Publications by authors named "Andrea Sboner"

100Publications

Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology.

Transl Oncol 2020 Nov 12;14(1):100944. Epub 2020 Nov 12.

Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States. Electronic address:

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http://dx.doi.org/10.1016/j.tranon.2020.100944DOI Listing
November 2020

Limitations of Detecting Genetic Variants from the RNA-Seq Data in Tissue and FNA Samples.

Thyroid 2020 Sep 18. Epub 2020 Sep 18.

Weill Cornell Medicine, 12295, Department of Pathology and Laboratory Medicine, New York, New York, United States.

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http://dx.doi.org/10.1089/thy.2020.0307DOI Listing
September 2020

Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome.

Arch Pathol Lab Med 2020 Dec;144(12):1535-1546

From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.

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http://dx.doi.org/10.5858/arpa.2019-0162-OADOI Listing
December 2020

Clinical features of neuroendocrine prostate cancer.

Eur J Cancer 2019 11 13;121:7-18. Epub 2019 Sep 13.

Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, NY, USA; Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ejca.2019.08.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6803064PMC
November 2019

CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis.

Cancer Cell 2019 04 28;35(4):603-617.e8. Epub 2019 Mar 28.

Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2019.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467783PMC
April 2019

The application of precision medicine in diagnosing familial Mediterranean fever.

Leuk Lymphoma 2019 08 30;60(8):2091-2093. Epub 2019 Jan 30.

a Department of Medicine , Weill Cornell Medicine , New York , NY , USA.

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https://www.tandfonline.com/doi/full/10.1080/10428194.2019.1
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http://dx.doi.org/10.1080/10428194.2019.1571204DOI Listing
August 2019

BRCA2-Associated Prostate Cancer in a Patient With Spinal and Bulbar Muscular Atrophy.

JCO Precis Oncol 2018 29;2. Epub 2018 Jun 29.

Weill Cornell Medicine; Weill Cornell Medicine-New York Presbyterian Hospital, New York, NY.

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http://dx.doi.org/10.1200/PO.18.00115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317373PMC
June 2018

ZFX Mediates Non-canonical Oncogenic Functions of the Androgen Receptor Splice Variant 7 in Castrate-Resistant Prostate Cancer.

Mol Cell 2018 10 27;72(2):341-354.e6. Epub 2018 Sep 27.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.08.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214474PMC
October 2018

Loss of an Androgen-Inactivating and Isoform-Specific HSD17B4 Splice Form Enables Emergence of Castration-Resistant Prostate Cancer.

Cell Rep 2018 01;22(3):809-819

Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.12.081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798464PMC
January 2018

Aberrant Activation of a Gastrointestinal Transcriptional Circuit in Prostate Cancer Mediates Castration Resistance.

Cancer Cell 2017 Dec 16;32(6):792-806.e7. Epub 2017 Nov 16.

Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728174PMC
December 2017

Clonal evolution of chemotherapy-resistant urothelial carcinoma.

Nat Genet 2016 12 17;48(12):1490-1499. Epub 2016 Oct 17.

Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.3692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5549141PMC
December 2016

N-Myc Induces an EZH2-Mediated Transcriptional Program Driving Neuroendocrine Prostate Cancer.

Cancer Cell 2016 10;30(4):563-577

Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Englander Institute for Precision Medicine, New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.09.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5540451PMC
October 2016

A primer on precision medicine informatics.

Brief Bioinform 2016 Jan 5;17(1):145-53. Epub 2015 Jun 5.

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http://dx.doi.org/10.1093/bib/bbv032DOI Listing
January 2016

Integrative clinical genomics of advanced prostate cancer.

Cell 2015 May;161(5):1215-1228

Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484602PMC
May 2015

ASEQ: fast allele-specific studies from next-generation sequencing data.

BMC Med Genomics 2015 Mar 1;8. Epub 2015 Mar 1.

Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy.

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http://dx.doi.org/10.1186/s12920-015-0084-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4363342PMC
March 2015

MAGI3-AKT3 fusion in breast cancer amended.

