Somak Roy

Somak Roy

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Somak Roy

Publications by authors named "Somak Roy"

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Interactive Browser-Based Genomics Data Visualization Tools for Translational and Clinical Laboratory Applications.

J Mol Diagn 2019 11 2;21(6):985-993. Epub 2019 Aug 2.

Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania. Electronic address:

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http://dx.doi.org/10.1016/j.jmoldx.2019.06.005DOI Listing
November 2019

Clinical Utility of GlioSeq Next-Generation Sequencing Test in Pediatric and Young Adult Patients With Brain Tumors.

J Neuropathol Exp Neurol 2019 Jun 10. Epub 2019 Jun 10.

Division of Molecular & Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.

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http://dx.doi.org/10.1093/jnen/nlz055DOI Listing
June 2019

Clinical Implementation and Validation of Automated Human Genome Variation Society (HGVS) Nomenclature System for Next-Generation Sequencing-Based Assays for Cancer.

J Mol Diagn 2018 09 21;20(5):628-634. Epub 2018 Jun 21.

Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; Informatics Subdivision Leadership, Association for Molecular Pathology, Bethesda, Maryland. Electronic address:

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http://dx.doi.org/10.1016/j.jmoldx.2018.05.006DOI Listing
September 2018

KRAS mutation is predictive of outcome in patients with pulmonary sarcomatoid carcinoma.

Histopathology 2018 Aug 7;73(2):207-214. Epub 2018 May 7.

Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1111/his.13505DOI Listing
August 2018

Next-Generation Sequencing Approach to Non-Small Cell Lung Carcinoma Yields More Actionable Alterations.

Arch Pathol Lab Med 2018 Mar 8;142(3):353-357. Epub 2017 Dec 8.

From the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee (Dr Mehrad); and the Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Drs Roy, Trejo Bittar, and Dacic).

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http://dx.doi.org/10.5858/arpa.2017-0046-OADOI Listing
March 2018

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists.

J Mol Diagn 2018 01 21;20(1):4-27. Epub 2017 Nov 21.

Next Generation Sequencing Bioinformatics Pipeline Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Department of Pathology and Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia.

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https://linkinghub.elsevier.com/retrieve/pii/S15251578173037
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http://dx.doi.org/10.1016/j.jmoldx.2017.11.003DOI Listing
January 2018

Authors' Reply.

J Mol Diagn 2018 01;20(1):125-126

Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.

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http://dx.doi.org/10.1016/j.jmoldx.2017.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5818630PMC
January 2018

Next-generation sequencing-based molecular characterization of primary urinary bladder adenocarcinoma.

Mod Pathol 2017 08 26;30(8):1133-1143. Epub 2017 May 26.

Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1038/modpathol.2017.33DOI Listing
August 2017

Big data from small samples: Informatics of next-generation sequencing in cytopathology.

Cancer Cytopathol 2017 Apr 5;125(4):236-244. Epub 2016 Dec 5.

Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.

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http://dx.doi.org/10.1002/cncy.21805DOI Listing
April 2017

Cytohistologic correlation of recurrent urothelial carcinoma detected in urinary diversion specimens.

Cancer Cytopathol 2017 Feb 14;125(2):120-127. Epub 2016 Oct 14.

Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.

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http://dx.doi.org/10.1002/cncy.21786DOI Listing
February 2017

Next-Generation Sequencing Informatics: Challenges and Strategies for Implementation in a Clinical Environment.

Arch Pathol Lab Med 2016 Sep 22;140(9):958-75. Epub 2016 Feb 22.

From the Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Drs Roy, LaFramboise, Nikiforov, Nikiforova, and Pantanowitz); the Department of Pathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); the Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri (Drs Pfeifer and Nagarajan); PierianDx, St Louis, Missouri (Dr Nagarajan); and the Department of Pathology and Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia (Dr Carter).

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http://dx.doi.org/10.5858/arpa.2015-0507-RADOI Listing
September 2016

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

Expert Rev Mol Diagn 2016 09 29;16(9):941-7. Epub 2016 Jul 29.

a Department of Pathology , University of Pittsburgh Medical Center , Pittsburgh , PA , USA.

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http://dx.doi.org/10.1080/14737159.2016.1206472DOI Listing
September 2016

Targeted next-generation sequencing panel (GlioSeq) provides comprehensive genetic profiling of central nervous system tumors.

