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Clinical Validation of a Cell-Free DNA Gene Panel.

Cheng J, Cao Y, MacLeay A, Lennerz JK, Baig A, Frazier RP, Lee J, Hu K, Pacula M, Meneses E, Robinson H, Batten JM, Brastianos PK, Heist RS, Bardia A, Le LP, Iafrate AJ.

J Mol Diagn. 2019 Apr 23. pii: S1525-1578(18)30562-2. doi: 10.1016/j.jmoldx.2019.02.008. [Epub ahead of print]


Clinically Integrated Molecular Diagnostics in Adenoid Cystic Carcinoma.

Thierauf J, Ramamurthy N, Jo VY, Robinson H, Frazier RP, Gonzalez J, Pacula M, Dominguez Meneses E, Nose V, Nardi V, Dias-Santagata D, Le LP, Lin DT, Faquin WC, Wirth LJ, Hess J, Iafrate AJ, Lennerz JK.

Oncologist. 2019 Mar 29. pii: theoncologist.2018-0515. doi: 10.1634/theoncologist.2018-0515. [Epub ahead of print]


VarGrouper: A Bioinformatic Tool for Local Haplotyping of Deletion-Insertion Variants from Next-Generation Sequencing Data after Variant Calling.

Schmidt RJ, Macleay A, Le LP.

J Mol Diagn. 2019 May;21(3):384-389. doi: 10.1016/j.jmoldx.2018.12.003. Epub 2019 Feb 20.


Clinicopathological and molecular features of SF3B1-mutated myeloproliferative neoplasms.

Boiocchi L, Hasserjian RP, Pozdnyakova O, Wong WJ, Lennerz JK, Le LP, Dias-Santagata D, Iafrate AJ, Hobbs GS, Nardi V.

Hum Pathol. 2019 Apr;86:1-11. doi: 10.1016/j.humpath.2018.11.022. Epub 2018 Dec 27.


Implementing the DICOM Standard for Digital Pathology.

Herrmann MD, Clunie DA, Fedorov A, Doyle SW, Pieper S, Klepeis V, Le LP, Mutter GL, Milstone DS, Schultz TJ, Kikinis R, Kotecha GK, Hwang DH, Andriole KP, Iafrate AJ, Brink JA, Boland GW, Dreyer KJ, Michalski M, Golden JA, Louis DN, Lennerz JK.

J Pathol Inform. 2018 Nov 2;9:37. doi: 10.4103/jpi.jpi_42_18. eCollection 2018.


Clinical Utility of Rapid EGFR Genotyping in Advanced Lung Cancer.

Dagogo-Jack I, Azzolli CG, Fintelmann F, Mino-Kenudson M, Farago AF, Gainor JF, Jiang G, Piotrowska Z, Heist RS, Lennes IT, Temel JS, Mooradian MJ, Lin JJ, Digumarthy SR, Batten JM, Robinson H, Nose V, Rivera M, Nardi V, Dias-Santagata D, Le LP, Sequist LV, Pitman M, Shepard JO, Shaw AT, Iafrate AJ, Lennerz JK.

JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.17.00299. Epub 2018 Jul 24.


Artificial Intelligence Approach for Variant Reporting.

Zomnir MG, Lipkin L, Pacula M, Meneses ED, MacLeay A, Duraisamy S, Nadhamuni N, Al Turki SH, Zheng Z, Rivera M, Nardi V, Dias-Santagata D, Iafrate AJ, Le LP, Lennerz JK.

JCO Clin Cancer Inform. 2018;2. doi: 10.1200/CCI.16.00079. Epub 2018 Mar 22.


A Nanopore Sequencing-Based Assay for Rapid Detection of Gene Fusions.

Jeck WR, Lee J, Robinson H, Le LP, Iafrate AJ, Nardi V.

J Mol Diagn. 2019 Jan;21(1):58-69. doi: 10.1016/j.jmoldx.2018.08.003. Epub 2018 Sep 28.


