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Benjamin R. Kipp, Ph.D.

  1. Clinical Molecular Geneticist
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Publications

  1. Atiq MA, Balan J, Blackburn PR, Gross JM, Voss JS, Jin L, Fadra N, Davila JI, Pitel BA, Siqueira Parrilha Terra SB, Minn KT, Jackson RA, Hofich CD, Willkomm KS, Peterson BJ, Clausen SN, Rumilla KM, Gupta S, Lo YC, Ida CM, Molligan JF, Thangaiah JJ, Petersen MJ, Sukov WR, Guo R, Giannini C, Schoolmeester JK 2nd, Fritchie K, Inwards CY, Folpe AL, Oliveira AM, Torres-Mora J, Kipp BR, Halling KC. SARCP, a Clinical Next-Generation Sequencing Assay for the Detection of Gene Fusions in Sarcomas: A Description of the First 652 Cases. J Mol Diagn. 2024 Nov 7 Epub 2024 Nov 07
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  2. Villalba JA, Terra SB, Pitel B, Knight SM, Kipp BR, Boland JM. Clinicopathologic and Molecular Characteristics of Resected Thoracic Mass Lesions in the Pediatric Population: A 25-Year Institutional Experience From a Tertiary Care Center. Arch Pathol Lab Med. 2024 Nov 1; 148 (11):1209-1217
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  3. Aggarwal M, Simadibrata DM, Kipp BR, Prokop LJ, Barr Fritcher EG, Schneider A, Cooley MA, Gores GJ, Eaton J, Roberts LR, Chandrasekhara V. Diagnostic Accuracy Performance of Fluorescence In Situ Hybridization (FISH) for Biliary Strictures: A Systematic Review and Meta-Analysis. J Clin Med. 2024 Oct 28; 13 (21)
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  4. Furtado LV, Bifulco C, Dolderer D, Hsiao SJ, Kipp BR, Lindeman NI, Ritterhouse LL, Temple-Smolkin RL, Zehir A, Nowak JA. Recommendations for Tumor Mutational Burden Assay Validation and Reporting: A Joint Consensus Recommendation of the Association for Molecular Pathology, College of American Pathologists, and Society for Immunotherapy of Cancer. J Mol Diagn. 2024 Aug; 26 (8):653-668 Epub 2024 June 06
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  5. Furtado LV, Bifulco C, Dolderer D, Hsiao SJ, Kipp BR, Lindeman NI, Ritterhouse LL, Temple-Smolkin RL, Zehir A, Nowak JA. A joint consensus recommendation of the Association for Molecular Pathology, College of American Pathologists, and Society for Immunotherapy of Cancer. Journal of Molecular Diagnostics. 2024 Aug; 26 (8):653-68
  6. Mun DG, Bhat FA, Joshi N, Sandoval L, Ding H, Jain A, Peterson JA, Kang T, Pujari GP, Tomlinson JL, Budhraja R, Zenka RM, Kannan N, Kipp BR, Dasari S, Gaspar-Maia A, Smoot RL, Kandasamy RK, Pandey A. Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry. Commun Biol. 2024 Jul 19; 7 (1):884 Epub 2024 July 19
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  7. Blommel JH, Roforth MM, Jerde CR, Karsten CA, Bridgeman AR, Voss JS, Boccuto L, Ivankovic DS, Sarasua SM, Kipp BR, Murphy SJ. Evaluating User Experience and DNA Yield from Self-Collection Devices. J Appl Lab Med. 2024 Jul 1; 9 (4):704-715
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  8. Cooley MA, Schneider AR, Barr Fritcher EG, Milosevic D, Levy MJ, Bridgeman AR, Martin JA, Petersen BT, Abu Dayyeh BK, Storm AC, Law RJ, Vargas EJ, Garimella V, Zemla T, Jenkins SM, Yin J, Gores GJ, Roberts LR, Kipp BR, Chandrasekhara V. Utility of methylated DNA markers for the diagnosis of malignant biliary strictures. Hepatology. 2024 Jun 21 Epub 2024 June 21
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  9. Nielson KJ, Rowsey R, Dasari S, Sukov WR, Kipp BR, Raghunathan A, Whaley RD, Ebare K, Stanton ML, Reynolds JP, Sharma V, Thompson RH, Boorjian SA, Leibovich BC, Hernandez LH, Jimenez RE, Cheville JC, Gupta S. Single nucleotide polymorphism (SNP) chromosomal microarray as a diagnostic tool for mucinous tubular and spindle cell carcinoma: A validation study. Hum Pathol. 2024 Apr; 146:57-65 Epub 2024 Apr 12
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  10. Majumdar R, Taye B, Bjornberg C, Giljork M, Lynch D, Farah F, Abdullah I, Osiecki K, Yousaf I, Luckstein A, Turri W, Sampathkumar P, Moyer AM, Kipp BR, Cattaneo R, Sussman CR, Navaratnarajah CK. From pandemic to endemic: Divergence of COVID-19 positive-tests and hospitalization numbers from SARS-CoV-2 RNA levels in wastewater of Rochester, Minnesota. Heliyon. 2024 Mar 30; 10 (6):e27974 Epub 2024 Mar 11
