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Identification of a Novel ZBTB20-JAK2 Fusion by Mate-Pair Sequencing in a Young Adult With B-Lymphoblastic Leukemia/Lymphoma.

Peterson JF, Blackburn PR, Webley MR, Pearce KE, Williamson CM, Vasmatzis G, Smadbeck JB, Bieliauskas SL, Reichard KK, Ketterling RP, Baughn LB, Greipp PT.

Mayo Clin Proc. 2019 Jul;94(7):1381-1384. doi: 10.1016/j.mayocp.2019.04.030. No abstract available.


Elucidating a false-negative MYC break-apart fluorescence in situ hybridization probe study by next-generation sequencing in a patient with high-grade B-cell lymphoma with IGH/MYC and IGH/BCL2 rearrangements.

Peterson JF, Pitel BA, Smoley SA, Vasmatzis G, Smadbeck JB, Greipp PT, Ketterling RP, Macon WR, Baughn LB.

Cold Spring Harb Mol Case Stud. 2019 Jun 3;5(3). pii: a004077. doi: 10.1101/mcs.a004077. Print 2019 Jun.


Using genomics to differentiate multiple primaries from metastatic lung cancer.

Murphy SJ, Harris FR, Kosari F, Terra S, Nasir A, Johnson SH, Serla V, Smadbeck JB, Halling GC, Karagouga G, Sukov B, Leventakos K, Yang P, Peikert T, Mansfield AS, Wigle DA, Yi ES, Kipp BR, Vasmatzis G, Aubry MC.

J Thorac Oncol. 2019 May 16. pii: S1556-0864(19)30374-0. doi: 10.1016/j.jtho.2019.05.008. [Epub ahead of print]


Immune Cell Infiltration May Be a Key Determinant of Long-Term Survival in Small Cell Lung Cancer.

Muppa P, Parrilha Terra SBS, Sharma A, Mansfield AS, Aubry MC, Bhinge K, Asiedu MK, de Andrade M, Janaki N, Murphy SJ, Nasir A, Van Keulen V, Vasmatzis G, Wigle DA, Yang P, Yi ES, Peikert T, Kosari F.

J Thorac Oncol. 2019 Jul;14(7):1286-1295. doi: 10.1016/j.jtho.2019.03.028. Epub 2019 May 9.


Characterization of a cryptic IGH/CCND1 rearrangement in a case of mantle cell lymphoma with negative CCND1 FISH studies.

Peterson JF, Baughn LB, Ketterling RP, Pitel BA, Smoley SA, Vasmatzis G, Smadbeck JB, Greipp PT, Mangaonkar AA, Thompson CA, Parikh SA, Chen D, Viswanatha DS.

Blood Adv. 2019 Apr 23;3(8):1298-1302. doi: 10.1182/bloodadvances.2019031450. No abstract available.


A comparison of adult rhabdomyosarcoma and high-grade neuroendocrine carcinoma of the urinary bladder reveals novel PPP1R12A fusions in rhabdomyosarcoma.

Gupta S, Sosa CP, Kosari F, Folpe A, Bhinge KN, Yang L, Agahi A, Johnson SH, Frank I, Boorjian SA, Hansel DE, Al-Ahmadie HA, Reuter VE, Vasmatzis G, Jimenez RE, Herrera-Hernandez L, Cheville JC.

Hum Pathol. 2019 Jun;88:48-59. doi: 10.1016/j.humpath.2019.03.007. Epub 2019 Apr 1.


Detection of a cryptic NUP214/ABL1 gene fusion by mate-pair sequencing (MPseq) in a newly diagnosed case of pediatric T-lymphoblastic leukemia.

Peterson JF, Pitel BA, Smoley SA, Smadbeck JB, Johnson SH, Vasmatzis G, Koon SJ, Webley MR, McGrath M, Bayerl MG, Baughn LB, Rowsey RA, Ketterling RP, Greipp PT, Hoppman NL.

Cold Spring Harb Mol Case Stud. 2019 Apr 1;5(2). pii: a003533. doi: 10.1101/mcs.a003533. Print 2019 Apr.


Shared and unique genomic structural variants of different histological components within testicular germ cell tumours identified with mate pair sequencing.