Neuro Oncol 2016 Mar 17;18(3):379-87. Epub 2015 Dec 17.

Department of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).

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http://dx.doi.org/10.1093/neuonc/nov289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767245PMC
March 2016

Molecular Pathology Informatics.

Authors:
Somak Roy

Clin Lab Med 2016 Mar;36(1):57-66

Department of Pathology, Molecular and Genomic Pathology, University of Pittsburgh Medical Center, 3477 Euler way, Pittsburgh, PA 15213, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cll.2015.09.007DOI Listing
March 2016

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Authors:
W Marston Linehan Paul T Spellman Christopher J Ricketts Chad J Creighton Suzanne S Fei Caleb Davis David A Wheeler Bradley A Murray Laura Schmidt Cathy D Vocke Myron Peto Abu Amar M Al Mamun Eve Shinbrot Anurag Sethi Samira Brooks W Kimryn Rathmell Angela N Brooks Katherine A Hoadley A Gordon Robertson Denise Brooks Reanne Bowlby Sara Sadeghi Hui Shen Daniel J Weisenberger Moiz Bootwalla Stephen B Baylin Peter W Laird Andrew D Cherniack Gordon Saksena Scott Haake Jun Li Han Liang Yiling Lu Gordon B Mills Rehan Akbani Mark D M Leiserson Benjamin J Raphael Pavana Anur Donald Bottaro Laurence Albiges Nandita Barnabas Toni K Choueiri Bogdan Czerniak Andrew K Godwin A Ari Hakimi Thai H Ho James Hsieh Michael Ittmann William Y Kim Bhavani Krishnan Maria J Merino Kenna R Mills Shaw Victor E Reuter Ed Reznik Carl S Shelley Brian Shuch Sabina Signoretti Ramaprasad Srinivasan Pheroze Tamboli George Thomas Satish Tickoo Kenneth Burnett Daniel Crain Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph D Paulauskis Robert J Penny Candace Shelton W Troy Shelton Mark Sherman Eric Thompson Peggy Yena Melissa T Avedon Jay Bowen Julie M Gastier-Foster Mark Gerken Kristen M Leraas Tara M Lichtenberg Nilsa C Ramirez Tracie Santos Lisa Wise Erik Zmuda John A Demchok Ina Felau Carolyn M Hutter Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C Zenklusen Jiashan Zhang Brenda Ayala Julien Baboud Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Adrian Ally Miruna Balasundaram Saianand Balu Rameen Beroukhim Tom Bodenheimer Christian Buhay Yaron S N Butterfield Rebecca Carlsen Scott L Carter Hsu Chao Eric Chuah Amanda Clarke Kyle R Covington Mahmoud Dahdouli Ninad Dewal Noreen Dhalla Harsha V Doddapaneni Jennifer A Drummond Stacey B Gabriel Richard A Gibbs Ranabir Guin Walker Hale Alicia Hawes D Neil Hayes Robert A Holt Alan P Hoyle Stuart R Jefferys Steven J M Jones Corbin D Jones Divya Kalra Christie Kovar Lora Lewis Jie Li Yussanne Ma Marco A Marra Michael Mayo Shaowu Meng Matthew Meyerson Piotr A Mieczkowski Richard A Moore Donna Morton Lisle E Mose Andrew J Mungall Donna Muzny Joel S Parker Charles M Perou Jeffrey Roach Jacqueline E Schein Steven E Schumacher Yan Shi Janae V Simons Payal Sipahimalani Tara Skelly Matthew G Soloway Carrie Sougnez Angela Tam Donghui Tan Nina Thiessen Umadevi Veluvolu Min Wang Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Jane Zhou Jason Bedford Fengju Chen Yao Fu Mark Gerstein David Haussler Katayoon Kasaian Phillip Lai Shiyun Ling Amie Radenbaugh David Van Den Berg John N Weinstein Jingchun Zhu Monique Albert Iakovina Alexopoulou Jeremiah J Andersen J Todd Auman John Bartlett Sheldon Bastacky Julie Bergsten Michael L Blute Lori Boice Roni J Bollag Jeff Boyd Erik Castle Ying-Bei Chen John C Cheville Erin Curley Benjamin Davies April DeVolk Rajiv Dhir Laura Dike John Eckman Jay Engel Jodi Harr Ronald Hrebinko Mei Huang Lori Huelsenbeck-Dill Mary Iacocca Bruce Jacobs Michael Lobis Jodi K Maranchie Scott McMeekin Jerome Myers Joel Nelson Jeremy Parfitt Anil Parwani Nicholas Petrelli Brenda Rabeno Somak Roy Andrew L Salner Joel Slaton Melissa Stanton R Houston Thompson Leigh Thorne Kelinda Tucker Paul M Weinberger Cynthia Winemiller Leigh Anne Zach Rosemary Zuna