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  11. Dasari S, McCarthy MR, Wojcik AA, Pitel BA, Samaddar A, Tekin B, Whaley RD, Raghunathan A, Hernandez LH, Jimenez RE, Stish BJ, Thompson RH, Leibovich BC, Boorjian SA, Jeffrey Karnes R, Childs DS, Quevedo JF, Kwon ED, Pagliaro LC, Costello BA, Halling KC, Cheville JC, Kipp BR, Gupta S. Genomic attributes of prostate cancer across primary and metastatic noncastrate and castrate resistant disease states: a next generation sequencing study of 183 patients. Prostate Cancer Prostatic Dis. 2024 Feb 27. [Epub ahead of print]
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  12. Walsh JR, Sun G, Balan J, Hardcastle J, Vollenweider J, Jerde C, Rumilla K, Koellner C, Koleilat A, Hasadsri L, Kipp B, Jenkinson G, Klee E. A supervised learning method for classifying methylation disorders. BMC Bioinformatics. 2024 Feb 12; 25 (1):66
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  13. Dehner CA, Torres-Mora J, Gupta S, Kipp BR, Halling KC, Chen S, Warmke LM, Michal M, Alani A, Yu W, Kovacs K, Obeidin F, Iwenofu OH, Satturwar S, Meis JM, Folpe AL. Sarcomas Harboring EWSR1::PATZ1 Fusions: A Clinicopathologic Study of 17 Cases. Mod Pathol. 2024 Feb; 37 (2):100400 Epub 2023 Dec 01
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  14. Blommel JH, Boccuto L, Ivankovic DS, Sarasua SM, Kipp BR, Karon BS. SARS-CoV-2 emergency use authorization published sensitivity differences do not correlate with positivity rate in a hospital/reference laboratory setting. Diagn Microbiol Infect Dis. 2024 Feb; 108 (2):116157 Epub 2023 Dec 10
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  15. Gagnon MF, Schoolmeester JK, Dasari S, Kipp BR, Cheville JC, Gupta S. Molecular alterations in primary and metastatic PEComa: insights from the AACR project GENIE data set. Hum Pathol 2024 Jan; 143:75-76 Epub 2023 Oct 06
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  16. Marya NB, Hartley C, Powers PD, Bois MC, Kerr SE, Graham RP, Levy MJ, UMass-Mayo Clinic AI Cytopathology Consortium, Gleeson F, Abu Dayyeh BK, Bofill-Garcia A, Chandrasekhara V, Gores G, Kipp B, Law RJ, Petersen B, Roberts LR, Storm AC, Vargas Valls EJ. Development of a Computer-aided Prediction Tool for Evaluating Brushing Samples of Biliary Strictures. Clin Gastroenterol Hepatol. 2024 Jan; 22 (1):185-187.e3 Epub 2023 Mar 24
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  17. Vizcaino MA, Folpe AL, Huffman H, Panchal RR, Nielsen GP, Kipp BR, Turakulov R, Aldape K, Giannini C. Pseudoendocrine sarcoma: clinicopathologic, molecular, and epigenetic features of one case. Virchows Arch. 2023 Dec; 483 (6):899-904 Epub 2023 Nov 13
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  18. Karon BS, Donato LJ, Moyer AM, Wockenfus AM, Kelley BR, Majumdar R, Kipp BR, Yao JD. Evaluation of the analytical sensitivity of ACON and LumiraDx SARS-CoV-2 rapid antigen tests using samples with presumed Omicron variant. Diagn Microbiol Infect Dis. 2023 Sep; 107(1):115977. Epub 2023 May 03.
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  19. Oliveira JL, Thompson CH, Saravanaperumal SA, Koganti T, Jenkinson G, Hein MS, Kohorst MA, Hasadsri L, Nguyen PL, Matern D, Kipp BR, Klee EW, Wieben ED, Hoyer JD, Rangan A. epsilongamma-Thalassemia, a New Hemoglobinopathy Category. Clin Chem. 2023 Jul 5; 69 (7):711-717
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  20. Blommel JH, Jenkinson G, Binnicker MJ, Karon BS, Boccuto L, Ivankovic DS, Sarasua SM, Kipp BR. Authorized SARS-CoV-2 molecular methods show wide variability in the limit of detection. Diagn Microbiol Infect Dis. 2023 Mar; 105 (3):115880 Epub 2022 Dec 15
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  21. Gonzalez-Bosquet J, Weroha SJ, Bakkum-Gamez JN, Weaver AL, McGree ME, Dowdy SC, Famuyide AO, Kipp BR, Halling KC, Yadav S, Couch FJ, Podratz KC. Prognostic stratification of endometrial cancers with high microsatellite instability or no specific molecular profile. Front Oncol. 2023; 13:1105504. Epub 2023 May 23.