Bryce AH, Egan JB, Smadbeck JB, Johnson SH, Murphy SJ, Harris FR, Halling GC, Terra SBSP, Cheville J, Pagliaro L, Leibovich B, Costello BA, Vasmatzis G.

Sci Rep. 2019 Mar 5;9(1):3586. doi: 10.1038/s41598-019-39956-y.


Proposal for Modification of Cahan's Criteria Utilizing Molecular Genetic Analyses for Cases without Baseline Histopathology: A Unique Method Applicable to Primary Radiosurgery.

Rusheen AE, Smadbeck JB, Schimmenti LA, Klee EW, Link MJ, Vasmatzis G, Carlson ML.

J Neurol Surg B Skull Base. 2019 Feb;80(1):10-17. doi: 10.1055/s-0038-1655759. Epub 2018 May 31.


Acute leukemias harboring KMT2A/MLLT10 fusion: a 10-year experience from a single genomics laboratory.

Peterson JF, Sukov WR, Pitel BA, Smoley SA, Pearce KE, Meyer RG, Williamson CM, Smadbeck JB, Vasmatzis G, Hoppman NL, Greipp PT, Baughn LB, Ketterling RP.

Genes Chromosomes Cancer. 2019 Aug;58(8):567-577. doi: 10.1002/gcc.22741. Epub 2019 Mar 19.


Large Chromosomal Rearrangements Yield Biomarkers to Distinguish Low-Risk From Intermediate- and High-Risk Prostate Cancer.

Vasmatzis G, Kosari F, Murphy SJ, Terra S, Kovtun IV, Harris FR, Zarei S, Smadbeck JB, Johnson SH, Gaitatzes AG, Therneau TM, Rangel LJ, Knudson RA, Greipp P, Sukov WR, Knutson DL, Kloft-Nelson SM, Karnes RJ, Cheville JC.

Mayo Clin Proc. 2019 Jan;94(1):27-36. doi: 10.1016/j.mayocp.2018.06.028.


False-negative rates for MYC fluorescence in situ hybridization probes in B-cell neoplasms.

King RL, McPhail ED, Meyer RG, Vasmatzis G, Pearce K, Smadbeck JB, Ketterling RP, Smoley SA, Greipp PT, Hoppman NL, Peterson JF, Baughn LB.

Haematologica. 2019 Jun;104(6):e248-e251. doi: 10.3324/haematol.2018.207290. Epub 2018 Dec 6. No abstract available.


Targeting HER2 in patient-derived xenograft ovarian cancer models sensitizes tumors to chemotherapy.

Harris FR, Zhang P, Yang L, Hou X, Leventakos K, Weroha SJ, Vasmatzis G, Kovtun IV.

Mol Oncol. 2019 Feb;13(2):132-152. doi: 10.1002/1878-0261.12414. Epub 2018 Dec 21.


Constitutional chromosome rearrangements that mimic the 2017 world health organization "acute myeloid leukemia with recurrent genetic abnormalities": A study of three cases and review of the literature.

Peterson JF, Pitel BA, Smoley SA, Smadbeck JB, Johnson SH, Vasmatzis G, Pearce KE, He R, Kelemen K, Al-Mondhiry HAB, Lamparella NE, Hoppman NL, Kearney HM, Baughn LB, Ketterling RP, Greipp PT.

Cancer Genet. 2019 Jan;230:37-46. doi: 10.1016/j.cancergen.2018.11.005. Epub 2018 Nov 20. Review.


Enhanced mRNA FISH with compact quantum dots.

Liu Y, Le P, Lim SJ, Ma L, Sarkar S, Han Z, Murphy SJ, Kosari F, Vasmatzis G, Cheville JC, Smith AM.

Nat Commun. 2018 Oct 26;9(1):4461. doi: 10.1038/s41467-018-06740-x.


Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma.

Mansfield AS, Peikert T, Smadbeck JB, Udell JBM, Garcia-Rivera E, Elsbernd L, Erskine CL, Van Keulen VP, Kosari F, Murphy SJ, Ren H, Serla VV, Schaefer Klein JL, Karagouga G, Harris FR, Sosa C, Johnson SH, Nevala W, Markovic SN, Bungum AO, Edell ES, Dong H, Cheville JC, Aubry MC, Jen J, Vasmatzis G.

