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Items: 1 to 50 of 147

1.

A novel histological index for evaluation of environmental enteric dysfunction identifies geographic-specific features of enteropathy among children with suboptimal growth.

Liu TC, VanBuskirk K, Ali SA, Kelly MP, Holtz LR, Yilmaz OH, Sadiq K, Iqbal N, Amadi B, Syed S, Ahmed T, Moore S, Ndao IM, Isaacs MH, Pfeifer JD, Atlas H, Tarr PI, Denno DM, Moskaluk CA.

PLoS Negl Trop Dis. 2020 Jan 13;14(1):e0007975. doi: 10.1371/journal.pntd.0007975. [Epub ahead of print]

2.

Preanalytics and Precision Pathology: Pathology Practices to Ensure Molecular Integrity of Cancer Patient Biospecimens for Precision Medicine.

Compton CC, Robb JA, Anderson MW, Berry AB, Birdsong GG, Bloom KJ, Branton PA, Crothers JW, Cushman-Vokoun AM, Hicks DG, Khoury JD, Laser J, Marshall CB, Misialek MJ, Natale KE, Nowak JA, Olson D, Pfeifer JD, Schade A, Vance GH, Walk EE, Yohe SL.

Arch Pathol Lab Med. 2019 Nov;143(11):1346-1363. doi: 10.5858/arpa.2019-0009-SA. Epub 2019 Jul 22.

PMID:
31329478
3.

Optimization of Population Frequency Cutoffs for Filtering Common Germline Polymorphisms from Tumor-Only Next-Generation Sequencing Data.

McNulty SN, Parikh BA, Duncavage EJ, Heusel JW, Pfeifer JD.

J Mol Diagn. 2019 Sep;21(5):903-912. doi: 10.1016/j.jmoldx.2019.05.005. Epub 2019 Jun 25.

PMID:
31251990
4.

Identity determination in diagnostic surgical pathology.

Pfeifer JD.

Semin Diagn Pathol. 2019 Sep;36(5):355-365. doi: 10.1053/j.semdp.2019.06.001. Epub 2019 Jun 4. Review.

PMID:
31196743
5.

Pitfalls in molecular diagnostics.

Sun L, Pfeifer JD.

Semin Diagn Pathol. 2019 Sep;36(5):342-354. doi: 10.1053/j.semdp.2019.06.002. Epub 2019 Jun 4. Review.

PMID:
31182318
6.

Tumor Mutation Burden and Checkpoint Immunotherapy Markers in NUT Midline Carcinoma.

He M, Chernock R, Zhou S, Gondim M, Dehner LP, Pfeifer JD.

Appl Immunohistochem Mol Morphol. 2019 Jun 7. doi: 10.1097/PAI.0000000000000781. [Epub ahead of print]

PMID:
31180909
7.

Tumor mutation burden, DNA mismatch repair status and checkpoint immunotherapy markers in primary and relapsed malignant rhabdoid tumors.

Abro B, Kaushal M, Chen L, Wu R, Dehner LP, Pfeifer JD, He M.

Pathol Res Pract. 2019 Jun;215(6):152395. doi: 10.1016/j.prp.2019.03.023. Epub 2019 Apr 18.

PMID:
31047727
8.

Long-term outcomes of follicular variant vs classic papillary thyroid carcinoma.

Henke LE, Pfeifer JD, Baranski TJ, DeWees T, Grigsby PW.

Endocr Connect. 2018 Dec 1;7(12):1226-1235. doi: 10.1530/EC-18-0264.

9.

Soft Tissue Sarcoma, Version 2.2018, NCCN Clinical Practice Guidelines in Oncology.

von Mehren M, Randall RL, Benjamin RS, Boles S, Bui MM, Ganjoo KN, George S, Gonzalez RJ, Heslin MJ, Kane JM, Keedy V, Kim E, Koon H, Mayerson J, McCarter M, McGarry SV, Meyer C, Morris ZS, O'Donnell RJ, Pappo AS, Paz IB, Petersen IA, Pfeifer JD, Riedel RF, Ruo B, Schuetze S, Tap WD, Wayne JD, Bergman MA, Scavone JL.