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  22. Vaubel RA, Kumar R, Weiskittel TM, Jenkins S, Dasari S, Uhm JH, Lachance DH, Brown PD, Van Gompel JJ, Jenkins RB, Kipp BR, Sukov WR, Giannini C, Johnson DR, Raghunathan A. Genomic markers of recurrence risk in atypical meningioma following gross total resection. Neurooncol Adv. 2023 Jan-Dec; 5 (1):vdad004 Epub 2023 Jan 10
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  23. Sridharan V, Neyaz A, Chogule A, Baiev I, Reyes S, Barr Fritcher EG, Lennerz JK, Sukov W, Kipp B, Ting DT, Deshpande V, Goyal L. FGFR mRNA Expression in Cholangiocarcinoma and Its Correlation with FGFR2 Fusion Status and Immune Signatures. Clin Cancer Res. 2022 Dec 15; 28 (24):5431-5439
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  24. Hogenson TL, Xie H, Phillips WJ, Toruner MD, Li JJ, Horn IP, Kennedy DJ, Almada LL, Marks DL, Carr RM, Toruner M, Sigafoos AN, Koenig-Kappes AN, Olson RL, Tolosa EJ, Zhang C, Li H, Doles JD, Bleeker J, Barrett MT, Boyum JH, Kipp BR, Mahipal A, Hubbard JM, Scheffler Hanson TJ, Petersen GM, Dasari S, Oberg AL, Truty MJ, Graham RP, Levy MJ, Zhu M, Billadeau DD, Adjei AA, Dusetti N, Iovanna JL, Bekaii-Saab TS, Ma WW, Fernandez-Zapico ME. Culture media composition influences patient-derived organoid ability to predict therapeutic responses in gastrointestinal cancers. JCI Insight. 2022 Nov 22; 7 (22)
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  25. Ji H, Barr Fritcher EG, Yin J, Bainter TM, Zemla TJ, Gores GJ, Halling KC, Kipp BR, Roberts LR. Evaluating the Significance of Pancreatobiliary Fluorescence In Situ Hybridization Polysomy on Prognosis in De Novo Cholangiocarcinoma. Clin Transl Gastroenterol. 2022 Oct 1; 13 (10):e00523 Epub 2022 Oct 01
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  26. Byeon SK, Madugundu AK, Garapati K, Ramarajan MG, Saraswat M, Kumar-M P, Hughes T, Shah R, Patnaik MM, Chia N, Ashrafzadeh-Kian S, Yao JD, Pritt BS, Cattaneo R, Salama ME, Zenka RM, Kipp BR, Grebe SKG, Singh RJ, Sadighi Akha AA, Algeciras-Schimnich A, Dasari S, Olson JE, Walsh JR, Venkatakrishnan AJ, Jenkinson G, O'Horo JC, Badley AD, Pandey A. Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study. Lancet Digit Health. 2022 Sep; 4 (9):e632-e645 Epub 2022 July 11
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  27. Milosevic D, Moyer AM, Majumdar R, Kipp BR, Yao JD. A reverse-transcription droplet digital PCR assay to detect and quantify SARS-CoV-2 RNA in upper respiratory tract specimens. J Clin Virol. 2022 Aug; 153:105216. Epub 2022 Jun 08.
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  28. Uson Junior PLS, DeLeon TT, Bogenberger JM, Pai RK, Kosiorek HE, Yin J, Ahn DH, Sonbol MB, Bekaii-Saab T, Mansfield AS, Buetow K, Gores GJ, Smoot R, Vasmatzis G, Kipp BR, Mahipal A, Baker AT, Babiker H, Barro O, Dumbauld C, Zhou Y, Aslam FN, Barrett M, Jacobs B, Meurice N, Arora M, Petit J, Elliott N, Nagalo B, Salomao MA, Borad MJ. FGFR2-IIIb Expression by Immunohistochemistry Has High Specificity in Cholangiocarcinoma with FGFR2 Genomic Alterations. Dig Dis Sci. 2022 Aug; 67(8):3797-3805. Epub 2021 Nov 13.
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  29. Majumdar R, Vrana JA, Koepplin JW, Milosevic D, Roden AC, Garcia JJ, Kipp BR, Moyer AM. SARS-CoV-2 RNA detection in Formalin-Fixed Paraffin-Embedded (FFPE) tissue by droplet digital PCR (ddPCR). Clin Chim Acta. 2022 Jul 01; 532:181-187. Epub 2022 May 10.
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  30. Rahi H, Olave MC, Fritchie KJ, Greipp PT, Halling KC, Kipp BR, Graham RP. Gene fusions in gastrointestinal tract cancers. Genes Chromosomes Cancer. 2022 May; 61(5):285-297.
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  31. Maus A, Renuse S, Kemp J, Madugundu AK, Vanderboom PM, Blommel J, Jerde C, Dasari S, Kipp BR, Singh RJ, Grebe SK, Pandey A. Targeted Detection of SARS-CoV-2 Nucleocapsid Sequence Variants by Mass Spectrometric Analysis of Tryptic Peptides. J Proteome Res. 2022 Jan 7; 21 (1):142-150 Epub 2021 Nov 15
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  32. Maus A, Renuse S, Kemp J, Moehnke K, Mangalaparthi KK, Chavan S, Madugundu AK, Vanderboom PM, Dasari S, Kipp BR, Singh RJ, Grebe SK, Pandey A. Comparison of anti-peptide and anti-protein antibody-based purification techniques for detection of SARS-CoV-2 by targeted LC-MS/MS. Advances in Sample Preparation. 2022; 2:100018
  33. Gonzalez-Bosquet J, Weroha SJ, Bakkum-Gamez JN, Weaver AL, McGree ME, Dowdy SC, Famuyide AO, Kipp BR, Halling KC, Yadav S, Couch FJ, Podratz KC. ECPPF (E2F1, CCNA2, POLE, PPP2R1A, FBXW7) stratification: Profiling high-risk subtypes of histomorphologically low-risk and treatment-insensitive endometrioid endometrial cancer. PLoS One. 2022; 17(12):e0278408. Epub 2022 Dec 01.
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  34. Rangan A, Hein MS, Jenkinson WG, Koganti T, Aleff RA, Hilker CA, Blommel JH, Porter TR, Swanson KC, Lundquist P, Nguyen PL, Shi M, He R, Viswanatha DS, Jen J, Klee EW, Kipp BR, Hoyer JD, Wieben ED, Oliveira JL. Improved Characterization of Complex beta-Globin Gene Cluster Structural Variants Using Long-Read Sequencing. J Mol Diagn. 2021 Dec; 23 (12):1732-1740
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  35. Karon BS, Donato LJ, Bridgeman AR, Blommel JH, Kipp B, Maus A, Renuse S, Kemp J, Madugundu AK, Vanderboom PM, Chavan S, Dasari S, Singh RJ, Grebe SK, Pandey A. Analytical Sensitivity and Specificity of Four Point of Care Rapid Antigen Diagnostic Tests for SARS-CoV-2 Using Real-Time Quantitative PCR, Quantitative Droplet Digital PCR, and a Mass Spectrometric Antigen Assay as Comparator Methods. Clin Chem. 2021 Nov 1; 67 (11):1545-1553
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  36. Mangalaparthi KK, Chavan S, Madugundu AK, Renuse S, Vanderboom PM, Maus AD, Kemp J, Kipp BR, Grebe SK, Singh RJ, Pandey A. A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples. Clin Proteomics 2021 Oct 22; 18 (1):25
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  37. Sankaranarayanan S, Balan J, Walsh JR, Wu Y, Minnich S, Piazza A, Osborne C, Oliver GR, Lesko J, Bates KL, Khezeli K, Block DR, DiGuardo M, Kreuter J, O'Horo JC, Kalantari J, Klee EW, Salama ME, Kipp B, Morice WG, Jenkinson G. COVID-19 Mortality Prediction From Deep Learning in a Large Multistate Electronic Health Record and Laboratory Information System Data Set: Algorithm Development and Validation. J Med Internet Res. 2021 Sep 28; 23(9):e30157.