J Thorac Oncol. 2019 Feb;14(2):276-287. doi: 10.1016/j.jtho.2018.10.001. Epub 2018 Oct 10.


Mate pair sequencing improves detection of genomic abnormalities in acute myeloid leukemia.

Aypar U, Smoley SA, Pitel BA, Pearce KE, Zenka RM, Vasmatzis G, Johnson SH, Smadbeck JB, Peterson JF, Geiersbach KB, Van Dyke DL, Thorland EC, Jenkins RB, Ketterling RP, Greipp PT, Kearney HM, Hoppman NL, Baughn LB.

Eur J Haematol. 2019 Jan;102(1):87-96. doi: 10.1111/ejh.13179. Epub 2018 Nov 22.


Use of mate-pair sequencing to characterize a complex cryptic BCR/ABL1 rearrangement observed in a newly diagnosed case of chronic myeloid leukemia.

Peterson JF, Pitel BA, Smoley SA, Smadbeck JB, Johnson SH, Vasmatzis G, Kearney HM, Greipp PT, Hoppman NL, Baughn LB, Ketterling RP.

Hum Pathol. 2018 Sep 26. pii: S0046-8177(18)30372-1. doi: 10.1016/j.humpath.2018.09.010. [Epub ahead of print]


UCH-L1 bypasses mTOR to promote protein biosynthesis and is required for MYC-driven lymphomagenesis in mice.

Hussain S, Bedekovics T, Liu Q, Hu W, Jeon H, Johnson SH, Vasmatzis G, May DG, Roux KJ, Galardy PJ.

Blood. 2018 Dec 13;132(24):2564-2574. doi: 10.1182/blood-2018-05-848515. Epub 2018 Sep 26.


Next Generation Sequencing of Sporadic Vestibular Schwannoma: Necessity of Biallelic NF2 Inactivation and Implications of Accessory Non-NF2 Variants.

Carlson ML, Smadbeck JB, Link MJ, Klee EW, Vasmatzis G, Schimmenti LA.

Otol Neurotol. 2018 Oct;39(9):e860-e871. doi: 10.1097/MAO.0000000000001932.


Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples.

Vasmatzis G, Wang X, Smadbeck JB, Murphy SJ, Geiersbach KB, Johnson SH, Gaitatzes AG, Asmann YW, Kosari F, Borad MJ, Serie DJ, McLaughlin SA, Kachergus JM, Necela BM, Thompson EA.

BMC Cancer. 2018 Jul 13;18(1):738. doi: 10.1186/s12885-018-4594-0.


YAP Tyrosine Phosphorylation and Nuclear Localization in Cholangiocarcinoma Cells Are Regulated by LCK and Independent of LATS Activity.

Sugihara T, Werneburg NW, Hernandez MC, Yang L, Kabashima A, Hirsova P, Yohanathan L, Sosa C, Truty MJ, Vasmatzis G, Gores GJ, Smoot RL.

Mol Cancer Res. 2018 Oct;16(10):1556-1567. doi: 10.1158/1541-7786.MCR-18-0158. Epub 2018 Jun 14.


Frequently rearranged and overexpressed δ-catenin is responsible for low sensitivity of prostate cancer cells to androgen receptor and β-catenin antagonists.

Zhang P, Schaefer-Klein J, Cheville JC, Vasmatzis G, Kovtun IV.

Oncotarget. 2018 May 11;9(36):24428-24442. doi: 10.18632/oncotarget.25319. eCollection 2018 May 11.


Copy number variant analysis using genome-wide mate-pair sequencing.

Smadbeck JB, Johnson SH, Smoley SA, Gaitatzes A, Drucker TM, Zenka RM, Kosari F, Murphy SJ, Hoppman N, Aypar U, Sukov WR, Jenkins RB, Kearney HM, Feldman AL, Vasmatzis G.

Genes Chromosomes Cancer. 2018 Sep;57(9):459-470. doi: 10.1002/gcc.5. Epub 2018 Jul 30.