Molecular characterization of apocrine salivary duct carcinoma.

Am J Surg Pathol 2015 Jun;39(6):744-52

Departments of *Pathology §Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA †Department of Pathology, Southern California Permanente Medical Group, Woodland Hills, CA ‡Department of Pathology, University Health Network, Toronto, ON, Canada.

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http://dx.doi.org/10.1097/PAS.0000000000000410DOI Listing
June 2015

Molecular Pathology Informatics.

Authors:
Somak Roy

Surg Pathol Clin 2015 Jun 7;8(2):187-94. Epub 2015 Apr 7.

Department of Pathology, Molecular and Genomic Pathology, University of Pittsburgh Medical Center, 3477 Euler way, Pittsburgh, PA 15213, USA. Electronic address:

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http://dx.doi.org/10.1016/j.path.2015.02.013DOI Listing
June 2015

Smartphone adapters for digital photomicrography.

J Pathol Inform 2014 30;5(1):24. Epub 2014 Jul 30.

Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.4103/2153-3539.137728DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141421PMC
September 2014

SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory.

J Mol Diagn 2014 Jan 9;16(1):11-22. Epub 2013 Nov 9.

Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania. Electronic address:

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http://dx.doi.org/10.1016/j.jmoldx.2013.08.005DOI Listing
January 2014

Amylase α-1A (AMY1A): a novel immunohistochemical marker to differentiate chromophobe renal cell carcinoma from benign oncocytoma.

Am J Surg Pathol 2013 Dec;37(12):1824-30

*Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA †Department of Pathology, East Carolina University, Greenville, NC.

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http://dx.doi.org/10.1097/PAS.0000000000000108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557609PMC
December 2013

Targeted next-generation sequencing panel (ThyroSeq) for detection of mutations in thyroid cancer.

J Clin Endocrinol Metab 2013 Nov 26;98(11):E1852-60. Epub 2013 Aug 26.

Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, Pennsylvania 15261.

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http://dx.doi.org/10.1210/jc.2013-2292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816258PMC
November 2013

Spindle cell carcinoma of the larynx with rhabdomyoblastic heterologous element: a rare form of divergent differentiation.

Head Neck Pathol 2013 Sep 9;7(3):263-7. Epub 2012 Oct 9.

Department of Pathology, University of Pittsburgh Medical Center, 3550 Terrace street, A711, Scaife hall, Pittsburgh, PA 15261, USA.

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http://dx.doi.org/10.1007/s12105-012-0402-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738762PMC
September 2013

Frozen section diagnosis: is there discordance between what pathologists say and what surgeons hear?

Am J Clin Pathol 2013 Sep;140(3):363-9

Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1309/AJCPHUE5ENZDU4DJDOI Listing
September 2013

Primary bladder adenocarcinoma versus metastatic colorectal adenocarcinoma: a persisting diagnostic challenge.

Diagn Pathol 2012 Nov 2;7:151. Epub 2012 Nov 2.

Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA.

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http://dx.doi.org/10.1186/1746-1596-7-151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502416PMC
November 2012

A novel case of concurrent renal tumors: chromophobe renal cell carcinoma and carcinoid tumor of the kidney with brief review of renal neuroendocrine tumors.

Int J Surg Pathol 2012 Oct 27;20(5):531-5. Epub 2012 Mar 27.

Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15261, USA.

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http://dx.doi.org/10.1177/1066896912438588DOI Listing
October 2012

Adenocarcinoma of the urinary bladder.

Arch Pathol Lab Med 2011 Dec;135(12):1601-5

Department of Pathology, University of Pittsburgh Medical Center, Pennsylvania 15261, USA.

