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Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples.

Borsu L, Intrieri J, Thampi L, Yu H, Riely G, Nafa K, Chandramohan R, Ladanyi M, Arcila ME.

J Mol Diagn. 2016 Nov;18(6):903-911. doi: 10.1016/j.jmoldx.2016.07.004.


GNAS Mutations in Fibrous Dysplasia: A Comparative Study of Standard Sequencing and Locked Nucleic Acid PCR Sequencing on Decalcified and Nondecalcified Formalin-fixed Paraffin-embedded Tissues.

Jour G, Oultache A, Sadowska J, Mitchell T, Healey J, Nafa K, Hameed M.

Appl Immunohistochem Mol Morphol. 2016 Oct;24(9):660-667.


The molecular landscape of extraskeletal osteosarcoma: A clinicopathological and molecular biomarker study.

Jour G, Wang L, Middha S, Zehir A, Chen W, Sadowska J, Healey J, Agaram NP, Choi L, Nafa K, Hameed M.

J Pathol Clin Res. 2015 Oct 29;2(1):9-20. doi: 10.1002/cjp2.29.


Genomic aberrations frequently alter chromatin regulatory genes in chordoma.

Wang L, Zehir A, Nafa K, Zhou N, Berger MF, Casanova J, Sadowska J, Lu C, Allis CD, Gounder M, Chandhanayingyong C, Ladanyi M, Boland PJ, Hameed M.

Genes Chromosomes Cancer. 2016 Jul;55(7):591-600. doi: 10.1002/gcc.22362.


Locked Nucleic Acid Probes (LNA) for Enhanced Detection of Low-Level, Clinically Significant Mutations.

Nafa K, Hameed M, Arcila ME.

Methods Mol Biol. 2016;1392:71-82. doi: 10.1007/978-1-4939-3360-0_8.


Epidermal growth factor receptor exon 20 insertions in advanced lung adenocarcinomas: Clinical outcomes and response to erlotinib.

Naidoo J, Sima CS, Rodriguez K, Busby N, Nafa K, Ladanyi M, Riely GJ, Kris MG, Arcila ME, Yu HA.

Cancer. 2015 Sep 15;121(18):3212-20. doi: 10.1002/cncr.29493.


Consistent copy number changes and recurrent PRKAR1A mutations distinguish Melanotic Schwannomas from Melanomas: SNP-array and next generation sequencing analysis.

Wang L, Zehir A, Sadowska J, Zhou N, Rosenblum M, Busam K, Agaram N, Travis W, Arcila M, Dogan S, Berger MF, Cheng DT, Ladanyi M, Nafa K, Hameed M.

Genes Chromosomes Cancer. 2015 May 29. doi: 10.1002/gcc.22254.


Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology.

Cheng DT, Mitchell TN, Zehir A, Shah RH, Benayed R, Syed A, Chandramohan R, Liu ZY, Won HH, Scott SN, Brannon AR, O'Reilly C, Sadowska J, Casanova J, Yannes A, Hechtman JF, Yao J, Song W, Ross DS, Oultache A, Dogan S, Borsu L, Hameed M, Nafa K, Arcila ME, Ladanyi M, Berger MF.

J Mol Diagn. 2015 May;17(3):251-64. doi: 10.1016/j.jmoldx.2014.12.006.


Additional Primary Malignancies in Patients with Gastrointestinal Stromal Tumor (GIST): A Clinicopathologic Study of 260 Patients with Molecular Analysis and Review of the Literature.

Hechtman JF, DeMatteo R, Nafa K, Chi P, Arcila ME, Dogan S, Oultache A, Chen W, Hameed M.

Ann Surg Oncol. 2015 Aug;22(8):2633-9. doi: 10.1245/s10434-014-4332-z. Review.


Novel oncogene and tumor suppressor mutations in KIT and PDGFRA wild type gastrointestinal stromal tumors revealed by next generation sequencing.

Hechtman JF, Zehir A, Mitchell T, Borsu L, Singer S, Tap W, Oultache A, Ladanyi M, Nafa K.

Genes Chromosomes Cancer. 2015 Mar;54(3):177-84. doi: 10.1002/gcc.22230.


Detection of mutations in myeloid malignancies through paired-sample analysis of microdroplet-PCR deep sequencing data.