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  38. Ida CM, Johnson DR, Nair AA, Davila J, Kollmeyer TM, Minn K, Fadra NM, Balcom JR, Fung KA, Kim DK, Kaufmann TJ, Kipp BR, Halling KC, Jenkins RB, Giannini C. Polymorphous Low-Grade Neuroepithelial Tumor of the Young (PLNTY): Molecular Profiling Confirms Frequent MAPK Pathway Activation. J Neuropathol Exp Neurol. 2021 Sep 27; 80 (9):821-829
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  39. Pryzbylski AL, Kollmeyer TM, Praska CE, Raghunathan A, Jentoft ME, Giannini C, Vaubel RA, Halling KC, Zheng G, DiGuardo MA, Kipp BR, Jenkins RB, Ida CM. Non-canonical IDH Mutation Frequency in IDH1-R132H-Negative Glioblastoma Patients Older Than 54 Years. J Neuropathol Exp Neurol 2021 Sep 10; 80 (8):804-806
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  40. Yang JD, Ghoz H, Aboelsoud MM, Taylor WR, Yab TC, Berger CK, Cao X, Foote PH, Giama NH, Barr Fritcher EG, Mahoney DW, Moser CD, Smyrk TC, Kipp BR, Gores GJ, Roberts LR, Kisiel JB. DNA Methylation Markers for Detection of Cholangiocarcinoma: Discovery, Validation, and Clinical Testing in Biliary Brushings and Plasma. Hepatol Commun. 2021 Aug; 5 (8):1448-1459 Epub 2021 May 03
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  41. Renuse S, Vanderboom PM, Maus AD, Kemp JV, Gurtner KM, Madugundu AK, Chavan S, Peterson JA, Madden BJ, Mangalaparthi KK, Mun DG, Singh S, Kipp BR, Dasari S, Singh RJ, Grebe SK, Pandey A. A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens. EBioMedicine. 2021 Jul; 69:103465 Epub 2021 July 03
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  42. Yonkus JA, Alva-Ruiz R, Abdelrahman AM, Leiting JL, Schneider AR, Grotz TE, Cleary SP, Smoot RL, Nagorney DM, Kendrick ML, Kipp BR, Truty MJ. Molecular Peritoneal Staging for Pancreatic Ductal Adenocarcinoma Using Mutant KRAS Droplet-Digital Polymerase Chain Reaction: Results of a Prospective Clinical Trial. J Am Coll Surg. 2021 Jul; 233 (1):73-80.e1 Epub 2021 May 20
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  43. Gonzalez-Bosquet J, Bakkum-Gamez JN, Weaver AL, McGree ME, Dowdy SC, Famuyide AO, Kipp BR, Halling KC, Couch FJ, Podratz KC. PP2A and E3 ubiquitin ligase deficiencies: Seminal biological drivers in endometrial cancer. Gynecol Oncol. 2021 Jul; 162 (1):182-189 Epub 2021 Apr 16
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  44. Roden AC, Vrana JA, Koepplin JW, Hudson AE, Norgan AP, Jenkinson G, Yamaoka S, Ebihara H, Monroe R, Szabolcs MJ, Majumdar R, Moyer AM, Garcia JJ, Kipp BR. Comparison of In Situ Hybridization, Immunohistochemistry, and Reverse Transcription-Droplet Digital Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Testing in Tissue. Arch Pathol Lab Med. 2021 Jul 1; 145 (7):785-796
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  45. DiGuardo MA, Davila JI, Jackson RA, Nair AA, Fadra N, Minn KT, Atiq MA, Zarei S, Blommel JH, Knight SM, Jen J, Eckloff BW, Voss JS, Rumilla KM, Kerr SE, Lam-Himlin DM, Bellizzi AM, Graham RP, Kipp BR, Jenkins RB, Halling KC. RNA-Seq Reveals Differences in Expressed Tumor Mutation Burden in Colorectal and Endometrial Cancers with and without Defective DNA-Mismatch Repair. J Mol Diagn. 2021 May; 23(5):555-564. Epub 2021 Feb 04.