Nature 2015 Apr;520(7547):E11-2

Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10065, USA.

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http://dx.doi.org/10.1038/nature14265DOI Listing
April 2015

The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer.

Nat Commun 2014 Nov 21;5:5383. Epub 2014 Nov 21.

1] Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, 413 East 69th Street, Room 1402, New York, New York 10021, USA [2] Institute for Precision Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, New York 10021, USA.

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http://dx.doi.org/10.1038/ncomms6383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4241506PMC
November 2014

PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors.

Nat Genet 2014 Nov 21;46(11):1227-32. Epub 2014 Sep 21.

1] Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA. [2] Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA. [3] Department of Medicine, Weill Cornell Medical College, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.3095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249650PMC
November 2014

Organoid cultures derived from patients with advanced prostate cancer.

Cell 2014 Sep 4;159(1):176-187. Epub 2014 Sep 4.

Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medical College and New York-Presbyterian Hospital, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.08.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237931PMC
September 2014

MTSS1 is a metastasis driver in a subset of human melanomas.

Nat Commun 2014 Mar 17;5:3465. Epub 2014 Mar 17.

1] Division of Immunology, Allergy and Infectious Diseases (DIAID), Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria [2] Center for Molecular Medicine (CeMM), Austrian Academy of Sciences, 1090 Vienna, Austria.

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http://dx.doi.org/10.1038/ncomms4465DOI Listing
March 2014

SPOP mutations in prostate cancer across demographically diverse patient cohorts.

Neoplasia 2014 Jan;16(1):14-20

Department of Pathology and Laboratory Medicine, Institute of Precision Medicine, Weill Medical College of Cornell University, New York, NY ; Department of Urology, Weill Medical College of Cornell University, New York, NY ; Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3924544PMC
http://dx.doi.org/10.1593/neo.131704DOI Listing
January 2014

Identification of molecular tumor markers in renal cell carcinomas with TFE3 protein expression by RNA sequencing.

Neoplasia 2013 Nov;15(11):1231-40

Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland ; Life Science Zurich PhD Program on Molecular and Translational Biomedicine, Zurich, Switzerland ; Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3859447PMC
http://dx.doi.org/10.1593/neo.131544DOI Listing
November 2013

Novel MIR143-NOTCH fusions in benign and malignant glomus tumors.

Genes Chromosomes Cancer 2013 Nov 2;52(11):1075-87. Epub 2013 Sep 2.

Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, NY.

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http://dx.doi.org/10.1002/gcc.22102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889711PMC
November 2013

Re: Stoehr et al. Lack of evidence for frequent MED12 p.L1224F mutation in prostate tumours from Caucasian patients. J Pathol 2013; 230: 453-456.

J Pathol 2013 Oct;231(2):271

Department of Urology, Weill Cornell Medical College, New York, NY, 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.

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http://dx.doi.org/10.1002/path.4216DOI Listing
October 2013

Identifying an ERG-positive subclass with clinical progression using expression profiling.

Eur Urol 2013 Dec 26;64(6):951-2. Epub 2013 Mar 26.

Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Institute for Precision Medicine of Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY, USA.

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http://dx.doi.org/10.1016/j.eururo.2013.03.036DOI Listing
December 2013

Epigenomic alterations in localized and advanced prostate cancer.

Neoplasia 2013 Apr;15(4):373-83

Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612910PMC
http://dx.doi.org/10.1593/neo.122146DOI Listing
April 2013

Recurrent NCOA2 gene rearrangements in congenital/infantile spindle cell rhabdomyosarcoma.

Genes Chromosomes Cancer 2013 Jun 5;52(6):538-50. Epub 2013 Mar 5.

Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York Presbyterian Hospital, New York, NY 10065, USA.

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https://rubinlab.med.cornell.edu/profiler_images/articles/NC
Web Search
http://doi.wiley.com/10.1002/gcc.22050
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http://dx.doi.org/10.1002/gcc.22050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734530PMC
June 2013

IQSeq: integrated isoform quantification analysis based on next-generation sequencing.