Clinicopathologic Features of Non-Small-Cell Lung Cancer Harboring an NTRK Gene Fusion.

Farago AF, Taylor MS, Doebele RC, Zhu VW, Kummar S, Spira AI, Boyle TA, Haura EB, Arcila ME, Benayed R, Aisner DL, Horick NK, Lennerz JK, Le LP, Iafrate AJ, Ou SI, Shaw AT, Mino-Kenudson M, Drilon A.

JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.18.00037. Epub 2018 Jul 23.


Impact of EML4-ALK Variant on Resistance Mechanisms and Clinical Outcomes in ALK-Positive Lung Cancer.

Lin JJ, Zhu VW, Yoda S, Yeap BY, Schrock AB, Dagogo-Jack I, Jessop NA, Jiang GY, Le LP, Gowen K, Stephens PJ, Ross JS, Ali SM, Miller VA, Johnson ML, Lovly CM, Hata AN, Gainor JF, Iafrate AJ, Shaw AT, Ou SI.

J Clin Oncol. 2018 Apr 20;36(12):1199-1206. doi: 10.1200/JCO.2017.76.2294. Epub 2018 Jan 26.


Expressed Gene Fusions as Frequent Drivers of Poor Outcomes in Hormone Receptor-Positive Breast Cancer.

Matissek KJ, Onozato ML, Sun S, Zheng Z, Schultz A, Lee J, Patel K, Jerevall PL, Saladi SV, Macleay A, Tavallai M, Badovinac-Crnjevic T, Barrios C, Beşe N, Chan A, Chavarri-Guerra Y, Debiasi M, Demirdögen E, Egeli Ü, Gökgöz S, Gomez H, Liedke P, Tasdelen I, Tolunay S, Werutsky G, St Louis J, Horick N, Finkelstein DM, Le LP, Bardia A, Goss PE, Sgroi DC, Iafrate AJ, Ellisen LW.

Cancer Discov. 2018 Mar;8(3):336-353. doi: 10.1158/2159-8290.CD-17-0535. Epub 2017 Dec 14.


Feasibility of Ultra-High-Throughput Functional Screening of Melanoma Biopsies for Discovery of Novel Cancer Drug Combinations.

Friedman AA, Xia Y, Trippa L, Le LP, Igras V, Frederick DT, Wargo JA, Tanabe KK, Lawrence DP, Neuberg DS, Flaherty KT, Fisher DE.

Clin Cancer Res. 2017 Aug 15;23(16):4680-4692. doi: 10.1158/1078-0432.CCR-16-3029. Epub 2017 Apr 26.


KIF13B-NRG1 Gene Fusion and KRAS Amplification in a Case of Natural Progression of Lung Cancer.

Xia D, Le LP, Iafrate AJ, Lennerz J.

Int J Surg Pathol. 2017 May;25(3):238-240. doi: 10.1177/1066896917693092.


Clinical and radiographic response following targeting of BCAN-NTRK1 fusion in glioneuronal tumor.

Alvarez-Breckenridge C, Miller JJ, Nayyar N, Gill CM, Kaneb A, D'Andrea M, Le LP, Lee J, Cheng J, Zheng Z, Butler WE, Multani P, Chow Maneval E, Ha Paek S, Toyota BD, Dias-Santagata D, Santagata S, Romero J, Shaw AT, Farago AF, Yip S, Cahill DP, Batchelor TT, Iafrate AJ, Brastianos PK.

NPJ Precis Oncol. 2017 Mar 20;1(1):5. doi: 10.1038/s41698-017-0009-y. eCollection 2017.


Diffuse large B-cell lymphoma with concurrent high MYC and BCL2 expression shows evidence of active B-cell receptor signaling by quantitative immunofluorescence.

Bogusz AM, Kovach AE, Le LP, Feng D, Baxter RH, Sohani AR.

PLoS One. 2017 Feb 17;12(2):e0172364. doi: 10.1371/journal.pone.0172364. eCollection 2017.