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  46. Gong B, Li D, Kusko R, Novoradovskaya N, Zhang Y, Wang S, Pabon-Pena C, Zhang Z, Lai K, Cai W, LoCoco JS, Lader E, Richmond TA, Mittal VK, Liu LC, Johann DJ Jr, Willey JC, Bushel PR, Yu Y, Xu C, Chen G, Burgess D, Cawley S, Giorda K, Haseley N, Qiu F, Wilkins K, Arib H, Attwooll C, Babson K, Bao L, Bao W, Lucas AB, Best H, Bhandari A, Bisgin H, Blackburn J, Blomquist TM, Boardman L, Burgher B, Butler DJ, Chang CJ, Chaubey A, Chen T, Chierici M, Chin CR, Close D, Conroy J, Cooley Coleman J, Craig DJ, Crawford E, Del Pozo A, Deveson IW, Duncan D, Eterovic AK, Fan X, Foox J, Furlanello C, Ghosal A, Glenn S, Guan M, Haag C, Hang X, Happe S, Hennigan B, Hipp J, Hong H, Horvath K, Hu J, Hung LY, Jarosz M, Kerkhof J, Kipp B, Kreil DP, Labaj P, Lapunzina P, Li P, Li QZ, Li W, Li Z, Liang Y, Liu S, Liu Z, Ma C, Marella N, Martin-Arenas R, Megherbi DB, Meng Q, Mieczkowski PA, Morrison T, Muzny D, Ning B, Parsons BL, Paweletz CP, Pirooznia M, Qu W, Raymond A, Rindler P, Ringler R, Sadikovic B, Scherer A, Schulze E, Sebra R, Shaknovich R, Shi Q, Shi T, Silla-Castro JC, Smith M, Lopez MS, Song P, Stetson D, Strahl M, Stuart A, Supplee J, Szankasi P, Tan H, Tang LY, Tao Y, Thakkar S, Thierry-Mieg D, Thierry-Mieg J, Thodima VJ, Thomas D, Tichy B, Tom N, Garcia EV, Verma S, Walker K, Wang C, Wang J, Wang Y, Wen Z, Wirta V, Wu L, Xiao C, Xiao W, Xu S, Yang M, Ying J, Yip SH, Zhang G, Zhang S, Zhao M, Zheng Y, Zhou X, Mason CE, Mercer T, Tong W, Shi L, Jones W, Xu J. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biol. 2021 Apr 16; 22 (1):109
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  47. Murphy SJ, Levy MJ, Smadbeck JB, Karagouga G, McCune AF, Harris FR, Udell JB, Johnson SH, Kerr SE, Cheville JC, Kipp BR, Vasmatzis G, Gleeson FC. Theragnostic chromosomal rearrangements in treatment-naive pancreatic ductal adenocarcinomas obtained via endoscopic ultrasound. J Cell Mol Med. 2021 Apr; 25 (8):4110-4123 Epub 2021 Mar 11
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  48. Murphy S, Smadbeck J, Eckloff B, Lee Y, Johnson S, Karagouga G, Serla V, Sharma A, Sikkink R, Voss J, Harris F, Kline JS, Kosari F, Feldman A, Wieben E, Aubry MC, Kipp B, Jen J, Cheville J, Vasmatzis G. Chromosomal Junction Detection from Whole-Genome Sequencing on Formalin-Fixed, Paraffin-Embedded Tumors. J Mol Diagn. 2021 Apr; 23 (4):375-388 Epub 2020 Dec 31
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  49. Vizcaino MA, Giannini C, Chang HT, Kipp BR, Fritchie K, Vaubel R. Intracranial angiomatoid fibrous histiocytoma with rhabdoid features: a mimic of rhabdoid meningioma. Brain Tumor Pathol. 2021 Apr; 38(2):138-144. Epub 2021 Jan 12.
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  50. Boland JM, Lee HE, Barr Fritcher EG, Voss JS, Jessen E, Davila JI, Kipp BR, Graham RP, Maleszewski JJ, Yi ES. Molecular Genetic Landscape of Sclerosing Pneumocytomas. Am J Clin Pathol. 2021 Feb 11; 155(3):397-404.
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  51. Bois MC, Boire NA, Layman AJ, Aubry MC, Alexander MP, Roden AC, Hagen CE, Quinton RA, Larsen C, Erben Y, Majumdar R, Jenkins SM, Kipp BR, Lin PT, Maleszewski JJ. COVID-19-Associated Nonocclusive Fibrin Microthrombi in the Heart. Circulation. 2021 Jan 19; 143(3):230-243. Epub 2020 Nov 16.
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  52. Zhao Y, Yu H, Ida CM, Halling KC, Kipp BR, Geiersbach K, Rumilla KM, Gupta S, Lin MT, Zheng G. Assessment of RAS Dependency for BRAF Alterations Using Cancer Genomic Databases. JAMA Netw Open. 2021 Jan 04; 4(1):e2035479.
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  53. Vaubel R, Zschernack V, Tran QT, Jenkins S, Caron A, Milosevic D, Smadbeck J, Vasmatzis G, Kandels D, Gnekow A, Kramm C, Jenkins R, Kipp BR, Rodriguez FJ, Orr BA, Pietsch T, Giannini C. Biology and grading of pleomorphic xanthoastrocytoma-what have we learned about it? Brain Pathol. 2021 Jan; 31 (1):20-32 Epub 2020 Aug 04
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  54. Balan J, Jenkinson G, Nair A, Saha N, Koganti T, Voss J, Zysk C, Barr Fritcher EG, Ross CA, Giannini C, Raghunathan A, Kipp BR, Jenkins R, Ida C, Halling KC, Blackburn PR, Dasari S, Oliver GR, Klee EW. SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA. Front Genet. 2021; 12:739054. Epub 2021 Oct 22.
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  55. Stephens Z, Milosevic D, Kipp B, Grebe S, Iyer RK, Kocher JA. PB-Motif-A Method for Identifying Gene/Pseudogene Rearrangements With Long Reads: An Application to CYP21A2 Genotyping. Front Genet. 2021; 12:716586 Epub 2021 July 28
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  56. Bosquet JG, Zhang Q, Cliby WA, Bakkum-Gamez JN, Cen L, Dowdy SC, Sherman ME, Weroha SJ, Clayton AC, Kipp BR, Halling KC, Couch FJ, Podratz KC. Association of a novel endometrial cancer biomarker panel with prognostic risk, platinum insensitivity, and targetable therapeutic options. PLoS One. 2021; 16 (1):e0245664 Epub 2021 Jan 27
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  57. Murphy SJ, Harris FR, Smadbeck JB, Serla V, Karagouga G, Johnson SH, Kosari F, Pierson KE, Bungum AO, Edell ES, Mansfield AS, Wigle DA, Kipp BR, Vasmatzis G, Aubry MC. Optimizing clinical cytology touch preparations for next generation sequencing. Genomics. 2020 Nov; 112(6):5313-5323. Epub 2020 Nov 02.