Cheng DT, Cheng J, Mitchell TN, Syed A, Zehir A, Mensah NY, Oultache A, Nafa K, Levine RL, Arcila ME, Berger MF, Hedvat CV.

J Mol Diagn. 2014 Sep;16(5):504-18. doi: 10.1016/j.jmoldx.2014.05.006.


Induction of sarcomas by mutant IDH2.

Lu C, Venneti S, Akalin A, Fang F, Ward PS, Dematteo RG, Intlekofer AM, Chen C, Ye J, Hameed M, Nafa K, Agaram NP, Cross JR, Khanin R, Mason CE, Healey JH, Lowe SW, Schwartz GK, Melnick A, Thompson CB.

Genes Dev. 2013 Sep 15;27(18):1986-98. doi: 10.1101/gad.226753.113.


Use of touch imprint cytology as a simple method to enrich tumor cells for molecular analysis.

Dogan S, Becker JC, Rekhtman N, Tang LH, Nafa K, Ladanyi M, Klimstra DS.

Cancer Cytopathol. 2013 Jul;121(7):354-60. doi: 10.1002/cncy.21292.


EGFR exon 20 insertion mutations in lung adenocarcinomas: prevalence, molecular heterogeneity, and clinicopathologic characteristics.

Arcila ME, Nafa K, Chaft JE, Rekhtman N, Lau C, Reva BA, Zakowski MF, Kris MG, Ladanyi M.

Mol Cancer Ther. 2013 Feb;12(2):220-9. doi: 10.1158/1535-7163.MCT-12-0620.


Dedifferentiation in gastrointestinal stromal tumor to an anaplastic KIT-negative phenotype: a diagnostic pitfall: morphologic and molecular characterization of 8 cases occurring either de novo or after imatinib therapy.

Antonescu CR, Romeo S, Zhang L, Nafa K, Hornick JL, Nielsen GP, Mino-Kenudson M, Huang HY, Mosquera JM, Dei Tos PA, Fletcher CD.

Am J Surg Pathol. 2013 Mar;37(3):385-92. doi: 10.1097/PAS.0b013e31826c1761.


Prevalence, clinicopathologic associations, and molecular spectrum of ERBB2 (HER2) tyrosine kinase mutations in lung adenocarcinomas.

Arcila ME, Chaft JE, Nafa K, Roy-Chowdhuri S, Lau C, Zaidinski M, Paik PK, Zakowski MF, Kris MG, Ladanyi M.

Clin Cancer Res. 2012 Sep 15;18(18):4910-8. doi: 10.1158/1078-0432.CCR-12-0912.


Melanocytic tumor with GNA11 p.Q209L mutation mimicking a foramen magnum meningioma.

Strom RG, Shvartsbeyn M, Rosenblum MK, Hameed MR, Nafa K, Mikolaenko I, Babu RP.

Clin Neurol Neurosurg. 2012 Oct;114(8):1197-200. doi: 10.1016/j.clineuro.2012.02.030. No abstract available.


EGFR exon 19 insertions: a new family of sensitizing EGFR mutations in lung adenocarcinoma.

He M, Capelletti M, Nafa K, Yun CH, Arcila ME, Miller VA, Ginsberg MS, Zhao B, Kris MG, Eck MJ, Jänne PA, Ladanyi M, Oxnard GR.

Clin Cancer Res. 2012 Mar 15;18(6):1790-7. doi: 10.1158/1078-0432.CCR-11-2361.


BRAF mutation analysis of fine-needle aspiration biopsies of papillary thyroid carcinoma: impact on diagnosis and prognosis.

Colanta A, Lin O, Tafe L, Ghossein R, Nafa K, Mitchell T, Ladanyi M, Arcila M.

Acta Cytol. 2011;55(6):563-9. doi: 10.1159/000333272.


Oncogene mutation profiling of pediatric solid tumors reveals significant subsets of embryonal rhabdomyosarcoma and neuroblastoma with mutated genes in growth signaling pathways.

Shukla N, Ameur N, Yilmaz I, Nafa K, Lau CY, Marchetti A, Borsu L, Barr FG, Ladanyi M.

Clin Cancer Res. 2012 Feb 1;18(3):748-57. doi: 10.1158/1078-0432.CCR-11-2056.

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