Analytical Validation of the Next-Generation Sequencing Assay for a Nationwide Signal-Finding Clinical Trial: Molecular Analysis for Therapy Choice Clinical Trial.

Lih CJ, Harrington RD, Sims DJ, Harper KN, Bouk CH, Datta V, Yau J, Singh RR, Routbort MJ, Luthra R, Patel KP, Mantha GS, Krishnamurthy S, Ronski K, Walther Z, Finberg KE, Canosa S, Robinson H, Raymond A, Le LP, McShane LM, Polley EC, Conley BA, Doroshow JH, Iafrate AJ, Sklar JL, Hamilton SR, Williams PM.

J Mol Diagn. 2017 Mar;19(2):313-327. doi: 10.1016/j.jmoldx.2016.10.007. Epub 2017 Feb 7.


Next-generation sequencing adds value to the preoperative diagnosis of pancreatic cysts.

Rosenbaum MW, Jones M, Dudley JC, Le LP, Iafrate AJ, Pitman MB.

Cancer Cytopathol. 2017 Jan;125(1):41-47. doi: 10.1002/cncy.21775. Epub 2016 Sep 20.


Health Care Infrastructure for Financially Sustainable Clinical Genomics.

Lennerz JK, McLaughlin HM, Baron JM, Rasmussen D, Sumbada Shin M, Berners-Lee N, Miller Batten J, Swoboda KJ, Gala MK, Winter HS, Schmahmann JD, Sweetser DA, Boswell M, Pacula M, Stenzinger A, Le LP, Hynes W, Rehm HL, Klibanski A, Black-Schaffer SW, Golden JA, Louis DN, Weiss ST, Iafrate AJ.

J Mol Diagn. 2016 Sep;18(5):697-706. doi: 10.1016/j.jmoldx.2016.04.003. Epub 2016 Jul 25.


Molecular Mechanisms of Resistance to First- and Second-Generation ALK Inhibitors in ALK-Rearranged Lung Cancer.

Gainor JF, Dardaei L, Yoda S, Friboulet L, Leshchiner I, Katayama R, Dagogo-Jack I, Gadgeel S, Schultz K, Singh M, Chin E, Parks M, Lee D, DiCecca RH, Lockerman E, Huynh T, Logan J, Ritterhouse LL, Le LP, Muniappan A, Digumarthy S, Channick C, Keyes C, Getz G, Dias-Santagata D, Heist RS, Lennerz J, Sequist LV, Benes CH, Iafrate AJ, Mino-Kenudson M, Engelman JA, Shaw AT.

Cancer Discov. 2016 Oct;6(10):1118-1133. Epub 2016 Jul 18.


Acquired Resistance to Crizotinib in NSCLC with MET Exon 14 Skipping.

Heist RS, Sequist LV, Borger D, Gainor JF, Arellano RS, Le LP, Dias-Santagata D, Clark JW, Engelman JA, Shaw AT, Iafrate AJ.

J Thorac Oncol. 2016 Aug;11(8):1242-1245. doi: 10.1016/j.jtho.2016.06.013. Epub 2016 Jun 22.


Colorectal cancer in Crohn's colitis is comparable to sporadic colorectal cancer.

Lennerz JK, van der Sloot KWJ, Le LP, Batten JM, Han JY, Fan KC, Siegel CA, Srivastava A, Park DY, Chen JH, Sands BE, Korzenik JR, Odze RD, Dias-Santagata D, Borger DR, Khalili H, Iafrate AJ, Lauwers GY.

Int J Colorectal Dis. 2016 May;31(5):973-982. doi: 10.1007/s00384-016-2574-x. Epub 2016 Mar 30.


Next-Generation Sequencing and Fluorescence in Situ Hybridization Have Comparable Performance Characteristics in the Analysis of Pancreaticobiliary Brushings for Malignancy.

Dudley JC, Zheng Z, McDonald T, Le LP, Dias-Santagata D, Borger D, Batten J, Vernovsky K, Sweeney B, Arpin RN, Brugge WR, Forcione DG, Pitman MB, Iafrate AJ.