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  58. Zarei S, Voss JS, Jin L, Jenkins SM, Bryce AH, Erickson LA, Bell DA, Kipp BR, Flotte TJ. Mutational Profile in Vulvar, Vaginal, and Urethral Melanomas: Review of 37 Cases With Focus on Primary Tumor Site. Int J Gynecol Pathol. 2020 Nov; 39 (6):587-594
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  59. Gleeson FC, Levy MJ, Jackson RA, Murphy SJ, Halling KC, Kipp BR, Graham RP, Zhang L. Lipocalin-2 Expression in Pancreas Adenocarcinoma Tumor Microenvironment Via Endoscopic Ultrasound Fine Needle Biopsy Is Feasible and May Reveal a Therapeutic Target. Pancreas 2020 Nov/Dec; 49 (10):e98-e99
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  60. Bible KC, Menefee ME, Lin CC, Millward MJ, Maples WJ, Goh BC, Karlin NJ, Kane MA, Adkins DR, Molina JR, Donehower RC, Lim WT, Flynn PJ, Richardson RL, Traynor AM, Rubin J, LoRusso PM, Smallridge RC, Burton JK, Suman VJ, Kumar A, Voss JS, Rumilla KM, Kipp BR, Chintakuntlawar AV, Harris P, Erlichman C. An International Phase 2 Study of Pazopanib in Progressive and Metastatic Thyroglobulin Antibody Negative Radioactive Iodine Refractory Differentiated Thyroid Cancer. Thyroid. 2020 Sep; 30 (9):1254-1262 Epub 2020 July 29
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  61. Bois MC, Milosevic D, Kipp BR, Maleszewski JJ. KRAS Mutations in Papillary Fibroelastomas: A Study of 50 Cases With Etiologic and Diagnostic Implications. Am J Surg Pathol. 2020 May; 44 (5):626-632
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  62. Jethwa KR, Jang S, Mullikin TC, Harmsen WS, Petersen MM, Olivier KR, Park SS, Neben-Wittich MA, Hubbard JM, Sandhyavenu H, Whitaker TJ, Waltman LA, Kipp BR, Merrell KW, Haddock MG, Hallemeier CL. Association of tumor genomic factors and efficacy for metastasis-directed stereotactic body radiotherapy for oligometastatic colorectal cancer. Radiother Oncol. 2020 May; 146:29-36 Epub 2020 Feb 27
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  63. Mehta N, Johnston JM, Hein M, Kipp BR, Coon L, Savedra ME, Hoyer JD, He R, Rangan A, Shi M, Oliveira JL. Further Characterization of Hb Bronovo [alpha103(G10)His-->Leu; HBA2: c.311A>T] and First Report of the Homozygous State. Hemoglobin. 2020 May; 44 (3):174-178 Epub 2020 June 18
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  139. Barr Fritcher EG, Kipp BR, Voss JS, Clayton AC, Lindor KD, Halling KC, Gores GJ. Primary sclerosing cholangitis patients with serial polysomy fluorescence in situ hybridization results are at increased risk of cholangiocarcinoma. Am J Gastroenterol. 2011 Nov; 106(11):2023-8. Epub 2011 Aug 16.
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  140. Kipp BR, Roellinger SE, Lundquist PA, Highsmith WE, Dawson DB. Development and clinical implementation of a combination deletion PCR and multiplex ligation-dependent probe amplification assay for detecting deletions involving the human alpha-globin gene cluster. J Mol Diagn. 2011 Sep; 13 (5):549-57 Epub 2011 June 25
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  141. Kipp BR, Fritcher EG, Clayton AC, Gores GJ, Roberts LR, Zhang J, Levy MJ, Halling KC. Comparison of KRAS mutation analysis and FISH for detecting pancreatobiliary tract cancer in cytology specimens collected during endoscopic retrograde cholangiopancreatography. J Mol Diagn. 2010 Nov; 12(6):780-6. Epub 2010 Sep 23.
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  142. Campion MB, Kipp BR, Humphrey SK, Zhang J, Clayton AC, Henry MR. Improving cellularity and quality of liquid-based cytology slides processed from pancreatobiliary tract brushings. Diagn Cytopathol. 2010 Sep; 38(9):627-32.
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  143. Oberg TN, Kipp BR, Vrana JA, Bartholet MK, Fales CJ, Garcia R, McDonald AN, Rosas BL, Henry MR, Clayton AC. Comparison of p16INK4a and ProEx C immunostaining on cervical ThinPrep cytology and biopsy specimens. Diagn Cytopathol. 2010 Aug; 38(8):564-72.
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  144. Voss JS, Kipp BR, Campion MB, Sokolova IA, Henry MR, Halling KC, Clayton AC. Assessment of fluorescence in situ hybridization and hybrid capture 2 analyses of cervical cytology specimens diagnosed as low grade squamous intraepithelial lesion for the detection of high grade cervical intraepithelial neoplasia. Anal Quant Cytol Histol. 2010 Jun; 32 (3):121-30
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  145. Gleeson FC, Kipp BR, Caudill JL, Clain JE, Clayton AC, Halling KC, Henry MR, Rajan E, Topazian MD, Wang KK, Wiersema MJ, Zhang J, Levy MJ. False positive endoscopic ultrasound fine needle aspiration cytology: incidence and risk factors. Gut. 2010 May; 59 (5):586-93
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  146. Voss JS, Kipp BR, Halling KC, Henry MR, Jett JR, Clayton AC, Rickman OB. Fluorescence in situ hybridization testing algorithm improves lung cancer detection in bronchial brushing specimens. Am J Respir Crit Care Med. 2010 Mar 1; 181(5):478-85. Epub 2009 Dec 10.
