palanca-Wessels C, Anderson J, Reid BJ, Rabinovitch PS. Molecular phenotype of spontaneously arising 4N (G2-tetraploid) intermediates of neoplastic progression in Barrett's esophagus. Cancer Res. 2003 Jul 15; 63(14):4211-7.
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  42. Barrett MT, Glogovac J, Prevo LJ, Reid BJ, Porter P, Rabinovitch PS. High-quality RNA and DNA from flow cytometrically sorted human epithelial cells and tissues. Biotechniques. 2002 Apr; 32(4):888-90, 892, 894, 896.
  43. Barrett MT, Yeung KY, Ruzzo WL, Hsu L, Blount PL, Sullivan R, Zarbl H, Delrow J, Rabinovitch PS, Reid BJ. Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae. Neoplasia. 2002 Mar-Apr; 4(2):121-8.
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  44. Sweetser DA, Chen CS, Blomberg AA, Flowers DA, Galipeau PC, Barrett MT, Heerema NA, Buckley J, Woods WG, Bernstein ID, Reid BJ. Loss of heterozygosity in childhood de novo acute myelogenous leukemia. Blood. 2001 Aug 15; 98(4):1188-94.
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  45. Barrett MT, Sanchez CA, Prevo LJ, Wong DJ, Galipeau PC, Paulson TG, Rabinovitch PS, Reid BJ. Evolution of neoplastic cell lineages in Barrett oesophagus. Nat Genet. 1999 May; 22(1):106-9.
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  46. Funk JO, Schiller PI, Barrett MT, Wong DJ, Kind P, Sander CA. p16INK4a expression is frequently decreased and associated with 9p21 loss of heterozygosity in sporadic melanoma. J Cutan Pathol. 1998 Jul; 25(6):291-6.
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  47. Foster SA, Wong DJ, Barrett MT, Galloway DA. Inactivation of p16 in human mammary epithelial cells by CpG island methylation. Mol Cell Biol. 1998 Apr; 18(4):1793-801.
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  48. Palanca-Wessels MC, Barrett MT, Galipeau PC, Rohrer KL, Reid BJ, Rabinovitch PS. Genetic analysis of long-term Barrett's esophagus epithelial cultures exhibiting cytogenetic and ploidy abnormalities. Gastroenterology. 1998 Feb; 114(2):295-304.
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  49. Wong DJ, Barrett MT, Stoger R, Emond MJ, Reid BJ. p16INK4a promoter is hypermethylated at a high frequency in esophageal adenocarcinomas. Cancer Res. 1997 Jul 1; 57(13):2619-22.
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  50. Barrett MT, Sanchez CA, Galipeau PC, Neshat K, Emond M, Reid BJ. Allelic loss of 9p21 and mutation of the CDKN2/p16 gene develop as early lesions during neoplastic progression in Barrett's esophagus. Oncogene. 1996 Nov 7; 13(9):1867-73.
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  51. Barrett MT, Schutte M, Kern SE, Reid BJ. Allelic loss and mutational analysis of the DPC4 gene in esophageal adenocarcinoma. Cancer Res. 1996 Oct 1; 56(19):4351-3.
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  52. Galipeau PC, Cowan DS, Sanchez CA, Barrett MT, Emond MJ, Levine DS, Rabinovitch PS, Reid BJ. 17p (p53) allelic losses, 4N (G2/tetraploid) populations, and progression to aneuploidy in Barrett's esophagus. Proc Natl Acad Sci U S A. 1996 Jul 9; 93(14):7081-4.
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  53. Barrett MT, Galipeau PC, Sanchez CA, Emond MJ, Reid BJ. Determination of the frequency of loss of heterozygosity in esophageal adenocarcinoma by cell sorting, whole genome amplification and microsatellite polymorphisms. Oncogene. 1996 May 2; 12(9):1873-8.
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  54. Reid BJ, Barrett MT, Galipeau PC, Sanchez CA, Neshat K, Cowan DS, Levine DS. Barrett's esophagus: ordering the events that lead to cancer. European Journal of Cancer Prevention. 1996; 5(Supplement 2):57-65.
  55. Barrett MT, Reid BJ, Joslyn G. Genotypic analysis of multiple loci in somatic cells by whole genome amplification. Nucleic Acids Res. 1995 Sep 11; 23(17):3488-92.
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  56. Andrulis IL, Barrett MT. DNA methylation patterns associated with asparagine synthetase expression in asparagine-overproducing and -auxotrophic cells. Mol Cell Biol. 1989 Jul; 9(7):2922-7.
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