J Natl Compr Canc Netw. 2018 May;16(5):536-563. doi: 10.6004/jnccn.2018.0025.

PMID:
29752328
10.

Clinical outcomes and differential effects of PI3K pathway mutation in obese versus non-obese patients with cervical cancer.

Grigsby P, Elhammali A, Ruiz F, Markovina S, McLellan MD, Miller CA, Chundury A, Ta NL, Rashmi R, Pfeifer JD, Fulton RS, DeWees T, Schwarz JK.

Oncotarget. 2017 Dec 23;9(3):4061-4073. doi: 10.18632/oncotarget.23664. eCollection 2018 Jan 9.

11.

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 May;31(5):791-808. doi: 10.1038/modpathol.2017.181. Epub 2018 Jan 12.

12.

Serum squamous cell carcinoma antigen as an early indicator of response during therapy of cervical cancer.

Markovina S, Wang S, Henke LE, Luke CJ, Pak SC, DeWees T, Pfeifer JD, Schwarz JK, Liu W, Chen S, Mutch D, Wang X, Powell MA, Siegel BA, Dehdashti F, Silverman GA, Grigsby PW.

Br J Cancer. 2018 Jan;118(1):72-78. doi: 10.1038/bjc.2017.390. Epub 2017 Nov 7.

13.

Routine use of clinical exome-based next-generation sequencing for evaluation of patients with thrombotic microangiopathies.

Gaut JP, Jain S, Pfeifer JD, Vigh-Conrad KA, Corliss M, Sharma MK, Heusel JW, Cottrell CE.

Mod Pathol. 2017 Dec;30(12):1739-1747. doi: 10.1038/modpathol.2017.90. Epub 2017 Jul 28.

14.

Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings.

Lubin IM, Aziz N, Babb LJ, Ballinger D, Bisht H, Church DM, Cordes S, Eilbeck K, Hyland F, Kalman L, Landrum M, Lockhart ER, Maglott D, Marth G, Pfeifer JD, Rehm HL, Roy S, Tezak Z, Truty R, Ullman-Cullere M, Voelkerding KV, Worthey EA, Zaranek AW, Zook JM.

J Mol Diagn. 2017 May;19(3):417-426. doi: 10.1016/j.jmoldx.2016.12.001. Epub 2017 Mar 18.

15.

Association of Li-Fraumeni Syndrome With Small Cell Carcinoma of the Ovary, Hypercalcemic Type and Concurrent Pleomorphic Liposarcoma of the Cervix.

Tandon B, Hagemann IS, Maluf HM, Pfeifer JD, Al-Kateb H.

Int J Gynecol Pathol. 2017 Nov;36(6):593-599. doi: 10.1097/PGP.0000000000000365.

PMID:
28177947
16.

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.

PMID:
28093192
17.

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.

18.

Molecular digital pathology: progress and potential of exchanging molecular data.

Roy S, Pfeifer JD, LaFramboise WA, Pantanowitz L.

Expert Rev Mol Diagn. 2016 Sep;16(9):941-7. doi: 10.1080/14737159.2016.1206472. Epub 2016 Jul 29. Review.

PMID:
27471996
19.

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.

PMID:
27388684
20.

Soft Tissue Sarcoma, Version 2.2016, NCCN Clinical Practice Guidelines in Oncology.

von Mehren M, Randall RL, Benjamin RS, Boles S, Bui MM, Conrad EU 3rd, Ganjoo KN, George S, Gonzalez RJ, Heslin MJ, Kane JM 3rd, Koon H, Mayerson J, McCarter M, McGarry SV, Meyer C, O'Donnell RJ, Pappo AS, Paz IB, Petersen IA, Pfeifer JD, Riedel RF, Schuetze S, Schupak KD, Schwartz HS, Tap WD, Wayne JD, Bergman MA, Scavone J.