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  147. Kipp BR, Ketterling RP, Oberg TN, Cousin MA, Plagge AM, Wiktor AE, Ihrke JM, Meyers CH, Morice WG, Halling KC, Clayton AC. Comparison of fluorescence in situ hybridization, p57 immunostaining, flow cytometry, and digital image analysis for diagnosing molar and nonmolar products of conception. Am J Clin Pathol. 2010 Feb; 133(2):196-204.
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  148. Abdelmoneim SS, Talwalkar J, Sethi S, Kamath P, Fathalla MM, Kipp BR, Campion MB, Clayton AC, Halling KC, Shah VH. A prospective pilot study of circulating endothelial cells as a potential new biomarker in portal hypertension. Liver Int. 2010 Feb; 30 (2):191-7 Epub 2009 Oct 19
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  149. Song M, Ruth A, Policht FA, Bubendorf L, Feichter G, Kipp BR, Halling KC, Sokolova IA. Dysplastic cells in cytological cervical samples show a high incidence of chromosomal abnormalities. Diagn Cytopathol. 2010 Jan; 38(1):28-33.
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  150. Voss JS, Kipp BR, Campion MB, Sokolova IA, Henry MR, Halling KC, Clayton AC. Comparison of fluorescence in situ hybridization, hybrid capture 2 and polymerase chain reaction for the detection of high-risk human papillomavirus in cervical cytology specimens. Anal Quant Cytol Histol. 2009 Aug; 31: (4)208-16.
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  151. Kipp BR, Pereira TC, Souza PC, Gleeson FC, Levy MJ, Clayton AC. Comparison of EUS-guided FNA and Trucut biopsy for diagnosing and staging abdominal and mediastinal neoplasms. Diagn Cytopathol. 2009 Aug; 37: (8)549-56.
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  152. Minot DM, Kipp BR, Root RM, Meyer RG, Reynolds CA, Nassar A, Henry MR, Clayton AC. Automated cellular imaging system III for assessing HER2 status in breast cancer specimens: development of a standardized scoring method that correlates with FISH. Am J Clin Pathol. 2009 Jul; 132(1):133-8.
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  153. Fritcher EG, Kipp BR, Halling KC, Oberg TN, Bryant SC, Tarrell RF, Gores GJ, Levy MJ, Clayton AC, Sebo TJ, Roberts LR. A multivariable model using advanced cytologic methods for the evaluation of indeterminate pancreatobiliary strictures. Gastroenterology. 2009 Jun; 136(7):2180-6. Epub 2009 Feb 14.
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  154. Kipp BR, Tanasescu M, Else TA, Bryant SC, Karnes RJ, Sebo TJ, Halling KC. Quantitative fluorescence in situ hybridization and its ability to predict bladder cancer recurrence and progression to muscle-invasive bladder cancer. J Mol Diagn. 2009 Mar; 11 (2):148-54 Epub 2009 Jan 29
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  155. Kipp BR, Tyner HL, Campion MB, Voss JS, Karnes RJ, Sebo TJ, Halling KC, Zhang J. Chromosomal alterations detected by fluorescence in situ hybridization in urothelial carcinoma and rarer histologic variants of bladder cancer. Am J Clin Pathol. 2008 Oct; 130 (4):552-9
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  156. Voss JS, Kipp BR, Krueger AK, Clayton AC, Halling KC, Karnes RJ, Henry MR, Sebo TJ. Changes in specimen preparation method may impact urine cytologic evaluation. Am J Clin Pathol. 2008 Sep; 130(3):428-33.
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  157. Halling KC, Kipp BR. Bladder cancer detection using FISH (UroVysion assay). Adv Anat Pathol. 2008 Sep; 15(5):279-86.
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  158. Kipp BR, Medeiros F, Campion MB, Distad TJ, Peterson LM, Keeney GL, Halling KC, Clayton AC. Direct uterine sampling with the Tao brush sampler using a liquid-based preparation method for the detection of endometrial cancer and atypical hyperplasia: a feasibility study. Cancer. 2008 Aug 25; 114(4):228-35.
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  159. Fritcher EG, Brankley SM, Kipp BR, Voss JS, Campion MB, Morrison LE, Legator MS, Lutzke LS, Wang KK, Sebo TJ, Halling KC. A comparison of conventional cytology, DNA ploidy analysis, and fluorescence in situ hybridization for the detection of dysplasia and adenocarcinoma in patients with Barrett's esophagus. Hum Pathol. 2008 Aug; 39 (8):1128-35 Epub 2008 July 07
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  160. Brankley SM, Adams EJ, Christensen MR, Everts CR, Lund JD, Oberg TN, Plagge AM, Zieman AH, Kipp BR, Halling KC. A study of the reproducibility of a fluorescence in situ hybridization bladder cancer detection assay. Anal Quant Cytol Histol. 2008 Jun; 30(3):145-51.
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  161. Levy MJ, Baron TH, Clayton AC, Enders FB, Gostout CJ, Halling KC, Kipp BR, Petersen BT, Roberts LR, Rumalla A, Sebo TJ, Topazian MD, Wiersema MJ, Gores GJ. Prospective evaluation of advanced molecular markers and imaging techniques in patients with indeterminate bile duct strictures. Am J Gastroenterol. 2008 May; 103 (5):1263-73
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  162. Kipp BR, Halling KC, Campion MB, Wendel AJ, Karnes RJ, Zhang J, Sebo TJ. Assessing the value of reflex fluorescence in situ hybridization testing in the diagnosis of bladder cancer when routine urine cytological examination is equivocal. J Urol. 2008 Apr; 179 (4):1296-301; discussion 1301 Epub 2008 Mar 04
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  163. Sokolova I, Algeciras-Schimnich A, Song M, Sitailo S, Policht F, Kipp BR, Voss JS, Halling KC, Ruth A, King W, Underwood D, Brainard J, Morrison L. Chromosomal biomarkers for detection of human papillomavirus associated genomic instability in epithelial cells of cervical cytology specimens. J Mol Diagn. 2007 Nov; 9(5):604-11.