YAP-associated chromosomal instability and cholangiocarcinoma in mice.

Rizvi S, Fischbach SR, Bronk SF, Hirsova P, Krishnan A, Dhanasekaran R, Smadbeck JB, Smoot RL, Vasmatzis G, Gores GJ.

Oncotarget. 2017 Dec 22;9(5):5892-5905. doi: 10.18632/oncotarget.23638. eCollection 2018 Jan 19.


Novel targeted therapy strategies for biliary tract cancers and hepatocellular carcinoma.

DeLeon TT, Ahn DH, Bogenberger JM, Anastasiadis PZ, Arora M, Ramanathan RK, Aqel BA, Vasmatzis G, Truty MJ, Oklu R, Bekaii-Saab TS, Borad MJ.

Future Oncol. 2018 Mar;14(6):553-566. doi: 10.2217/fon-2017-0451. Epub 2018 Feb 20. Review.


SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing (MPseq).

Johnson SH, Smadbeck JB, Smoley SA, Gaitatzes A, Murphy SJ, Harris FR, Drucker TM, Zenka RM, Pitel BA, Rowsey RA, Hoppman NL, Aypar U, Sukov WR, Jenkins RB, Feldman AL, Kearney HM, Vasmatzis G.

Cancer Genet. 2018 Feb;221:1-18. doi: 10.1016/j.cancergen.2017.11.009. Epub 2017 Dec 2.


Pathways Impacted by Genomic Alterations in Pulmonary Carcinoid Tumors.

Asiedu MK, Thomas CF Jr, Dong J, Schulte SC, Khadka P, Sun Z, Kosari F, Jen J, Molina J, Vasmatzis G, Kuang R, Aubry MC, Yang P, Wigle DA.

Clin Cancer Res. 2018 Apr 1;24(7):1691-1704. doi: 10.1158/1078-0432.CCR-17-0252. Epub 2018 Jan 19.


Genome U-Plot: a whole genome visualization.

Gaitatzes A, Johnson SH, Smadbeck JB, Vasmatzis G.

Bioinformatics. 2018 May 15;34(10):1629-1634. doi: 10.1093/bioinformatics/btx829.


Identification of a pyruvate-to-lactate signature in pancreatic intraductal papillary mucinous neoplasms.

Penheiter AR, Deelchand DK, Kittelson E, Damgard SE, Murphy SJ, O'Brien DR, Bamlet WR, Passow MR, Smyrk TC, Couch FJ, Vasmatzis G, Port JD, Marjańska M, Carlson SK.

Pancreatology. 2018 Jan;18(1):46-53. doi: 10.1016/j.pan.2017.11.006. Epub 2017 Nov 14.


Retention of Interstitial Genes between TMPRSS2 and ERG Is Associated with Low-Risk Prostate Cancer.

Murphy SJ, Kosari F, Karnes RJ, Nasir A, Johnson SH, Gaitatzes AG, Smadbeck JB, Rangel LJ, Vasmatzis G, Cheville JC.

Cancer Res. 2017 Nov 15;77(22):6157-6167. doi: 10.1158/0008-5472.CAN-17-0529. Epub 2017 Nov 10.


Genomic rearrangements in sporadic lymphangioleiomyomatosis: an evolving genetic story.

Murphy SJ, Terra SB, Harris FR, Nasir A, Voss JS, Smadbeck JB, Johnson SH, Serla V, Ryu JH, Yi ES, Kipp BR, Vasmatzis G, Carmona EM.

Mod Pathol. 2017 Sep;30(9):1223-1233. doi: 10.1038/modpathol.2017.52. Epub 2017 Jun 23.


Microbial Antigens Stimulate Metalloprotease-7 Secretion in Human B-Lymphocytes Using mTOR-Dependent and Independent Pathways.

Ali MF, Dasari H, Van Keulen VP, Cornec D, Vasmatzis G, Peikert T, Carmona EM.

Sci Rep. 2017 Jun 20;7(1):3869. doi: 10.1038/s41598-017-04199-2.


A novel cytogenetic and molecular characterization of renal metanephric adenoma: Identification of partner genes involved in translocation t(9;15)(p24;q24).

