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Subclones dominate at MDS progression following allogeneic hematopoietic cell transplant.

Jacoby MA, Duncavage EJ, Chang GS, Miller CA, Shao J, Elliott K, Robinson J, Fulton RS, Fronick CC, O'Laughlin M, Heath SE, Pusic I, Welch JS, Link DC, DiPersio JF, Westervelt P, Ley TJ, Graubert TA, Walter MJ.

JCI Insight. 2018 Mar 8;3(5). pii: 98962. doi: 10.1172/jci.insight.98962. [Epub ahead of print]


Cellular stressors contribute to the expansion of hematopoietic clones of varying leukemic potential.

Wong TN, Miller CA, Jotte MRM, Bagegni N, Baty JD, Schmidt AP, Cashen AF, Duncavage EJ, Helton NM, Fiala M, Fulton RS, Heath SE, Janke M, Luber K, Westervelt P, Vij R, DiPersio JF, Welch JS, Graubert TA, Walter MJ, Ley TJ, Link DC.

Nat Commun. 2018 Jan 31;9(1):455. doi: 10.1038/s41467-018-02858-0.


Loss of Toll-like receptor 2 results in accelerated leukemogenesis in the NUP98-HOXD13 mouse model of MDS.

Monlish DA, Bhatt ST, Duncavage EJ, Greenberg ZJ, Keller JL, Romine MP, Yang W, Aplan PD, Walter MJ, Schuettpelz LG.

Blood. 2018 Mar 1;131(9):1032-1035. doi: 10.1182/blood-2017-08-801944. Epub 2018 Jan 22. No abstract available.


Genomic heterogeneity of ALK fusion breakpoints in non-small-cell lung cancer.

Rosenbaum JN, Bloom R, Forys JT, Hiken J, Armstrong JR, Branson J, McNulty S, Velu PD, Pepin K, Abel H, Cottrell CE, Pfeifer JD, Kulkarni S, Govindan R, Konnick EQ, Lockwood CM, Duncavage EJ.

Mod Pathol. 2018 Jan 12. doi: 10.1038/modpathol.2017.181. [Epub ahead of print]


Authors' Reply.

Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A, Nikiforova MN.

J Mol Diagn. 2018 Jan;20(1):125-126. doi: 10.1016/j.jmoldx.2017.11.002.


Clinical Targeted Next-Generation Sequencing Shows Increased Mutational Load in Endometrioid-type Endometrial Adenocarcinoma With Deficient DNA Mismatch Repair.

Lee PJ, McNulty S, Duncavage EJ, Heusel JW, Hagemann IS.

Int J Gynecol Pathol. 2017 Oct 27. doi: 10.1097/PGP.0000000000000459. [Epub ahead of print]


FGFR2 amplification in colorectal adenocarcinoma.

Carter JH, Cottrell CE, McNulty SN, Vigh-Conrad KA, Lamp S, Heusel JW, Duncavage EJ.

Cold Spring Harb Mol Case Stud. 2017 Nov 21;3(6). pii: a001495. doi: 10.1101/mcs.a001495. Print 2017 Nov.


New Insight Into the Biology, Risk Stratification, and Targeted Treatment of Myelodysplastic Syndromes.

Haider M, Duncavage EJ, Afaneh KF, Bejar R, List AF.

Am Soc Clin Oncol Educ Book. 2017;37:480-494. doi: 10.14694/EDBK_175397.


Spectrum of mutations in leiomyosarcomas identified by clinical targeted next-generation sequencing.

Lee PJ, Yoo NS, Hagemann IS, Pfeifer JD, Cottrell CE, Abel HJ, Duncavage EJ.

Exp Mol Pathol. 2017 Feb;102(1):156-161. doi: 10.1016/j.yexmp.2017.01.012. Epub 2017 Jan 14.


Mutational landscape and response are conserved in peripheral blood of AML and MDS patients during decitabine therapy.

Duncavage EJ, Uy GL, Petti AA, Miller CA, Lee YS, Tandon B, Gao F, Fronick CC, O'Laughlin M, Fulton RS, Wilson RK, Jacoby MA, Cashen AF, Wartman LD, Walter MJ, Westervelt P, Link DC, DiPersio JF, Ley TJ, Welch JS.

