Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer.

[1]  P. Carroll,et al.  Initial treatment patterns and outcome of contemporary prostate cancer patients with bone metastases at initial presentation , 2007, Cancer.

[2]  S. Varambally,et al.  Induced Chromosomal Proximity and Gene Fusions in Prostate Cancer , 2009, Science.

[3]  C. Cooper,et al.  Novel, gross chromosomal alterations involving PTEN cooperate with allelic loss in prostate cancer , 2012, Modern Pathology.

[4]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[5]  D. Dearnaley,et al.  A model of the natural history of screen-detected prostate cancer, and the effect of radical treatment on overall survival , 2006, British Journal of Cancer.

[6]  J. Tchinda,et al.  Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. , 2006, Science.

[7]  Thomas Zichner,et al.  DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..

[8]  H. Schlüter,et al.  ERG Status Is Unrelated to PSA Recurrence in Radically Operated Prostate Cancer in the Absence of Antihormonal Therapy , 2011, Clinical Cancer Research.

[9]  H. Moch,et al.  Ki67 LABELLING INDEX: AN INDEPENDENT PREDICTOR OF PROGRESSION IN PROSTATE CANCER TREATED BY RADICAL PROSTATECTOMY , 1996, The Journal of pathology.

[10]  Martin J. Aryee,et al.  Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements , 2010, Nature Genetics.

[11]  Chawnshang Chang,et al.  Endocrine mechanisms of disease: Expression and degradation of androgen receptor: mechanism and clinical implication. , 2003, The Journal of clinical endocrinology and metabolism.

[12]  S. Nelson,et al.  BFAST: An Alignment Tool for Large Scale Genome Resequencing , 2009, PloS one.

[13]  Sebastian D. Mackowiak,et al.  miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades , 2011, Nucleic acids research.

[14]  Jie Zhang,et al.  Nuclear Receptor-Induced Chromosomal Proximity and DNA Breaks Underlie Specific Translocations in Cancer , 2009, Cell.

[15]  A. Sivachenko,et al.  Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer , 2012, Nature Genetics.

[16]  A. Knudson.  Mutation and cancer: statistical study of retinoblastoma. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Jianfeng Xu,et al.  Deletion of a Small Consensus Region at 6q15, Including the MAP3K7 Gene, Is Significantly Associated with High-Grade Prostate Cancers , 2007, Clinical Cancer Research.

[18]  H. Lähdesmäki,et al.  Overexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer , 2012, Oncogene.

[19]  David T. W. Jones,et al.  Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations , 2012, Cell.

[20]  Jin Woo Kim,et al.  DNA copy number alterations in prostate cancers: A combined analysis of published CGH studies , 2007, The Prostate.

[21]  D. Berney,et al.  Androgen-induced TMPRSS2:ERG fusion in nonmalignant prostate epithelial cells. , 2010, Cancer research.

[22]  Guidelines Eau.  EUROPEAN ASSOCIATION OF UROLOGY , 2003 .

[23]  Benjamin J. Raphael,et al.  The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer , 2012, Nature.

[24]  Andrew J Vickers,et al.  Long-term prediction of prostate cancer up to 25 years before diagnosis of prostate cancer using prostate kallikreins measured at age 44 to 50 years. , 2007, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[25]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[26]  J. Brooks,et al.  Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness , 2012, Oncogene.

[27]  N. Dubrawsky.  Cancer statistics , 1989, CA: a cancer journal for clinicians.

[28]  Stephen J. Salipante,et al.  Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers , 2011, Proceedings of the National Academy of Sciences.

[29]  Antony V. Cox,et al.  Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing , 2008, Nature Genetics.

[30]  D. Lin,et al.  Treatment and survival outcomes in young men diagnosed with prostate cancer , 2009, Cancer.

[31]  Beatrice S Knudsen,et al.  Mechanisms of prostate cancer initiation and progression. , 2010, Advances in cancer research.

[32]  Michael C. Rusch,et al.  CREST maps somatic structural variation in cancer genomes with base-pair resolution , 2011, Nature Methods.

[33]  C. Plass,et al.  Genomic deletion of PTEN is associated with tumor progression and early PSA recurrence in ERG fusion-positive and fusion-negative prostate cancer. , 2012, The American journal of pathology.

[34]  M. Stratton,et al.  The cancer genome , 2009, Nature.

[35]  T. Borodina,et al.  Transcriptome analysis by strand-specific sequencing of complementary DNA , 2009, Nucleic acids research.

[36]  A. Chokkalingam,et al.  Prostate cancer epidemiology. , 2006, Frontiers in bioscience : a journal and virtual library.

[37]  Tim Beißbarth,et al.  TMPRSS2-ERG -specific transcriptional modulation is associated with prostate cancer biomarkers and TGF-β signaling , 2011, BMC Cancer.

[38]  Arul M Chinnaiyan,et al.  Common gene rearrangements in prostate cancer. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[39]  James A Hanley,et al.  20-year outcomes following conservative management of clinically localized prostate cancer. , 2005, JAMA.

[40]  A. Jemal,et al.  Cancer statistics, 2012 , 2012, CA: a cancer journal for clinicians.

[41]  J. Eisman,et al.  Age-related changes in serum testosterone and sex hormone binding globulin in Australian men: longitudinal analyses of two geographically separate regional cohorts. , 2007, The Journal of clinical endocrinology and metabolism.

[42]  S. Terry,et al.  Complex regulation of human androgen receptor expression by Wnt signaling in prostate cancer cells , 2006, Oncogene.

[43]  J. Mckinlay,et al.  Normal, bound and nonbound testosterone levels in normally ageing men: results from the Massachusetts Male Ageing Study , 2005, Clinical endocrinology.

[44]  Marcel H. Schulz,et al.  A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome , 2008, Science.

[45]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[46]  Michael Rehli,et al.  Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. , 2006, Cancer research.

[47]  S. Balk,et al.  The Androgen Receptor Recruits Nuclear Receptor CoRepressor (N-CoR) in the Presence of Mifepristone via Its N and C Termini Revealing a Novel Molecular Mechanism for Androgen Receptor Antagonists* , 2005, Journal of Biological Chemistry.

[48]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[49]  Mark D. Johnson,et al.  Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion , 2011, Proceedings of the National Academy of Sciences.

[50]  S. Dhanasekaran,et al.  Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer , 2007, Nature.

[51]  Amy E. Hawkins,et al.  DNA sequencing of a cytogenetically normal acute myeloid leukemia genome , 2008, Nature.

[52]  Zhaohui S. Qin,et al.  An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. , 2010, Cancer cell.

[53]  C. Sander,et al.  Integrative genomic profiling of human prostate cancer. , 2010, Cancer cell.

[54]  Eric S. Lander,et al.  The genomic complexity of primary human prostate cancer , 2010, Nature.

[55]  A. Haese*,et al.  Clinical significance of p53 alterations in surgically treated prostate cancers , 2008, Modern Pathology.

[56]  Chawnshang Chang,et al.  Expression and Degradation of Androgen Receptor: Mechanism and Clinical Implication , 2003 .

[57]  Thomas Wiegel,et al.  EAU guidelines on prostate cancer. Part 1: screening, diagnosis, and treatment of clinically localised disease. , 2011, European urology.

[58]  Michael Moser,et al.  Altered corepressor SMRT expression and recruitment to target genes as a mechanism that change the response to androgens in prostate cancer progression. , 2012, Biochemical and biophysical research communications.