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http://dx.doi.org/10.5858/arpa.2009-0713-RSDOI Listing
December 2011

University of Pittsburgh Medical Center Remains Tracker: A novel application for tracking decedents and improving the autopsy workflow.

J Pathol Inform 2011 14;2:30. Epub 2011 Jun 14.

Department of Pathology, University of Pittsburgh Medical Center, A711 Scaife Hall 3550 Terrace Street, Pittsburgh, PA 15261, USA.

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http://dx.doi.org/10.4103/2153-3539.82055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3132995PMC
November 2011

Prostatic adenocarcinoma metastatic to pleomorphic liposarcoma, a "collision phenomenon": report of a case with review of pelvic collision tumors.

Patholog Res Int 2011 22;2011:173541. Epub 2011 Aug 22.

Department of Pathology, University of Pittsburgh Medical Center, A615, Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA.

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https://www.hindawi.com/archive/2011/173541/
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http://dx.doi.org/10.4061/2011/173541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166762PMC
November 2011

Idiopathic granulomatous orchitis.

Pathol Res Pract 2011 May 1;207(5):275-8. Epub 2011 Apr 1.

Department of Pathology, University of Pittsburgh Medical Center, United States.

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http://dx.doi.org/10.1016/j.prp.2011.02.005DOI Listing
May 2011

Highly cellular leiomyoma mimics a malignant small round-cell tumor: a diagnostic dilemma on frozen sections.

Taiwan J Obstet Gynecol 2010 Jun;49(2):203-5

Department of Pathology, Maulana Azad Medical College, New Delhi, India.

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http://dx.doi.org/10.1016/S1028-4559(10)60043-5DOI Listing
June 2010

Acinic cell carcinoma with extensive neuroendocrine differentiation: a diagnostic challenge.

Head Neck Pathol 2009 Jun 26;3(2):163-8. Epub 2009 Mar 26.

Department of Pathology, Maulana Azad Medical College, New Delhi, India.

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http://dx.doi.org/10.1007/s12105-009-0114-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715458PMC
June 2009

An acute myeloid leukemia M6b blast crisis with giant proerythroblasts in chronic myeloid leukemia.

J Pediatr Hematol Oncol 2009 Mar;31(3):220-1

Department of Pathology, Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India.

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http://dx.doi.org/10.1097/MPH.0b013e3181983c88DOI Listing
March 2009

Unusual presentation of metastatic amelanotic melanoma of unknown primary origin as a solitary breast lump.

Melanoma Res 2008 Dec;18(6):447-50

Department of Pathology, Maulana Azad Medical College, New Delhi, India.

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http://dx.doi.org/10.1097/CMR.0b013e328317f04bDOI Listing
December 2008

Aggressive angiomyxoma of the vulva presenting as a pedunculated swelling.

Indian J Pathol Microbiol 2008 Apr-Jun;51(2):259-60

Department of Pathology, Maulana Azad Medical College, New Delhi, India.

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http://dx.doi.org/10.4103/0377-4929.41677DOI Listing
September 2008

Primary carcinoid tumor of the ovary: a case report.

Arch Gynecol Obstet 2008 Jan 5;277(1):79-82. Epub 2007 Jul 5.

Department of Pathology, Maulana Azad Medical College, New Delhi, India.

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http://dx.doi.org/10.1007/s00404-007-0408-3DOI Listing
January 2008

Clear cell malignant myoepithelioma--breast presenting as a fungating mass.

Breast J 2007 Nov-Dec;13(6):618-20

Department of Pathology, Maulana Azad Medical College, New Delhi-110002, India.

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http://dx.doi.org/10.1111/j.1524-4741.2007.00493.xDOI Listing
December 2007

Fibroma with minor sex cord elements--an incidental finding in a normal sized ovary. A case report with literature review.

Diagn Pathol 2007 Dec 4;2:46. Epub 2007 Dec 4.

Department Of Pathology, Maulana Azad Medical College, New Delhi, India.

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http://dx.doi.org/10.1186/1746-1596-2-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2217290PMC
December 2007

Malignant peripheral nerve sheath tumor of the breast: case report.

World J Surg Oncol 2007 Dec 21;5:142. Epub 2007 Dec 21.

Department of Pathology, Maulana Azad Medical College and associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi 110002, India.

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http://dx.doi.org/10.1186/1477-7819-5-142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246134PMC
December 2007