Blood. 2017 Mar 9;129(10):1397-1401. doi: 10.1182/blood-2016-10-745273. Epub 2017 Jan 12. No abstract available.


Targeted Next-Generation Sequencing in Molecular Subtyping of Lower-Grade Diffuse Gliomas: Application of the World Health Organization's 2016 Revised Criteria for Central Nervous System Tumors.

Carter JH, McNulty SN, Cimino PJ, Cottrell CE, Heusel JW, Vigh-Conrad KA, Duncavage EJ.

J Mol Diagn. 2017 Mar;19(2):328-337. doi: 10.1016/j.jmoldx.2016.10.010. Epub 2016 Dec 30.


Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.

Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A, Nikiforova MN.

J Mol Diagn. 2017 Jan;19(1):4-23. doi: 10.1016/j.jmoldx.2016.10.002. Review.


TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes.

Welch JS, Petti AA, Miller CA, Fronick CC, O'Laughlin M, Fulton RS, Wilson RK, Baty JD, Duncavage EJ, Tandon B, Lee YS, Wartman LD, Uy GL, Ghobadi A, Tomasson MH, Pusic I, Romee R, Fehniger TA, Stockerl-Goldstein KE, Vij R, Oh ST, Abboud CN, Cashen AF, Schroeder MA, Jacoby MA, Heath SE, Luber K, Janke MR, Hantel A, Khan N, Sukhanova MJ, Knoebel RW, Stock W, Graubert TA, Walter MJ, Westervelt P, Link DC, DiPersio JF, Ley TJ.

N Engl J Med. 2016 Nov 24;375(21):2023-2036. doi: 10.1056/NEJMoa1605949.


In Silico Proficiency Testing for Clinical Next-Generation Sequencing.

Duncavage EJ, Abel HJ, Pfeifer JD.

J Mol Diagn. 2017 Jan;19(1):35-42. doi: 10.1016/j.jmoldx.2016.09.005. Epub 2016 Nov 15. Review.


Dynamic changes in the clonal structure of MDS and AML in response to epigenetic therapy.

Uy GL, Duncavage EJ, Chang GS, Jacoby MA, Miller CA, Shao J, Heath S, Elliott K, Reineck T, Fulton RS, Fronick CC, O'Laughlin M, Ganel L, Abboud CN, Cashen AF, DiPersio JF, Wilson RK, Link DC, Welch JS, Ley TJ, Graubert TA, Westervelt P, Walter MJ.

Leukemia. 2017 Apr;31(4):872-881. doi: 10.1038/leu.2016.282. Epub 2016 Oct 14.


Targeted sequencing informs the evaluation of normal karyotype cytopenic patients for low-grade myelodysplastic syndrome.

Duncavage EJ, O'Brien J, Vij K, Miller CA, Chang GS, Shao J, Jacoby MA, Heath S, Janke MR, Elliott K, Fulton RS, Fronick C, O'Laughlin M, Westervelt P, Ley TJ, Wilson RK, Walter MJ.

Leukemia. 2016 Dec;30(12):2422-2426. doi: 10.1038/leu.2016.247. Epub 2016 Aug 30. No abstract available.


A Model Study of In Silico Proficiency Testing for Clinical Next-Generation Sequencing.

Duncavage EJ, Abel HJ, Merker JD, Bodner JB, Zhao Q, Voelkerding KV, Pfeifer JD.

Arch Pathol Lab Med. 2016 Oct;140(10):1085-91. doi: 10.5858/arpa.2016-0194-CP. Epub 2016 Jul 7.


A common founding clone with TP53 and PTEN mutations gives rise to a concurrent germ cell tumor and acute megakaryoblastic leukemia.

Lu C, Riedell P, Miller CA, Hagemann IS, Westervelt P, Ozenberger BA, O'Laughlin M, Magrini V, Demeter RT, Duncavage EJ, Griffith M, Griffith OL, Wartman LD.

Cold Spring Harb Mol Case Stud. 2016 Jan;2(1):a000687. doi: 10.1101/mcs.a000687.


A genomic analysis of Philadelphia chromosome-negative AML arising in patients with CML.

Krysiak K, Christopher MJ, Skidmore ZL, Demeter RT, Magrini V, Kunisaki J, O'Laughlin M, Duncavage EJ, Miller CA, Ozenberger BA, Griffith M, Wartman LD, Griffith OL.

