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

[1]  Paul Theodor Pyl,et al.  HTSeq – A Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[2]  S. Orkin,et al.  Polycomb repressive complex 2 regulates normal hematopoietic stem cell function in a developmental-stage-specific manner. , 2014, Cell stem cell.

[3]  Noemi Andor,et al.  EXPANDS: expanding ploidy and allele frequency on nested subpopulations , 2013, Bioinform..

[4]  M. Berger,et al.  Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing. , 2013, Journal of visualized experiments : JoVE.

[5]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[6]  Wendy S. W. Wong,et al.  Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs , 2012, Bioinform..

[7]  Benjamin E. Gross,et al.  The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.

[8]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[9]  B. Pockaj,et al.  Malignant Peripheral Nerve Sheath Tumors (MPNST): The Mayo Clinic Experience , 2012, Annals of Surgical Oncology.

[10]  Kiran C. Bobba,et al.  The genetic basis of early T-cell precursor acute lymphoblastic leukaemia , 2012, Nature.

[11]  Marc Ladanyi,et al.  Advances in sarcoma genomics and new therapeutic targets , 2011, Nature Reviews Cancer.

[12]  H. Pasolli,et al.  EZH1 and EZH2 cogovern histone H3K27 trimethylation and are essential for hair follicle homeostasis and wound repair. , 2011, Genes & development.

[13]  D. Reinberg,et al.  The Polycomb complex PRC2 and its mark in life , 2011, Nature.

[14]  Stuart H. Orkin,et al.  A Myc Network Accounts for Similarities between Embryonic Stem and Cancer Cell Transcription Programs , 2010, Cell.

[15]  C. Antonescu,et al.  ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours , 2010, Nature.

[16]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[17]  H. Drexler,et al.  Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders , 2010, Nature Genetics.

[18]  R. Kuiper,et al.  Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes , 2010, Nature Genetics.

[19]  Terence P. Speed,et al.  TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays , 2010, BMC Bioinformatics.

[20]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[21]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[22]  S. Gygi,et al.  Defining the Human Deubiquitinating Enzyme Interaction Landscape , 2009, Cell.

[23]  J. Simon,et al.  Roles of the EZH2 histone methyltransferase in cancer epigenetics. , 2008, Mutation research.

[24]  D. Reinberg,et al.  Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. , 2008, Molecular cell.

[25]  Guo-Cheng Yuan,et al.  EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. , 2008, Molecular cell.

[26]  T. Mikkelsen,et al.  Genome-scale DNA methylation maps of pluripotent and differentiated cells , 2008, Nature.

[27]  S A Forbes,et al.  The Catalogue of Somatic Mutations in Cancer (COSMIC) , 2008, Current protocols in human genetics.

[28]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[29]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[30]  S. Dry,et al.  Validation of the postoperative nomogram for 12‐year sarcoma‐specific mortality , 2004, Cancer.

[31]  M. Pierotti,et al.  p15INK4b, p14ARF, and p16INK4a inactivation in sporadic and neurofibromatosis type 1-related malignant peripheral nerve sheath tumors. , 2003, Clinical cancer research : an official journal of the American Association for Cancer Research.

[32]  S. Dhanasekaran,et al.  The polycomb group protein EZH2 is involved in progression of prostate cancer , 2002, Nature.

[33]  B. Scheithauer,et al.  Deletions of the INK4A gene occur in malignant peripheral nerve sheath tumors but not in neurofibromas. , 1999, The American journal of pathology.

[34]  D. Louis,et al.  Malignant transformation of neurofibromas in neurofibromatosis 1 is associated with CDKN2A/p16 inactivation. , 1999, The American journal of pathology.

[35]  Jeng-Shin Lee,et al.  Chromosome 17p deletions and p53 gene mutations associated with the formation of malignant neurofibrosarcomas in von Recklinghausen neurofibromatosis. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[36]  R. Grimer,et al.  Management of Soft Tissue Sarcoma , 1990 .

[37]  W. R. Hart,et al.  Tumors of the peripheral nervous system. , 1970, Human pathology.

[38]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[39]  C. Antonescu,et al.  Malignant Peripheral Nerve Sheath Tumor (MPNST) and Triton Tumor , 2013 .

[40]  F. Rodriguez.  Peripheral nerve sheath tumors: the elegant chapter in surgical neuropathology , 2012, Acta Neuropathologica.

[41]  L. Qin,et al.  Oncologic Outcomes of Sporadic, Neurofibromatosis-Associated, and Radiation-Induced Malignant Peripheral Nerve Sheath Tumors , 2012, Annals of Surgical Oncology.

[42]  R. Arceci.  Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders , 2010 .

[43]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[44]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[45]  I. Ariel,et al.  Tumors of the peripheral nervous system , 1983, Seminars in surgical oncology.

[46]  J. Fleiss.  Measuring nominal scale agreement among many raters. , 1971 .