Andrea Sboner

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc The real cost of sequencing: higher than you think!
    Andrea Sboner
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 12:125. 2011
  2. pmc Molecular sampling of prostate cancer: a dilemma for predicting disease progression
    Andrea Sboner
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, NY, USA
    BMC Med Genomics 3:8. 2010
  3. pmc FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
    Andrea Sboner
    Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, New Haven, CT 06511, USA
    Genome Biol 11:R104. 2010
  4. pmc Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing
    Dorothee Pflueger
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10021, USA
    Genome Res 21:56-67. 2011
  5. pmc Distinct genomic aberrations associated with ERG rearranged prostate cancer
    Francesca Demichelis
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, NY 10065
    Genes Chromosomes Cancer 48:366-80. 2009
  6. pmc Novel ZC3H7B-BCOR, MEAF6-PHF1, and EPC1-PHF1 fusions in ossifying fibromyxoid tumors--molecular characterization shows genetic overlap with endometrial stromal sarcoma
    Cristina R Antonescu
    Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
    Genes Chromosomes Cancer 53:183-93. 2014
  7. pmc N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer
    Dorothee Pflueger
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10021, USA
    Neoplasia 11:804-11. 2009
  8. pmc Novel MIR143-NOTCH fusions in benign and malignant glomus tumors
    Juan Miguel Mosquera
    Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, NY
    Genes Chromosomes Cancer 52:1075-87. 2013
  9. pmc VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
    Lukas Habegger
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Bioinformatics 28:2267-9. 2012
  10. pmc Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets
    Himisha Beltran
    Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
    Cancer Discov 1:487-95. 2011