J Natl Compr Canc Netw. 2016 Jun;14(6):758-86.

PMID:
27283169
21.

Deja Visite: Specimen Provenance Issues in Next-Generation Sequencing.

Pfeifer JD.

Am J Clin Pathol. 2016 Mar;145(3):296-8. doi: 10.1093/ajcp/aqw037. No abstract available.

PMID:
27124910
22.

Use of short tandem repeat analysis in unusual presentations of trophoblastic tumors and their mimics.

Aranake-Chrisinger J, Huettner PC, Hagemann AR, Pfeifer JD.

Hum Pathol. 2016 Jun;52:92-100. doi: 10.1016/j.humpath.2016.01.005. Epub 2016 Feb 4.

PMID:
26980014
23.

Real-world data in the molecular era-finding the reality in the real world.

Dickson DJ, Pfeifer JD.

Clin Pharmacol Ther. 2016 Feb;99(2):186-97. doi: 10.1002/cpt.300. Epub 2016 Jan 12. Review.

PMID:
26565654
24.

Standards for Clinical Grade Genomic Databases.

Yohe SL, Carter AB, Pfeifer JD, Crawford JM, Cushman-Vokoun A, Caughron S, Leonard DG.

Arch Pathol Lab Med. 2015 Nov;139(11):1400-12. doi: 10.5858/arpa.2014-0568-CP.

PMID:
26516938
25.

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.

PMID:
26386089
26.

Diagnostic yield of targeted next generation sequencing in various cancer types: an information-theoretic approach.

Hagemann IS, O'Neill PK, Erill I, Pfeifer JD.

Cancer Genet. 2015 Sep;208(9):441-7. doi: 10.1016/j.cancergen.2015.05.030. Epub 2015 May 29.

PMID:
26227479
27.

Computational Pathology: A Path Ahead.

Louis DN, Feldman M, Carter AB, Dighe AS, Pfeifer JD, Bry L, Almeida JS, Saltz J, Braun J, Tomaszewski JE, Gilbertson JR, Sinard JH, Gerber GK, Galli SJ, Golden JA, Becich MJ.

Arch Pathol Lab Med. 2016 Jan;140(1):41-50. doi: 10.5858/arpa.2015-0093-SA. Epub 2015 Jun 22.

28.

Identification of major factors associated with failed clinical molecular oncology testing performed by next generation sequencing (NGS).

Al-Kateb H, Nguyen TT, Steger-May K, Pfeifer JD.

Mol Oncol. 2015 Nov;9(9):1737-43. doi: 10.1016/j.molonc.2015.05.004. Epub 2015 May 29.

29.

BRAF mutation is not predictive of long-term outcome in papillary thyroid carcinoma.

Henke LE, Pfeifer JD, Ma C, Perkins SM, DeWees T, El-Mofty S, Moley JF, Nussenbaum B, Haughey BH, Baranski TJ, Schwarz JK, Grigsby PW.

Cancer Med. 2015 Jun;4(6):791-9. doi: 10.1002/cam4.417. Epub 2015 Feb 25.

30.

The Cancer Genomics Resource List 2014.

Zutter MM, Bloom KJ, Cheng L, Hagemann IS, Kaufman JH, Krasinskas AM, Lazar AJ, Leonard DG, Lindeman NI, Moyer AM, Nikiforova MN, Nowak JA, Pfeifer JD, Sepulveda AR, Willis JE, Yohe SL.

Arch Pathol Lab Med. 2015 Aug;139(8):989-1008. doi: 10.5858/arpa.2014-0330-CP. Epub 2014 Dec 1.

31.

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.

32.