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  164. Levy MJ, Clain JE, Clayton A, Halling KC, Kipp BR, Rajan E, Roberts LR, Root RM, Sebo TJ, Topazian MD, Wang KK, Wiersema MJ, Gores GJ. Preliminary experience comparing routine cytology results with the composite results of digital image analysis and fluorescence in situ hybridization in patients undergoing EUS-guided FNA. Gastrointest Endosc. 2007 Sep; 66 (3):483-90
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  165. Halling KC, Kipp BR. Fluorescence in situ hybridization in diagnostic cytology. Hum Pathol. 2007 Aug; 38(8):1137-44.
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  166. Barr Fritcher EG, Kipp BR, Slezak JM, Moreno-Luna LE, Gores GJ, Levy MJ, Roberts LR, Halling KC, Sebo TJ. Correlating routine cytology, quantitative nuclear morphometry by digital image analysis, and genetic alterations by fluorescence in situ hybridization to assess the sensitivity of cytology for detecting pancreatobiliary tract malignancy. Am J Clin Pathol. 2007 Aug; 128(2):272-9.
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  167. DeHaan RD, Kipp BR, Smyrk TC, Abraham SC, Roberts LR, Halling KC. An assessment of chromosomal alterations detected by fluorescence in situ hybridization and p16 expression in sporadic and primary sclerosing cholangitis-associated cholangiocarcinomas. Hum Pathol. 2007 Mar; 38(3):491-9. Epub 2007 Jan 19.
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  168. Halling KC, Kipp BR. FISH in Diagnostic Cytology. Hum Pathol. 2007; 38(8):1137-44.
  169. Moreno Luna LE, Kipp B, Halling KC, Sebo TJ, Kremers WK, Roberts LR, Barr Fritcher EG, Levy MJ, Gores GJ. Advanced cytologic techniques for the detection of malignant pancreatobiliary strictures. Gastroenterology. 2006 Oct; 131 (4):1064-72 Epub 2006 Aug 16
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  170. Halling KC, Rickman OB, Kipp BR, Harwood AR, Doerr CH, Jett JR. A comparison of cytology and fluorescence in situ hybridization for the detection of lung cancer in bronchoscopic specimens. Chest. 2006 Sep; 130 (3):694-701
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  171. Kipp BR, Campion MB, Coffman E, Smith A, Tomisek JD, Browne GG, Panella JR, Desai R, Harwood AR, Halling KC. An evaluation of ThinPrep UroCyte filters for the preparation of slides for fluorescence in situ hybridization. Diagn Cytopathol. 2006 Jul; 34 (7):479-84
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  172. Brankley SM, Wang KK, Harwood AR, Miller DV, Legator MS, Lutzke LS, Kipp BR, Morrison LE, Halling KC. The development of a fluorescence in situ hybridization assay for the detection of dysplasia and adenocarcinoma in Barrett's esophagus. J Mol Diagn. 2006 May; 8 (2):260-7
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  173. Kipp BR, Sebo TJ, Griffin MD, Ihrke JM, Halling KC. Analysis of polyomavirus-infected renal transplant recipients' urine specimens: correlation of routine urine cytology, fluorescence in situ hybridization, and digital image analysis. Am J Clin Pathol. 2005 Dec; 124(6):854-61.
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  174. Kipp BR, Fritcher EG, del Rosario KM, Stevens CL, Sebo TJ, Halling KC. A systematic approach to identifying urothelial cells likely to be polysomic by fluorescence in situ hybridization. Anal Quant Cytol Histol. 2005 Dec; 27(6):317-22.
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  175. Kipp BR, Karnes RJ, Brankley SM, Harwood AR, Pankratz VS, Sebo TJ, Blute MM, Lieber MM, Zincke H, Halling KC. Monitoring intravesical therapy for superficial bladder cancer using fluorescence in situ hybridization. J Urol. 2005 Feb; 173: (2)401-4.
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  176. Debes JD, Sebo TJ, Heemers HV, Kipp BR, Haugen DL, Lohse CM, Tindall DJ. p300 modulates nuclear morphology in prostate cancer. Cancer Res. 2005 Feb 1; 65 (3):708-12
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  177. Kipp BR, Stadheim LM, Halling SA, Pochron NL, Harmsen S, Nagorney DM, Sebo TJ, Therneau TM, Gores GJ, de Groen PC, Baron TH, Levy MJ, Halling KC, Roberts LR. A comparison of routine cytology and fluorescence in situ hybridization for the detection of malignant bile duct strictures. Am J Gastroenterol. 2004 Sep; 99(9):1675-81.
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  178. Harewood GC, Baron TH, Stadheim LM, Kipp BR, Sebo TJ, Salomao DR. Prospective, blinded assessment of factors influencing the accuracy of biliary cytology interpretation. Am J Gastroenterol. 2004 Aug; 99 (8):1464-9
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  179. Baron TH, Harewood GC, Rumalla A, Pochron NL, Stadheim LM, Gores GJ, Therneau TM, De Groen PC, Sebo TJ, Salomao DR, Kipp BR. A prospective comparison of digital image analysis and routine cytology for the identification of malignancy in biliary tract strictures. Clin Gastroenterol Hepatol. 2004 Mar; 2 (3):214-9
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