Blood Cancer J. 2016 Apr 8;6:e413. doi: 10.1038/bcj.2016.18. No abstract available.


Implications of Tumor Clonal Heterogeneity in the Era of Next-Generation Sequencing.

Jacoby MA, Duncavage EJ, Walter MJ.

Trends Cancer. 2015 Dec;1(4):231-241. doi: 10.1016/j.trecan.2015.10.006. Epub 2015 Nov 25. Review.


Occult Specimen Contamination in Routine Clinical Next-Generation Sequencing Testing.

Sehn JK, Spencer DH, Pfeifer JD, Bredemeyer AJ, Cottrell CE, Abel HJ, Duncavage EJ.

Am J Clin Pathol. 2015 Oct;144(4):667-74. doi: 10.1309/AJCPR88WDJJLDMBN.


Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia.

Klco JM, Miller CA, Griffith M, Petti A, Spencer DH, Ketkar-Kulkarni S, Wartman LD, Christopher M, Lamprecht TL, Helton NM, Duncavage EJ, Payton JE, Baty J, Heath SE, Griffith OL, Shen D, Hundal J, Chang GS, Fulton R, O'Laughlin M, Fronick C, Magrini V, Demeter RT, Larson DE, Kulkarni S, Ozenberger BA, Welch JS, Walter MJ, Graubert TA, Westervelt P, Radich JP, Link DC, Mardis ER, DiPersio JF, Wilson RK, Ley TJ.

JAMA. 2015 Aug 25;314(8):811-22. doi: 10.1001/jama.2015.9643.


T-cell clonality assessment by next-generation sequencing improves detection sensitivity in mycosis fungoides.

Sufficool KE, Lockwood CM, Abel HJ, Hagemann IS, Schumacher JA, Kelley TW, Duncavage EJ.

J Am Acad Dermatol. 2015 Aug;73(2):228-36.e2. doi: 10.1016/j.jaad.2015.04.030. Epub 2015 Jun 3.


The utility of next-generation sequencing in diagnosis and monitoring of acute myeloid leukemia and myelodysplastic syndromes.

Duncavage EJ, Tandon B.

Int J Lab Hematol. 2015 May;37 Suppl 1:115-21. doi: 10.1111/ijlh.12361. Review.


Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo.

Shirai CL, Ley JN, White BS, Kim S, Tibbitts J, Shao J, Ndonwi M, Wadugu B, Duncavage EJ, Okeyo-Owuor T, Liu T, Griffith M, McGrath S, Magrini V, Fulton RS, Fronick C, O'Laughlin M, Graubert TA, Walter MJ.

Cancer Cell. 2015 May 11;27(5):631-43. doi: 10.1016/j.ccell.2015.04.008.


Whole Exome Sequencing Reveals the Order of Genetic Changes during Malignant Transformation and Metastasis in a Single Patient with NF1-plexiform Neurofibroma.

Hirbe AC, Dahiya S, Miller CA, Li T, Fulton RS, Zhang X, McDonald S, DeSchryver K, Duncavage EJ, Walrath J, Reilly KM, Abel HJ, Pekmezci M, Perry A, Ley TJ, Gutmann DH.

Clin Cancer Res. 2015 Sep 15;21(18):4201-11. doi: 10.1158/1078-0432.CCR-14-3049. Epub 2015 Apr 29.


A wide spectrum of EGFR mutations in glioblastoma is detected by a single clinical oncology targeted next-generation sequencing panel.

Cimino PJ, Bredemeyer A, Abel HJ, Duncavage EJ.

Exp Mol Pathol. 2015 Jun;98(3):568-73. doi: 10.1016/j.yexmp.2015.04.006. Epub 2015 Apr 22.


Next-generation sequencing of salivary high-grade neuroendocrine carcinomas identifies alterations in RB1 and the mTOR pathway.

Goyal B, Duncavage EJ, Martinez D, Lewis JS Jr, Chernock RD.

Exp Mol Pathol. 2014 Dec;97(3):572-8. doi: 10.1016/j.yexmp.2014.10.011. Epub 2014 Oct 29.


Clinical next-generation sequencing in patients with non-small cell lung cancer.