J Mol Diagn. 2016 Jan;18(1):124-30. doi: 10.1016/j.jmoldx.2015.08.002. Epub 2015 Nov 18.


Durable Clinical Response to Entrectinib in NTRK1-Rearranged Non-Small Cell Lung Cancer.

Farago AF, Le LP, Zheng Z, Muzikansky A, Drilon A, Patel M, Bauer TM, Liu SV, Ou SH, Jackman D, Costa DB, Multani PS, Li GG, Hornby Z, Chow-Maneval E, Luo D, Lim JE, Iafrate AJ, Shaw AT.

J Thorac Oncol. 2015 Dec;10(12):1670-4. doi: 10.1097/01.JTO.0000473485.38553.f0.


Identification of insertions in PTEN and TP53 in anaplastic thyroid carcinoma with angiogenic brain metastasis.

Sadow PM, Dias-Santagata D, Zheng Z, Lin DT, Le LP, Nucera C.

Endocr Relat Cancer. 2015 Dec;22(6):L23-8. doi: 10.1530/ERC-15-0198. No abstract available.


Detection of Dual IDH1 and IDH2 Mutations by Targeted Next-Generation Sequencing in Acute Myeloid Leukemia and Myelodysplastic Syndromes.

Platt MY, Fathi AT, Borger DR, Brunner AM, Hasserjian RP, Balaj L, Lum A, Yip S, Dias-Santagata D, Zheng Z, Le LP, Graubert TA, Iafrate AJ, Nardi V.

J Mol Diagn. 2015 Nov;17(6):661-8. doi: 10.1016/j.jmoldx.2015.06.004. Epub 2015 Aug 30.


Design of a Genomics Curriculum: Competencies for Practicing Pathologists.

Laudadio J, McNeal JL, Boyd SD, Le LP, Lockwood C, McCloskey CB, Sharma G, Voelkerding KV, Haspel RL.

Arch Pathol Lab Med. 2015 Jul;139(7):894-900. doi: 10.5858/arpa.2014-0253-CP.


Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer.

O'Brien TD, Jia P, Xia J, Saxena U, Jin H, Vuong H, Kim P, Wang Q, Aryee MJ, Mino-Kenudson M, Engelman JA, Le LP, Iafrate AJ, Heist RS, Pao W, Zhao Z.

Methods. 2015 Jul 15;83:118-27. doi: 10.1016/j.ymeth.2015.04.016. Epub 2015 Apr 23.


GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases.

Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK.

Nat Biotechnol. 2015 Feb;33(2):187-197. doi: 10.1038/nbt.3117. Epub 2014 Dec 16.


Molecular classification of MYC-driven B-cell lymphomas by targeted gene expression profiling of fixed biopsy specimens.

Carey CD, Gusenleitner D, Chapuy B, Kovach AE, Kluk MJ, Sun HH, Crossland RE, Bacon CM, Rand V, Dal Cin P, Le LP, Neuberg D, Sohani AR, Shipp MA, Monti S, Rodig SJ.

J Mol Diagn. 2015 Jan;17(1):19-30. doi: 10.1016/j.jmoldx.2014.08.006. Epub 2014 Nov 7.


Anchored multiplex PCR for targeted next-generation sequencing.

Zheng Z, Liebers M, Zhelyazkova B, Cao Y, Panditi D, Lynch KD, Chen J, Robinson HE, Shim HS, Chmielecki J, Pao W, Engelman JA, Iafrate AJ, Le LP.

Nat Med. 2014 Dec;20(12):1479-84. doi: 10.1038/nm.3729. Epub 2014 Nov 10.


Crizotinib in ROS1-rearranged non-small-cell lung cancer.

Shaw AT, Ou SH, Bang YJ, Camidge DR, Solomon BJ, Salgia R, Riely GJ, Varella-Garcia M, Shapiro GI, Costa DB, Doebele RC, Le LP, Zheng Z, Tan W, Stephenson P, Shreeve SM, Tye LM, Christensen JG, Wilner KD, Clark JW, Iafrate AJ.

