Genomic footprints of activated telomere maintenance mechanisms in cancer

[1]  Stefan M. Pfister,et al.  TelomereHunter – in silico estimation of telomere content and composition from cancer genomes , 2019, BMC Bioinformatics.

[2]  Peter J. Park,et al.  Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing , 2018, bioRxiv.

[3]  Katharina I. Deeg,et al.  Integrative genomic and transcriptomic analysis of leiomyosarcoma , 2018, Nature Communications.

[4]  Icgc,et al.  Pan-cancer analysis of whole genomes , 2017, bioRxiv.

[5]  Delia M. Braun,et al.  TelNet - a database for human and yeast genes involved in telomere maintenance , 2017, BMC Genetics.

[6]  J. Arthur,et al.  Comparative analysis of whole genome sequencing-based telomere length measurement techniques. , 2017, Methods.

[7]  Xin Hu,et al.  Systematic analysis of telomere length and somatic alterations in 31 cancer types , 2017, Nature Genetics.

[8]  Weihang Chai,et al.  Human MLH1 suppresses the insertion of telomeric sequences at intra-chromosomal sites in telomerase-expressing cells , 2016, Nucleic acids research.

[9]  M. Toyoda,et al.  DNA hypermethylation enhanced telomerase reverse transcriptase expression in human-induced pluripotent stem cells , 2017, Human Cell.

[10]  Roland Eils,et al.  Complex heatmaps reveal patterns and correlations in multidimensional genomic data , 2016, Bioinform..

[11]  P. Soares,et al.  The Role of ATRX in the Alternative Lengthening of Telomeres (ALT) Phenotype , 2016, Genes.

[12]  David T. W. Jones,et al.  TelomereHunter: telomere content estimation and characterization from whole genome sequencing data , 2016, bioRxiv.

[13]  David T. W. Jones,et al.  Telomere dysfunction and chromothripsis , 2016, International journal of cancer.

[14]  G. Reifenberger,et al.  The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary , 2016, Acta Neuropathologica.

[15]  Jing Liu,et al.  Whole-Genome Sequencing Reveals Diverse Models of Structural Variations in Esophageal Squamous Cell Carcinoma , 2016, American journal of human genetics.

[16]  Aziz Khan,et al.  dbSUPER: a database of super-enhancers in mouse and human genome , 2015, bioRxiv.

[17]  [World Health Organization classification of tumours of the central nervous system: a summary]. , 2016, Zhonghua bing li xue za zhi = Chinese journal of pathology.

[18]  Peter J. Campbell,et al.  Chromothripsis and Kataegis Induced by Telomere Crisis , 2015, Cell.

[19]  D. Zwijnenburg,et al.  Abstract PR06: TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors , 2016 .

[20]  K. Collins,et al.  Control of telomerase action at human telomeres , 2015, Nature Structural &Molecular Biology.

[21]  Simon C Watkins,et al.  Telomerase activation by genomic rearrangements in high-risk neuroblastoma , 2015, Nature.

[22]  S. Mittnacht,et al.  RB in DNA repair , 2015, Oncotarget.

[23]  Lilit Nersisyan,et al.  Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data , 2015, PloS one.

[24]  Thoas Fioretos,et al.  Activation of human telomerase reverse transcriptase through gene fusion in clear cell sarcoma of the kidney. , 2015, Cancer letters.

[25]  S. Gagos,et al.  Nuclear-Receptor-Mediated Telomere Insertion Leads to Genome Instability in ALT Cancers , 2015, Cell.

[26]  Aziz Khan,et al.  dbSUPER: a database of super-enhancers in mouse and human genome , 2015, bioRxiv.

[27]  R. Reddel Telomere Maintenance Mechanisms in Cancer: Clinical Implications , 2014, Current pharmaceutical design.

[28]  Richard Durbin,et al.  Estimating telomere length from whole genome sequence data , 2014, Nucleic acids research.

[29]  D. Sheer,et al.  The role of microhomology in genomic structural variation. , 2014, Trends in genetics : TIG.

[30]  Mark Hills,et al.  Telomere extension by telomerase and ALT generates variant repeats by mechanistically distinct processes , 2013, Nucleic acids research.

[31]  S. Bailey,et al.  TERT promoter mutation and aberrant hypermethylation are associated with elevated expression in medulloblastoma and characterise the majority of non-infant SHH subgroup tumours , 2014, Acta Neuropathologica.

[32]  P. O’Reilly,et al.  Identification of seven loci affecting mean telomere length and their association with disease , 2013, Nature Genetics.

[33]  Gary L. Gallia,et al.  TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal , 2013, Proceedings of the National Academy of Sciences.

[34]  Mallikarjun Patil,et al.  Checkpoint kinase 1 in DNA damage response and cell cycle regulation , 2013, Cellular and Molecular Life Sciences.

[35]  J. Korbel,et al.  Criteria for Inference of Chromothripsis in Cancer Genomes , 2013, Cell.

[36]  D. Schadendorf,et al.  TERT Promoter Mutations in Familial and Sporadic Melanoma , 2013, Science.

[37]  Lynda Chin,et al.  Highly Recurrent TERT Promoter Mutations in Human Melanoma , 2013, Science.

[38]  Jing-Pian Peng,et al.  Telomerase-Null Survivor Screening Identifies Novel Telomere Recombination Regulators , 2013, PLoS genetics.

[39]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[40]  R. Wilson,et al.  Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data , 2012, Genome Biology.

[41]  H. Pickett,et al.  Variant repeats are interspersed throughout the telomeres and recruit nuclear receptors in ALT cells , 2012, The Journal of cell biology.