Detail Information

Publications22

  1. pmc The real cost of sequencing: higher than you think!
    Andrea Sboner
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 12:125. 2011
    ..Advances in sequencing technology have led to a sharp decrease in the cost of 'data generation'. But is this sufficient to ensure cost-effective and efficient 'knowledge generation'?..
  2. pmc Molecular sampling of prostate cancer: a dilemma for predicting disease progression
    Andrea Sboner
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, NY, USA
    BMC Med Genomics 3:8. 2010
    ..Hence, we sought to develop a molecular panel for prostate cancer progression by reasoning that molecular profiles might further improve current clinical models...
  3. pmc FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
    Andrea Sboner
    Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, New Haven, CT 06511, USA
    Genome Biol 11:R104. 2010
    ..It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements...
  4. pmc Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing
    Dorothee Pflueger
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10021, USA
    Genome Res 21:56-67. 2011
    ..Future work will focus on determining if the ETS rearrangements in prostate cancer are associated or directly predispose to a rearrangement-prone phenotype...
  5. pmc Distinct genomic aberrations associated with ERG rearranged prostate cancer
    Francesca Demichelis
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, NY 10065
    Genes Chromosomes Cancer 48:366-80. 2009
    ..This study provides further support to define a distinct molecular subtype of prostate cancer based on the presence of ETS gene rearrangements...
  6. pmc Novel ZC3H7B-BCOR, MEAF6-PHF1, and EPC1-PHF1 fusions in ossifying fibromyxoid tumors--molecular characterization shows genetic overlap with endometrial stromal sarcoma
    Cristina R Antonescu
    Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
    Genes Chromosomes Cancer 53:183-93. 2014
    ..As similar gene fusions were reported in endometrial stromal sarcomas, we screened for potential gene abnormalities in JAZF1 and EPC1 by FISH and found two additional cases with EPC1-PHF1 fusions...
  7. pmc N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer
    Dorothee Pflueger
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10021, USA
    Neoplasia 11:804-11. 2009
    ..Broader implications of this study support the use of RNA sequencing to discover novel cancer translocations...
  8. pmc Novel MIR143-NOTCH fusions in benign and malignant glomus tumors
    Juan Miguel Mosquera
    Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, NY
    Genes Chromosomes Cancer 52:1075-87. 2013
    ..Only 1/18 angioleiomyomas showed NOTCH2 gene rearrangement, while all the myopericytomas and myofibroma/toses were negative. In summary, we describe novel NOTCH1-3 rearrangements in benign and malignant, visceral, and soft tissue GTs...
  9. pmc VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
    Lukas Habegger
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Bioinformatics 28:2267-9. 2012
    ..Finally, in order to enable on-demand access and to minimize unnecessary transfers of large data files, VAT can be run as a virtual machine in a cloud-computing environment...
  10. pmc Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets
    Himisha Beltran
    Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
    Cancer Discov 1:487-95. 2011
    ..We propose that alterations in Aurora kinase A and N-myc are involved in the development of NEPC, and future clinical trials will help determine from the efficacy of Aurora kinase inhibitor therapy...
  11. pmc Epigenomic alterations in localized and advanced prostate cancer
    Pei Chun Lin
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA
    Neoplasia 15:373-83. 2013
    ..These results warrant clinical evaluation in larger cohorts to help distinguish indolent PCa from advanced disease...
  12. pmc RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
    Lukas Habegger
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
    Bioinformatics 27:281-3. 2011
    ..Availability and implementation: RSEQtools is implemented in C and the source code is available at http://rseqtools.gersteinlab.org/...
  13. pmc Integrative annotation of variants from 1092 humans: application to cancer genomics
    Ekta Khurana
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Science 342:1235587. 2013
    ..g., certain deletions and enhancers). On the basis of these patterns, we developed a computational tool (FunSeq), whose application to ~90 cancer genomes reveals nearly a hundred candidate noncoding drivers. ..
  14. pmc IQSeq: integrated isoform quantification analysis based on next-generation sequencing
    Jiang Du
    Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 7:e29175. 2012
    ..This allows one to have a modular, "plugin-able" read-generation function to support the particularities of the many evolving sequencing technologies...
  15. pmc Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays
    Derek A Oldridge
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, NY 10065, USA
    Nucleic Acids Res 38:3275-86. 2010
    ..Our results are relevant to any array-based CNV study and provide guidelines to optimize performance based on study-specific objectives...
  16. pmc Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
    Science 330:1775-87. 2010
    ..Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome...
  17. pmc Novel YAP1-TFE3 fusion defines a distinct subset of epithelioid hemangioendothelioma
    Cristina R Antonescu
    Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Genes Chromosomes Cancer 52:775-84. 2013
    ..All tumors expressed endothelial markers, as well as strong nuclear TFE3. In summary, we are reporting a novel subset of EHE occurring in young adults, showing a distinct phenotype and YAP1-TFE3 fusions...
  18. pmc Genomics and privacy: implications of the new reality of closed data for the field
    Dov Greenbaum
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
    PLoS Comput Biol 7:e1002278. 2011
    ..However, teaching personal genomics with identifiable subjects in the university setting will, in turn, create additional privacy issues and social conundrums...
  19. pmc Recurrent NCOA2 gene rearrangements in congenital/infantile spindle cell rhabdomyosarcoma
    Juan Miguel Mosquera
    Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York Presbyterian Hospital, New York, NY 10065, USA
    Genes Chromosomes Cancer 52:538-50. 2013
    ..Our findings also support a relationship between NCOA2-rearranged spindle cell RMS occurring in young childhood and the so-called congenital RMS, which often displays rearrangements at 8q13 locus (NCOA2)...
  20. pmc Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays
    Ashish Agarwal
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    BMC Genomics 11:383. 2010
    ..Understanding the relative merits of these technologies will help researchers select the appropriate technology for their needs...
  21. doi request reprint Robust-linear-model normalization to reduce technical variability in functional protein microarrays
    Andrea Sboner
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    J Proteome Res 8:5451-64. 2009
    ..Hence, we show RLM normalization is better suited to protein arrays than approaches used for DNA microarrays...
  22. pmc SPOP mutations in prostate cancer across demographically diverse patient cohorts
    Mirjam Blattner
    Department of Pathology and Laboratory Medicine, Institute of Precision Medicine, Weill Medical College of Cornell University, New York, NY
    Neoplasia 16:14-20. 2014
    ..Recurrent mutations in the Speckle-Type POZ Protein (SPOP) gene occur in up to 15% of prostate cancers. However, the frequency and features of cancers with these mutations across different populations is unknown...