N Engl J Med. 2014 Nov 20;371(21):1963-71. doi: 10.1056/NEJMoa1406766. Epub 2014 Sep 27.


Computational pathology: an emerging definition.

Louis DN, Gerber GK, Baron JM, Bry L, Dighe AS, Getz G, Higgins JM, Kuo FC, Lane WJ, Michaelson JS, Le LP, Mermel CH, Gilbertson JR, Golden JA.

Arch Pathol Lab Med. 2014 Sep;138(9):1133-8. doi: 10.5858/arpa.2014-0034-ED. No abstract available.


Case records of the Massachusetts General Hospital. Case 24-2014. A 27-year-old man with severe osteoporosis and multiple bone fractures.

Mannstadt M, Lin AE, Le LP.

N Engl J Med. 2014 Jul 31;371(5):465-72. doi: 10.1056/NEJMcpc1404139. No abstract available.


Genotyping cancer-associated genes in chordoma identifies mutations in oncogenes and areas of chromosomal loss involving CDKN2A, PTEN, and SMARCB1.

Choy E, MacConaill LE, Cote GM, Le LP, Shen JK, Nielsen GP, Iafrate AJ, Garraway LA, Hornicek FJ, Duan Z.

PLoS One. 2014 Jul 1;9(7):e101283. doi: 10.1371/journal.pone.0101283. eCollection 2014.


Standardized decision support in next generation sequencing reports of somatic cancer variants.

Dienstmann R, Dong F, Borger D, Dias-Santagata D, Ellisen LW, Le LP, Iafrate AJ.

Mol Oncol. 2014 Jul;8(5):859-73. doi: 10.1016/j.molonc.2014.03.021. Epub 2014 Apr 4. Review.


The 2013 symposium on pathology data integration and clinical decision support and the current state of field.

Baron JM, Dighe AS, Arnaout R, Balis UJ, Black-Schaffer WS, Carter AB, Henricks WH, Higgins JM, Jackson BR, Kim J, Klepeis VE, Le LP, Louis DN, Mandelker D, Mermel CH, Michaelson JS, Nagarajan R, Platt ME, Quinn AM, Rao L, Shirts BH, Gilbertson JR.

J Pathol Inform. 2014 Jan 31;5(1):2. doi: 10.4103/2153-3539.126145. eCollection 2014.


Germline mutations in oncogene-induced senescence pathways are associated with multiple sessile serrated adenomas.

Gala MK, Mizukami Y, Le LP, Moriichi K, Austin T, Yamamoto M, Lauwers GY, Bardeesy N, Chung DC.

Gastroenterology. 2014 Feb;146(2):520-9.


Inactivation of the tumor suppressor WTX in a subset of pediatric tumors.

Akhavanfard S, Vargas SO, Han M, Nitta M, Chang CB, Le LP, Fazlollahi L, Nguyen Q, Ma Y, Cosper A, Dias-Santagata D, Han JY, Bergethon K, Borger DR, Ellisen LW, Pomeroy SL, Haber DA, Iafrate AJ, Rivera MN.

Genes Chromosomes Cancer. 2014 Jan;53(1):67-77. doi: 10.1002/gcc.22118. Epub 2013 Nov 5.


BRAF V600E status adds incremental value to current risk classification systems in predicting papillary thyroid carcinoma recurrence.

Prescott JD, Sadow PM, Hodin RA, Le LP, Gaz RD, Randolph GW, Stephen AE, Parangi S, Daniels GH, Lubitz CC.

Surgery. 2012 Dec;152(6):984-90. doi: 10.1016/j.surg.2012.08.039.


Apocrine-eccrine carcinomas: molecular and immunohistochemical analyses.

Le LP, Dias-Santagata D, Pawlak AC, Cosper AK, Nguyen AT, Selim MA, Deng A, Horick NK, Iafrate AJ, Mihm MC Jr, Hoang MP.

PLoS One. 2012;7(10):e47290. doi: 10.1371/journal.pone.0047290. Epub 2012 Oct 9.