Gastrointestinal stromal tumors, version 2.2014.

von Mehren M, Randall RL, Benjamin RS, Boles S, Bui MM, Casper ES, Conrad EU 3rd, DeLaney TF, Ganjoo KN, George S, Gonzalez RJ, Heslin MJ, Kane JM 3rd, Mayerson J, McGarry SV, Meyer C, O'Donnell RJ, Pappo AS, Paz IB, Pfeifer JD, Riedel RF, Schuetze S, Schupak KD, Schwartz HS, Van Tine BA, Wayne JD, Bergman MA, Sundar H.

J Natl Compr Canc Netw. 2014 Jun;12(6):853-62.

PMID:
24925196
33.

Mucosal melanoma: correlation of clinicopathologic, prognostic, and molecular features.

Gru AA, Becker N, Dehner LP, Pfeifer JD.

Melanoma Res. 2014 Aug;24(4):360-70. doi: 10.1097/CMR.0000000000000082.

PMID:
24870295
34.

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.

35.

Soft tissue sarcoma, version 2.2014.

von Mehren M, Randall RL, Benjamin RS, Boles S, Bui MM, Casper ES, Conrad EU 3rd, Delaney TF, Ganjoo KN, George S, Gonzalez RJ, Heslin MJ, Kane JM 3rd, Mayerson J, McGarry SV, Meyer C, O'Donnell RJ, Pappo AS, Paz IB, Pfeifer JD, Riedel RF, Schuetze S, Schupak KD, Schwartz HS, Van Tine BA, Wayne JD, Bergman MA, Sundar H; National Comprehensive Cancer Network.

J Natl Compr Canc Netw. 2014 Apr;12(4):473-83.

PMID:
24717567
36.

Progress and potential: training in genomic pathology.

Haspel RL, Olsen RJ, Berry A, Hill CE, Pfeifer JD, Schrijver I, Kaul KL.

Arch Pathol Lab Med. 2014 Apr;138(4):498-504. doi: 10.5858/arpa.2013-0359-SA. Review.

37.

BRAF V600E mutational status in pediatric thyroid cancer.

Henke LE, Perkins SM, Pfeifer JD, Ma C, Chen Y, DeWees T, Grigsby PW.

Pediatr Blood Cancer. 2014 Jul;61(7):1168-72. doi: 10.1002/pbc.24935. Epub 2014 Mar 27.

PMID:
24677749
38.
39.

Diagnostic utility of targeted next-generation sequencing in problematic cases.

Sehn JK, Hagemann IS, Pfeifer JD, Cottrell CE, Lockwood CM.

Am J Surg Pathol. 2014 Apr;38(4):534-41. doi: 10.1097/PAS.0000000000000161.

PMID:
24451277
40.

Stabilization of disease after targeted therapy in a thymic carcinoma with KIT mutation detected by clinical next-generation sequencing.

Hagemann IS, Govindan R, Javidan-Nejad C, Pfeifer JD, Cottrell CE.

J Thorac Oncol. 2014 Feb;9(2):e12-6. doi: 10.1097/JTO.0b013e3182a7d22e.

41.

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.

42.

Clinical next generation sequencing in cancer.

Pfeifer JD.

Cancer Genet. 2013 Dec;206(12):409-12. doi: 10.1016/j.cancergen.2013.10.004. Epub 2013 Oct 22. No abstract available.

PMID:
24345338
43.

Molecular techniques in anatomic pathology: an overview.

Wick MR, Nappi O, Pfeifer JD.

Semin Diagn Pathol. 2013 Nov;30(4):263-83. doi: 10.1053/j.semdp.2013.11.009. Epub 2013 Nov 19. Review. No abstract available.

PMID:
24342284
44.

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.

PMID:
24303327
45.

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.

46.

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.

47.

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.

PMID:
24196187
48.

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.

PMID:
24120702
49.

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.

50.

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing.

Liu C, Yang X, Duffy B, Mohanakumar T, Mitra RD, Zody MC, Pfeifer JD.

Nucleic Acids Res. 2013 Aug;41(14):e142. doi: 10.1093/nar/gkt481. Epub 2013 Jun 8.

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