[42]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[43]  R. Hruban,et al.  Loss of ATRX or DAXX expression and concomitant acquisition of the alternative lengthening of telomeres phenotype are late events in a small subset of MEN-1 syndrome pancreatic neuroendocrine tumors , 2012, Modern Pathology.

[44]  W. Hahn,et al.  Loss of ATRX, Genome Instability, and an Altered DNA Damage Response Are Hallmarks of the Alternative Lengthening of Telomeres Pathway , 2012, PLoS genetics.

[45]  E. Montgomery,et al.  Prevalence of the alternative lengthening of telomeres telomere maintenance mechanism in human cancer subtypes. , 2011, The American journal of pathology.

[46]  R. McLendon,et al.  Altered Telomeres in Tumors with ATRX and DAXX Mutations , 2011, Science.

[47]  N. Carter,et al.  Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development , 2011, Cell.

[48]  M. Shammas Telomeres, lifestyle, cancer, and aging , 2011, Current opinion in clinical nutrition and metabolic care.

[49]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[50]  Tania L. Slatter,et al.  Pilocytic astrocytomas have telomere-associated promyelocytic leukemia bodies without alternatively lengthened telomeres. , 2010, The American journal of pathology.

[51]  V. Avvedimento,et al.  Menin stimulates homology‐directed DNA repair , 2010, FEBS letters.

[52]  M. Lieber,et al.  The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. , 2010, Annual review of biochemistry.

[53]  R. Reddel,et al.  Alternative lengthening of telomeres: models, mechanisms and implications , 2010, Nature Reviews Genetics.

[54]  R. O'Sullivan,et al.  Telomeres: protecting chromosomes against genome instability , 2010, Nature Reviews Molecular Cell Biology.

[55]  F. Ishikawa,et al.  Unusual Telomeric DNAs in Human Telomerase-Negative Immortalized Cells , 2008, Molecular and Cellular Biology.

[56]  Max Kuhn,et al.  Building Predictive Models in R Using the caret Package , 2008 .

[57]  Tao Sun,et al.  Acquisition of granule neuron precursor identity is a critical determinant of progenitor cell competence to form Shh-induced medulloblastoma. , 2008, Cancer cell.

[58]  Ju Yan,et al.  Endings in the middle: current knowledge of interstitial telomeric sequences. , 2008, Mutation research.

[59]  B. Scheithauer,et al.  The 2007 WHO classification of tumours of the central nervous system , 2007, Acta Neuropathologica.

[60]  Victor V Lobanenkov,et al.  Dual role of DNA methylation inside and outside of CTCF-binding regions in the transcriptional regulation of the telomerase hTERT gene , 2007, Nucleic acids research.

[61]  Andy Liaw,et al.  Classification and Regression by randomForest , 2007 .

[62]  Martin Kupiec,et al.  A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[63]  G. Tang,et al.  Indian Hedgehog: A Mechanotransduction Mediator in Condylar Cartilage , 2004, Journal of dental research.

[64]  N. Carter,et al.  A DNA damage checkpoint response in telomere-initiated senescence , 2003, Nature.

[65]  F. Bosman,et al.  Hypermethylation of the human telomerase catalytic subunit (hTERT) gene correlates with telomerase activity , 2002, International journal of cancer.

[66]  H. Pickett,et al.  Molecular characterization of inter-telomere and intra-telomere mutations in human ALT cells , 2002, Nature Genetics.

[67]  J. Murnane,et al.  DNA amplification by breakage/fusion/bridge cycles initiated by spontaneous telomere loss in a human cancer cell line. , 2002, Neoplasia.

[68]  A. Levine,et al.  Surfing the p53 network , 2000, Nature.

[69]  A. Zetterberg,et al.  Frequent amplification of the telomerase reverse transcriptase gene in human tumors. , 2000, Cancer research.

[70]  J. Levine,et al.  Surfing the p53 network , 2000, Nature.

[71]  W. Poon,et al.  Telomerase expression in gliomas including the nonastrocytic tumors. , 1998, Human pathology.

[72]  P. Bryant,et al.  Chromosome healing, telomere capture and mechanisms of radiation-induced chromosome breakage. , 1998, International journal of radiation biology.

[73]  Bas van Steensel,et al.  Control of telomere length by the human telomeric protein TRF1 , 1997, Nature.

[74]  J. Shay,et al.  Telomerase activity is detected in pancreatic cancer but not in benign tumors. , 1997, Cancer research.

[75]  D. S. Coffey,et al.  Telomerase activity: a prevalent marker of malignant human prostate tissue. , 1996, Cancer research.

[76]  J. Shay,et al.  Telomerase activity in human germline and embryonic tissues and cells. , 1996, Developmental genetics.

[77]  A. Jeffreys,et al.  Mechanisms underlying telomere repeat turnover, revealed by hypervariable variant repeat distribution patterns in the human Xp/Yp telomere. , 1995, The EMBO journal.

[78]  D I Boomsma,et al.  Genetic determination of telomere size in humans: a twin study of three age groups. , 1994, American journal of human genetics.

[79]  H. Williams,et al.  Healing of broken human chromosomes by the addition of telomeric repeats. , 1994, American journal of human genetics.

[80]  P. Meltzer,et al.  Telomere capture stabilizes chromosome breakage , 1993, Nature Genetics.

[81]  A. Wilkie,et al.  A truncated human chromosome 16 associated with α thalassaemia is stabilized by addition of telomeric repeat (TTAGGG)n , 1990, Nature.

[82]  C. Harley,et al.  Telomeres shorten during ageing of human fibroblasts , 1990, Nature.

[83]  M. Dempster,et al.  Human telomeres contain at least three types of G-rich repeat distributed non-randomly. , 1989, Nucleic acids research.

[84]  B. Mcclintock,et al.  The Stability of Broken Ends of Chromosomes in Zea Mays. , 1941, Genetics.