Fibrosis-associated single-nucleotide polymorphisms in TGFB1 and CAV1 are not associated with the development of nephrogenic systemic fibrosis.

Le LP, Garibyan L, Lara D, Finberg KE, Iafrate AJ, Duncan LM, Kay J, Nazarian RM.

Am J Dermatopathol. 2013 May;35(3):351-6. doi: 10.1097/DAD.0b013e31826c5508.


Microcystic adnexal carcinoma versus desmoplastic trichoepithelioma: a comparative study.

Tse JY, Nguyen AT, Le LP, Hoang MP.

Am J Dermatopathol. 2013 Feb;35(1):50-5. doi: 10.1097/DAD.0b013e31825988df.


Adenoviral protein V promotes a process of viral assembly through nucleophosmin 1.

Ugai H, Dobbins GC, Wang M, Le LP, Matthews DA, Curiel DT.

Virology. 2012 Oct 25;432(2):283-95. doi: 10.1016/j.virol.2012.05.028. Epub 2012 Jun 18.


Clinical fellowship training in pathology informatics: A program description.

Gilbertson JR, McClintock DS, Lee RE, Onozato M, Kuo FC, Beckwith BA, Yagi Y, Dighe AS, Gudewicz TM, Le LP, Wilbur DC, Kim JY, Brodsky VB, Black-Schaffer S.

J Pathol Inform. 2012;3:11. doi: 10.4103/2153-3539.93893. Epub 2012 Mar 16.


EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas.

Ryan RJ, Nitta M, Borger D, Zukerberg LR, Ferry JA, Harris NL, Iafrate AJ, Bernstein BE, Sohani AR, Le LP.

PLoS One. 2011;6(12):e28585. doi: 10.1371/journal.pone.0028585. Epub 2011 Dec 14.


Mosaic amplification of multiple receptor tyrosine kinase genes in glioblastoma.

Snuderl M, Fazlollahi L, Le LP, Nitta M, Zhelyazkova BH, Davidson CJ, Akhavanfard S, Cahill DP, Aldape KD, Betensky RA, Louis DN, Iafrate AJ.

Cancer Cell. 2011 Dec 13;20(6):810-7. doi: 10.1016/j.ccr.2011.11.005. Epub 2011 Dec 1.


Malignant neurocristic hamartoma: a tumor distinct from conventional melanoma and malignant blue nevus.

Linskey KR, Dias-Santagata D, Nazarian RM, Le LP, Lam Q, Bellucci KS, Robinson-Bostom L, Mihm MC Jr, Hoang MP.

Am J Surg Pathol. 2011 Oct;35(10):1570-7. doi: 10.1097/PAS.0b013e31822389b7.


Recurrent chromosomal copy number alterations in sporadic chordomas.

Le LP, Nielsen GP, Rosenberg AE, Thomas D, Batten JM, Deshpande V, Schwab J, Duan Z, Xavier RJ, Hornicek FJ, Iafrate AJ.

PLoS One. 2011;6(5):e18846. doi: 10.1371/journal.pone.0018846. Epub 2011 May 13.


Proliferative nodules arising within congenital melanocytic nevi: a histologic, immunohistochemical, and molecular analyses of 43 cases.

Phadke PA, Rakheja D, Le LP, Selim MA, Kapur P, Davis A, Mihm MC Jr, Hoang MP.

Am J Surg Pathol. 2011 May;35(5):656-69. doi: 10.1097/PAS.0b013e31821375ea.


Clinicopathologic and molecular profiles of microsatellite unstable Barrett Esophagus-associated adenocarcinoma.

Farris AB 3rd, Demicco EG, Le LP, Finberg KE, Miller J, Mandal R, Fukuoka J, Cohen C, Gaissert HA, Zukerberg LR, Lauwers GY, Iafrate AJ, Mino-Kenudson M.

Am J Surg Pathol. 2011 May;35(5):647-55. doi: 10.1097/PAS.0b013e31820f18a2.


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