Hagemann IS, Devarakonda S, Lockwood CM, Spencer DH, Guebert K, Bredemeyer AJ, Al-Kateb H, Nguyen TT, Duncavage EJ, Cottrell CE, Kulkarni S, Nagarajan R, Seibert K, Baggstrom M, Waqar SN, Pfeifer JD, Morgensztern D, Govindan R.

Cancer. 2015 Feb 15;121(4):631-9. doi: 10.1002/cncr.29089. Epub 2014 Oct 24.


Clinical prognostic biomarkers in chronic lymphocytic leukemia and diffuse large B-cell lymphoma.

Chastain EC, Duncavage EJ.

Arch Pathol Lab Med. 2015 May;139(5):602-7. doi: 10.5858/arpa.2014-0086-RA. Epub 2014 Sep 23. Review.


Blasts-more than meets the eye: evaluation of post-induction day 21 bone marrow in CBFB rearranged acute leukemia.

Xu X, Duncavage EJ.

Int J Clin Exp Pathol. 2014 Jun 15;7(7):4498-502. eCollection 2014.


Copy number variants in clinical next-generation sequencing data can define the relationship between simultaneous tumors in an individual patient.

Sehn JK, Abel HJ, Duncavage EJ.

Exp Mol Pathol. 2014 Aug;97(1):69-73. doi: 10.1016/j.yexmp.2014.05.008. Epub 2014 Jun 2.


Detection of gene rearrangements in targeted clinical next-generation sequencing.

Abel HJ, Al-Kateb H, Cottrell CE, Bredemeyer AJ, Pritchard CC, Grossmann AH, Wallander ML, Pfeifer JD, Lockwood CM, Duncavage EJ.

J Mol Diagn. 2014 Jul;16(4):405-17. doi: 10.1016/j.jmoldx.2014.03.006. Epub 2014 May 9.


Malignant transformation of a desmoplastic infantile ganglioglioma in an infant carrier of a nonsynonymous TP53 mutation.

Prakash V, Batanian JR, Guzman MA, Duncavage EJ, Geller TJ.

Pediatr Neurol. 2014 Jul;51(1):138-43. doi: 10.1016/j.pediatrneurol.2014.02.012. Epub 2014 Feb 22.


Detection of viral pathogens in high grade gliomas from unmapped next-generation sequencing data.

Cimino PJ, Zhao G, Wang D, Sehn JK, Lewis JS Jr, Duncavage EJ.

Exp Mol Pathol. 2014 Jun;96(3):310-5. doi: 10.1016/j.yexmp.2014.03.010. Epub 2014 Apr 1.


CD163 immunohistochemistry is superior to CD68 in predicting outcome in classical Hodgkin lymphoma.

Klein JL, Nguyen TT, Bien-Willner GA, Chen L, Foyil KV, Bartlett NL, Duncavage EJ, Hassan A, Frater JL, Kreisel F.

Am J Clin Pathol. 2014 Mar;141(3):381-7. doi: 10.1309/AJCP61TLMXLSLJYS.


A comparison of deep sequencing of TCRG rearrangements vs traditional capillary electrophoresis for assessment of clonality in T-Cell lymphoproliferative disorders.

Schumacher JA, Duncavage EJ, Mosbruger TL, Szankasi PM, Kelley TW.

Am J Clin Pathol. 2014 Mar;141(3):348-59. doi: 10.1309/AJCP5TYGBVW4ZITR.


Retinoblastoma gene mutations detected by whole exome sequencing of Merkel cell carcinoma.

Cimino PJ, Robirds DH, Tripp SR, Pfeifer JD, Abel HJ, Duncavage EJ.

Mod Pathol. 2014 Aug;27(8):1073-87. doi: 10.1038/modpathol.2013.235. Epub 2014 Jan 10.


Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches.

Abel HJ, Duncavage EJ.

Cancer Genet. 2013 Dec;206(12):432-40. doi: 10.1016/j.cancergen.2013.11.002. Epub 2013 Nov 20. Review.


Clinical genomicist workstation.