Catic A, Kurtovic-Kozaric A, Johnson SH, Vasmatzis G, Pins MR, Kogan J.

Cancer Genet. 2017 Aug;214-215:9-15. doi: 10.1016/j.cancergen.2017.03.001. Epub 2017 Mar 16.


Management of Multifocal Lung Cancer: Results of a Survey.

Leventakos K, Peikert T, Midthun DE, Molina JR, Blackmon S, Nichols FC, Garces YI, Hallemeier CL, Murphy SJ, Vasmatzis G, Kratz SL, Holland WP, Thomas CF, Mullon JJ, Shen KR, Cassivi SD, Marks RS, Aubry MC, Adjei AA, Yang P, Allen MS, Edell ES, Wigle D, Mansfield AS.

J Thorac Oncol. 2017 Sep;12(9):1398-1402. doi: 10.1016/j.jtho.2017.05.013. Epub 2017 Jun 3.


EGFR mediates activation of RET in lung adenocarcinoma with neuroendocrine differentiation characterized by ASCL1 expression.

Bhinge K, Yang L, Terra S, Nasir A, Muppa P, Aubry MC, Yi J, Janaki N, Kovtun IV, Murphy SJ, Halling G, Rahi H, Mansfield A, de Andrade M, Yang P, Vasmatzis G, Peikert T, Kosari F.

Oncotarget. 2017 Apr 18;8(16):27155-27165. doi: 10.18632/oncotarget.15676.


TFEB-VEGFA (6p21.1) co-amplified renal cell carcinoma: a distinct entity with potential implications for clinical management.

Gupta S, Johnson SH, Vasmatzis G, Porath B, Rustin JG, Rao P, Costello BA, Leibovich BC, Thompson RH, Cheville JC, Sukov WR.

Mod Pathol. 2017 Jul;30(7):998-1012. doi: 10.1038/modpathol.2017.24. Epub 2017 Mar 24.


Mantle cell lymphoma with a novel t(11;12)(q13;p11.2): a proposed alternative mechanism of CCND1 up-regulation.

Menke JR, Vasmatzis G, Murphy S, Yang L, Menke DM, Tun HW, King RL, Smoley SA, Ketterling RP, Sukov WR.

Hum Pathol. 2017 Jun;64:207-212. doi: 10.1016/j.humpath.2017.01.001. Epub 2017 Jan 27.


Trinucleotide Repeat Expansion in the Transcription Factor 4 (TCF4) Gene Leads to Widespread mRNA Splicing Changes in Fuchs' Endothelial Corneal Dystrophy.

Wieben ED, Aleff RA, Tang X, Butz ML, Kalari KR, Highsmith EW, Jen J, Vasmatzis G, Patel SV, Maguire LJ, Baratz KH, Fautsch MP.

Invest Ophthalmol Vis Sci. 2017 Jan 1;58(1):343-352. doi: 10.1167/iovs.16-20900.


Common fragile sites (CFS) and extremely large CFS genes are targets for human papillomavirus integrations and chromosome rearrangements in oropharyngeal squamous cell carcinoma.

Gao G, Johnson SH, Vasmatzis G, Pauley CE, Tombers NM, Kasperbauer JL, Smith DI.

Genes Chromosomes Cancer. 2017 Jan;56(1):59-74. doi: 10.1002/gcc.22415. Epub 2016 Nov 1.


Chromoplectic TPM3-ALK rearrangement in a patient with inflammatory myofibroblastic tumor who responded to ceritinib after progression on crizotinib.

Mansfield AS, Murphy SJ, Harris FR, Robinson SI, Marks RS, Johnson SH, Smadbeck JB, Halling GC, Yi ES, Wigle D, Vasmatzis G, Jen J.

Ann Oncol. 2016 Nov;27(11):2111-2117. Epub 2016 Oct 14.


Custom Gene Capture and Next-Generation Sequencing to Resolve Discordant ALK Status by FISH and IHC in Lung Adenocarcinoma.

Jang JS, Wang X, Vedell PT, Wen J, Zhang J, Ellison DW, Evans JM, Johnson SH, Yang P, Sukov WR, Oliveira AM, Vasmatzis G, Sun Z, Jen J, Yi ES.