PLoS One 2012 6;7(1):e29175. Epub 2012 Jan 6.

Department of Computer Science, Yale University, New Haven, Connecticut, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029175PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3253133PMC
May 2012

Genomics and privacy: implications of the new reality of closed data for the field.

PLoS Comput Biol 2011 Dec 1;7(12):e1002278. Epub 2011 Dec 1.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1002278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228779PMC
December 2011

The real cost of sequencing: higher than you think!

Genome Biol 2011 Aug 25;12(8):125. Epub 2011 Aug 25.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2011-12-8-125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245608PMC
August 2011

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:
Mark B Gerstein Zhi John Lu Eric L Van Nostrand Chao Cheng Bradley I Arshinoff Tao Liu Kevin Y Yip Rebecca Robilotto Andreas Rechtsteiner Kohta Ikegami Pedro Alves Aurelien Chateigner Marc Perry Mitzi Morris Raymond K Auerbach Xin Feng Jing Leng Anne Vielle Wei Niu Kahn Rhrissorrakrai Ashish Agarwal Roger P Alexander Galt Barber Cathleen M Brdlik Jennifer Brennan Jeremy Jean Brouillet Adrian Carr Ming-Sin Cheung Hiram Clawson Sergio Contrino Luke O Dannenberg Abby F Dernburg Arshad Desai Lindsay Dick Andréa C Dosé Jiang Du Thea Egelhofer Sevinc Ercan Ghia Euskirchen Brent Ewing Elise A Feingold Reto Gassmann Peter J Good Phil Green Francois Gullier Michelle Gutwein Mark S Guyer Lukas Habegger Ting Han Jorja G Henikoff Stefan R Henz Angie Hinrichs Heather Holster Tony Hyman A Leo Iniguez Judith Janette Morten Jensen Masaomi Kato W James Kent Ellen Kephart Vishal Khivansara Ekta Khurana John K Kim Paulina Kolasinska-Zwierz Eric C Lai Isabel Latorre Amber Leahey Suzanna Lewis Paul Lloyd Lucas Lochovsky Rebecca F Lowdon Yaniv Lubling Rachel Lyne Michael MacCoss Sebastian D Mackowiak Marco Mangone Sheldon McKay Desirea Mecenas Gennifer Merrihew David M Miller Andrew Muroyama John I Murray Siew-Loon Ooi Hoang Pham Taryn Phippen Elicia A Preston Nikolaus Rajewsky Gunnar Rätsch Heidi Rosenbaum Joel Rozowsky Kim Rutherford Peter Ruzanov Mihail Sarov Rajkumar Sasidharan Andrea Sboner Paul Scheid Eran Segal Hyunjin Shin Chong Shou Frank J Slack Cindie Slightam Richard Smith William C Spencer E O Stinson Scott Taing Teruaki Takasaki Dionne Vafeados Ksenia Voronina Guilin Wang Nicole L Washington Christina M Whittle Beijing Wu Koon-Kiu Yan Georg Zeller Zheng Zha Mei Zhong Xingliang Zhou Julie Ahringer Susan Strome Kristin C Gunsalus Gos Micklem X Shirley Liu Valerie Reinke Stuart K Kim LaDeana W Hillier Steven Henikoff Fabio Piano Michael Snyder Lincoln Stein Jason D Lieb Robert H Waterston

Science 2010 Dec 22;330(6012):1775-87. Epub 2010 Dec 22.

Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/science.1196914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569PMC
December 2010

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.

Bioinformatics 2011 Jan 5;27(2):281-3. Epub 2010 Dec 5.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018817PMC
January 2011

Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays.

Nucleic Acids Res 2010 Jun 15;38(10):3275-86. Epub 2010 Feb 15.

Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, NY 10065, USA.

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http://dx.doi.org/10.1093/nar/gkq073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879534PMC
June 2010

Robust-linear-model normalization to reduce technical variability in functional protein microarrays.

J Proteome Res 2009 Dec;8(12):5451-64

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1021/pr900412kDOI Listing
December 2009