Sharma MK, Phillips J, Agarwal S, Wiggins WS, Shrivastava S, Koul SB, Bhattacharjee M, Houchins CD, Kalakota RR, George B, Meyer RR, Spencer DH, Lockwood CM, Nguyen TT, Duncavage EJ, Al-Kateb H, Cottrell CE, Godala S, Lokineni R, Sawant SM, Chatti V, Surampudi S, Sunkishala RR, Darbha R, Macharla S, Milbrandt JD, Virgin HW, Mitra RD, Head RD, Kulkarni S, Bredemeyer A, Pfeifer JD, Seibert K, Nagarajan R.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:156-7. eCollection 2013.


Targeted next-generation sequencing using fine-needle aspirates from adenocarcinomas of the lung.

Karnes HE, Duncavage EJ, Bernadt CT.

Cancer Cytopathol. 2014 Feb;122(2):104-13. doi: 10.1002/cncy.21361. Epub 2013 Nov 12.


Validation of a next-generation sequencing assay for clinical molecular oncology.

Cottrell CE, Al-Kateb H, Bredemeyer AJ, Duncavage EJ, Spencer DH, Abel HJ, Lockwood CM, Hagemann IS, O'Guin SM, Burcea LC, Sawyer CS, Oschwald DM, Stratman JL, Sher DA, Johnson MR, Brown JT, Cliften PF, George B, McIntosh LD, Shrivastava S, Nguyen TT, Payton JE, Watson MA, Crosby SD, Head RD, Mitra RD, Nagarajan R, Kulkarni S, Seibert K, Virgin HW 4th, Milbrandt J, Pfeifer JD.

J Mol Diagn. 2014 Jan;16(1):89-105. doi: 10.1016/j.jmoldx.2013.10.002. Epub 2013 Nov 6.


Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data.

Spencer DH, Tyagi M, Vallania F, Bredemeyer AJ, Pfeifer JD, Mitra RD, Duncavage EJ.

J Mol Diagn. 2014 Jan;16(1):75-88. doi: 10.1016/j.jmoldx.2013.09.003. Epub 2013 Nov 5.


MED12 exon 2 mutations in uterine and extrauterine smooth muscle tumors.

Schwetye KE, Pfeifer JD, Duncavage EJ.

Hum Pathol. 2014 Jan;45(1):65-70. doi: 10.1016/j.humpath.2013.08.005. Epub 2013 Nov 4.


Characterization of translocations in mesenchymal hamartoma and undifferentiated embryonal sarcoma of the liver.

Mathews J, Duncavage EJ, Pfeifer JD.

Exp Mol Pathol. 2013 Dec;95(3):319-24. doi: 10.1016/j.yexmp.2013.09.006. Epub 2013 Oct 10.


Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens.

Spencer DH, Sehn JK, Abel HJ, Watson MA, Pfeifer JD, Duncavage EJ.

J Mol Diagn. 2013 Sep;15(5):623-33. doi: 10.1016/j.jmoldx.2013.05.004. Epub 2013 Jun 26.


Detection of FLT3 internal tandem duplication in targeted, short-read-length, next-generation sequencing data.

Spencer DH, Abel HJ, Lockwood CM, Payton JE, Szankasi P, Kelley TW, Kulkarni S, Pfeifer JD, Duncavage EJ.

J Mol Diagn. 2013 Jan;15(1):81-93. doi: 10.1016/j.jmoldx.2012.08.001. Epub 2012 Nov 14.


Detection of Merkel cell polyomavirus in chronic lymphocytic leukemia T-cells.

Cimino PJ Jr, Bahler DW, Duncavage EJ.

Exp Mol Pathol. 2013 Feb;94(1):40-4. doi: 10.1016/j.yexmp.2012.09.019. Epub 2012 Sep 28.


Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia.

Duncavage EJ, Abel HJ, Szankasi P, Kelley TW, Pfeifer JD.

Mod Pathol. 2012 Jun;25(6):795-804. doi: 10.1038/modpathol.2012.29. Epub 2012 Mar 16.


Absence of Merkel cell polyomavirus in primary parotid high-grade neuroendocrine carcinomas regardless of cytokeratin 20 immunophenotype.

Chernock RD, Duncavage EJ, Gnepp DR, El-Mofty SK, Lewis JS Jr.

Am J Surg Pathol. 2011 Dec;35(12):1806-11. doi: 10.1097/PAS.0b013e318236a9b0.


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