J Thorac Oncol. 2016 Nov;11(11):1891-1900. doi: 10.1016/j.jtho.2016.06.001. Epub 2016 Jun 22.


Quantification of Somatic Chromosomal Rearrangements in Circulating Cell-Free DNA from Ovarian Cancers.

Harris FR, Kovtun IV, Smadbeck J, Multinu F, Jatoi A, Kosari F, Kalli KR, Murphy SJ, Halling GC, Johnson SH, Liu MC, Mariani A, Vasmatzis G.

Sci Rep. 2016 Jul 20;6:29831. doi: 10.1038/srep29831.


Integrated mate-pair and RNA sequencing identifies novel, targetable gene fusions in peripheral T-cell lymphoma.

Boddicker RL, Razidlo GL, Dasari S, Zeng Y, Hu G, Knudson RA, Greipp PT, Davila JI, Johnson SH, Porcher JC, Smadbeck JB, Eckloff BW, Billadeau DD, Kurtin PJ, McNiven MA, Link BK, Ansell SM, Cerhan JR, Asmann YW, Vasmatzis G, Feldman AL.

Blood. 2016 Sep 1;128(9):1234-45. doi: 10.1182/blood-2016-03-707141. Epub 2016 Jun 13.


Targeted next generation sequencing of endoscopic ultrasound acquired cytology from ampullary and pancreatic adenocarcinoma has the potential to aid patient stratification for optimal therapy selection.

Gleeson FC, Kerr SE, Kipp BR, Voss JS, Minot DM, Tu ZJ, Henry MR, Graham RP, Vasmatzis G, Cheville JC, Lazaridis KN, Levy MJ.

Oncotarget. 2016 Aug 23;7(34):54526-54536. doi: 10.18632/oncotarget.9440.


Molecular cytology genotyping of primary and metastatic GI stromal tumors by using a custom two-gene targeted next-generation sequencing panel with therapeutic intent.

Gleeson FC, Kerr SE, Kipp BR, Voss JS, Minot DM, Tu ZJ, Henry MR, Vasmatzis G, Cheville JC, Lazaridis KN, Levy MJ.

Gastrointest Endosc. 2016 Dec;84(6):950-958.e3. doi: 10.1016/j.gie.2016.04.027. Epub 2016 Apr 23.


Magnetophoretic-based microfluidic device for DNA Concentration.

Shim S, Shim J, Taylor WR, Kosari F, Vasmatzis G, Ahlquist DA, Bashir R.

Biomed Microdevices. 2016 Apr;18(2):28. doi: 10.1007/s10544-016-0051-5.


Integrated Genomic Analysis of Pancreatic Ductal Adenocarcinomas Reveals Genomic Rearrangement Events as Significant Drivers of Disease.

Murphy SJ, Hart SN, Halling GC, Johnson SH, Smadbeck JB, Drucker T, Lima JF, Rohakhtar FR, Harris FR, Kosari F, Subramanian S, Petersen GM, Wiltshire TD, Kipp BR, Truty MJ, McWilliams RR, Couch FJ, Vasmatzis G.

Cancer Res. 2016 Feb 1;76(3):749-61. doi: 10.1158/0008-5472.CAN-15-2198. Epub 2015 Dec 16.


Heterogeneity of Programmed Cell Death Ligand 1 Expression in Multifocal Lung Cancer.

Mansfield AS, Murphy SJ, Peikert T, Yi ES, Vasmatzis G, Wigle DA, Aubry MC.

Clin Cancer Res. 2016 May 1;22(9):2177-82. doi: 10.1158/1078-0432.CCR-15-2246. Epub 2015 Dec 14.


Integrated analysis of the genomic instability of PTEN in clinically insignificant and significant prostate cancer.

Murphy SJ, Karnes RJ, Kosari F, Castellar BE, Kipp BR, Johnson SH, Terra S, Harris FR, Halling GC, Klein JL, Nasir A, Bergstrahl E, Rangel LJ, Sukov WR, Vasmatzis G, Cheville JC.

Mod Pathol. 2016 Feb;29(2):143-56. doi: 10.1038/modpathol.2015.136. Epub 2015 Nov 27.

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