Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation

[1]  Benjamin J. Raphael,et al.  Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. , 2013, The New England journal of medicine.

[2]  M. Knowles,et al.  Oncogenic FGFR3 gene fusions in bladder cancer , 2012, Human molecular genetics.

[3]  Jun Wang,et al.  SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data , 2013, Genome Biology.

[4]  D. Brat,et al.  Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma , 2012, Science.

[5]  Joshua F. McMichael,et al.  The Origin and Evolution of Mutations in Acute Myeloid Leukemia , 2012, Cell.

[6]  Huanming Yang,et al.  Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma , 2011, Nature Genetics.

[7]  Huanming Yang,et al.  Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder , 2011, Nature Genetics.

[8]  Hongtao Yu,et al.  Mutational Inactivation of STAG2 Causes Aneuploidy in Human Cancer , 2011, Science.

[9]  A. Tsalenko,et al.  Visualization of Fine-Scale Genomic Structure by Oligonucleotide-Based High-Resolution FISH , 2010, Cytogenetic and Genome Research.

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

[11]  J. Montie,et al.  Bladder Cancer in 2010: How Far have We Come? , 2010, Ca.

[12]  Paolo Vineis,et al.  A sequence variant at 4p16.3 confers susceptibility to urinary bladder cancer , 2010, Nature Genetics.

[13]  N. Samani,et al.  Whole Genome Survey of Copy Number Variation in the Spontaneously Hypertensive Rat: Relationship to Quantitative Trait Loci, Gene Expression, and Blood Pressure , 2010, Hypertension.

[14]  Albert Jeltsch,et al.  BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences , 2010, BMC Bioinformatics.

[15]  W. Gregory,et al.  Spectrum of Phosphatidylinositol 3-Kinase Pathway Gene Alterations in Bladder Cancer , 2009, Clinical Cancer Research.

[16]  Ken Chen,et al.  VarScan: variant detection in massively parallel sequencing of individual and pooled samples , 2009, Bioinform..

[17]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

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

[19]  Derek Y. Chiang,et al.  High-resolution mapping of copy-number alterations with massively parallel sequencing , 2009, Nature Methods.

[20]  I. Vernos,et al.  The TACC proteins: TACC-ling microtubule dynamics and centrosome function. , 2008, Trends in cell biology.

[21]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[22]  G. Parmigiani,et al.  Chromatid cohesion defects may underlie chromosome instability in human colorectal cancers , 2008, Proceedings of the National Academy of Sciences.

[23]  E. Lander,et al.  Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma , 2007, Proceedings of the National Academy of Sciences.

[24]  Guy Cavet,et al.  Comment on "The Consensus Coding Sequences of Human Breast and Colorectal Cancers" , 2007, Science.

[25]  G. Parmigiani,et al.  The Consensus Coding Sequences of Human Breast and Colorectal Cancers , 2006, Science.

[26]  R. Cheney,et al.  Genetic alterations in urothelial bladder carcinoma , 2006, Cancer.

[27]  Geert J. P. L. Kops,et al.  On the road to cancer: aneuploidy and the mitotic checkpoint , 2005, Nature Reviews Cancer.

[28]  Xue-Ru Wu.  Urothelial tumorigenesis: a tale of divergent pathways , 2005, Nature Reviews Cancer.

[29]  Adel H Jebar,et al.  FGFR3 and Ras gene mutations are mutually exclusive genetic events in urothelial cell carcinoma , 2005, Oncogene.

[30]  Bing Zhang,et al.  WebGestalt: an integrated system for exploring gene sets in various biological contexts , 2005, Nucleic Acids Res..

[31]  Long-Cheng Li,et al.  MethPrimer: designing primers for methylation PCRs , 2002, Bioinform..

[32]  D. Chopin,et al.  Frequent activating mutations of FGFR3 in human bladder and cervix carcinomas , 1999, Nature Genetics.

[33]  M. Knowles,et al.  Mutation of the 9q34 gene TSC1 in sporadic bladder cancer , 1999, Oncogene.

[34]  A. Jemal,et al.  Global cancer statistics , 2011, CA: a cancer journal for clinicians.

[35]  D. Banerjee,et al.  Resistance Mechanisms to Methotrexate in Tumors , 1996, Stem cells.

[36]  M. Williamson,et al.  p16 (CDKN2) is a major deletion target at 9p21 in bladder cancer. , 1995, Human molecular genetics.

[37]  D. S. Prestridge.  Predicting Pol II promoter sequences using transcription factor binding sites. , 1995, Journal of molecular biology.

[38]  C. Cordon-Cardo,et al.  p53 mutations in human bladder cancer: Genotypic versus phenotypic patterns , 1994, International journal of cancer.

[39]  M. Knowles,et al.  Loss of heterozygosity at the RB locus is frequent and correlates with muscle invasion in bladder carcinoma. , 1991, Oncogene.