Ultradeep Sequencing of a Human Ultraconserved Region Reveals Somatic and Constitutional Genomic Instability

Ultradeep sequencing of genomes permits the detection of very low-level genomic instability in non-neoplastic tissues of patients with the most common form of inherited colorectal cancer.

[1]  L. Loeb,et al.  Mutator phenotype may be required for multistage carcinogenesis. , 1991, Cancer research.

[2]  G. Thomas,et al.  [Genetic predisposition to colorectal cancer]. , 1993, Annales de gastroenterologie et d'hepatologie.

[3]  Robin J. Leach,et al.  Mutations of a mutS homolog in hereditary nonpolyposis colorectal cancer , 1993, Cell.

[4]  Bert Vogelstein,et al.  Hypermutability and mismatch repair deficiency in RER+ tumor cells , 1993, Cell.

[5]  H T Lynch,et al.  Hereditary Nonpolyposis Colorectal Cancer Patients Replication Errors in Benign and Malignant Tumors from , 2006 .

[6]  A. Chapelle,et al.  Loss of the wild type MLH1 gene is a feature of hereditary nonpolyposis colorectal cancer , 1994, Nature Genetics.

[7]  R. Iggo,et al.  A rapid PCR fidelity assay. , 1994, Nucleic acids research.

[8]  R. Fleischmann,et al.  Mutation of a mutL homolog in hereditary colon cancer. , 1994, Science.

[9]  K. Kinzler,et al.  Mismatch repair deficiency in phenotypically normal human cells , 1995, Science.

[10]  J. Braman,et al.  PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. , 1996, Nucleic acids research.

[11]  L. Aaltonen,et al.  Semiautomated assessment of loss of heterozygosity and replication error in tumors. , 1996, Cancer research.

[12]  T. Iwama,et al.  Molecular nature of colon tumors in hereditary nonpolyposis colon cancer, familial polyposis, and sporadic colon cancer. , 1996, Gastroenterology.

[13]  K. Maruyama,et al.  Loss or Somatic Mutations of hMSH2 Occur in Hereditary Nonpolyposis Colorectal Cancers with hMSH2 Germline Mutations , 1996, Japanese journal of cancer research : Gann.

[14]  W. Thilly,et al.  Fidelity and mutational spectrum of Pfu DNA polymerase on a human mitochondrial DNA sequence. , 1997, Genome research.

[15]  A. Lindblom,et al.  Tumorigenesis in colorectal tumors from patients with hereditary non-polyposis colorectal cancer , 1997, Human Genetics.

[16]  Peter Beighton,et al.  de la Chapelle, A. , 1997 .

[17]  A. de la Chapelle,et al.  Mutations predisposing to hereditary nonpolyposis colorectal cancer. , 1997, Advances in cancer research.

[18]  J. Kur,et al.  Cloning and expression in Escherichia coli of the recombinant his-tagged DNA polymerases from Pyrococcus furiosus and Pyrococcus woesei. , 1998, Protein expression and purification.

[19]  S Srivastava,et al.  A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. , 1998, Cancer research.

[20]  J. Kur,et al.  Cloning and Expression inEscherichia coliof the Recombinant His-Tagged DNA Polymerases fromPyrococcus furiosusandPyrococcus woesei , 1998 .

[21]  A. de la Chapelle,et al.  Genetic and epigenetic modification of MLH1 accounts for a major share of microsatellite-unstable colorectal cancers. , 2000, The American journal of pathology.

[22]  D. Schaid,et al.  The frequency of hereditary defective mismatch repair in a prospective series of unselected colorectal carcinomas. , 2001, American journal of human genetics.

[23]  D. Glavač,et al.  Causes of microsatellite instability in colorectal tumors: implications for hereditary non-polyposis colorectal cancer screening. , 2001, Cancer genetics and cytogenetics.

[24]  S. Leung,et al.  Germline, somatic and epigenetic events underlying mismatch repair deficiency in colorectal and HNPCC-related cancers , 2002, Oncogene.

[25]  E. Ito,et al.  Mutations and aberrant DNA methylation of the PROX1 gene in hematologic malignancies , 2003, Genes, chromosomes & cancer.

[26]  D. Haussler,et al.  Ultraconserved Elements in the Human Genome , 2004, Science.

[27]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[28]  Il-Jin Kim,et al.  [Hereditary colorectal cancer]. , 2005, The Korean journal of gastroenterology = Taehan Sohwagi Hakhoe chi.

[29]  J. Bielas,et al.  Quantification of random genomic mutations , 2005, Nature Methods.

[30]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[31]  G. Capellá,et al.  Low levels of microsatellite instability characterize MLH1 and MSH2 HNPCC carriers before tumor diagnosis. , 2005, Human molecular genetics.

[32]  Laurent Excoffier,et al.  Conserved noncoding sequences are selectively constrained and not mutation cold spots , 2006, Nature Genetics.

[33]  G. Church,et al.  Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants , 2006, Nature Genetics.

[34]  Frank Diehl,et al.  BEAMing up for detection and quantification of rare sequence variants , 2006, Nature Methods.

[35]  Thomas LaFramboise,et al.  Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing , 2006, Nature Medicine.

[36]  P. Radice,et al.  A human cell-based assay to evaluate the effects of alterations in the MLH1 mismatch repair gene. , 2006, Cancer research.

[37]  H. Friess,et al.  Role of lymphangiogenesis and lymphangiogenic factors during pancreatic cancer progression and lymphatic spread. , 2006, International journal of oncology.

[38]  T. Yoshimoto,et al.  A Homeobox Protein, Prox1, Is Involved in the Differentiation, Proliferation, and Prognosis in Hepatocellular Carcinoma , 2006, Clinical Cancer Research.

[39]  Alan M. Moses,et al.  In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.

[40]  P. Lynch New Issues in Genetic Counseling of Hereditary Colon Cancer , 2007, Clinical Cancer Research.

[41]  M. Hellmich,et al.  Epigenetic silencing of the candidate tumor suppressor gene PROX1 in sporadic breast cancer. , 2005, International journal of cancer.

[42]  M. Ronaghi,et al.  Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. , 2007, Genome research.

[43]  K. Søreide Molecular Testing for Microsatellite Instability and DNA Mismatch Repair Defects in Hereditary and Sporadic Colorectal Cancers – Ready for Prime Time? , 2007, Tumor Biology.

[44]  A. Sparks,et al.  The Genomic Landscapes of Human Breast and Colorectal Cancers , 2007, Science.

[45]  P. Møller,et al.  Guidelines for the clinical management of Lynch syndrome (hereditary non-polyposis cancer) , 2007, Journal of Medical Genetics.

[46]  Thomas D. Schmittgen,et al.  Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. , 2007, Cancer cell.

[47]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[48]  L. Aaltonen,et al.  No evidence for dual role of loss of heterozygosity in hereditary non-polyposis colorectal cancer , 2007, Oncogene.

[49]  Susan M. Huse,et al.  Accuracy and quality of massively parallel DNA pyrosequencing , 2007, Genome Biology.

[50]  David Haussler,et al.  Human Genome Ultraconserved Elements Are Ultraselected , 2007, Science.

[51]  Axel Visel,et al.  Deletion of Ultraconserved Elements Yields Viable Mice , 2007, PLoS biology.

[52]  D. Busam,et al.  An Integrated Genomic Analysis of Human Glioblastoma Multiforme , 2008, Science.

[53]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[54]  M. Stratton,et al.  Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing , 2008, Proceedings of the National Academy of Sciences.

[55]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[56]  Jussi Taipale,et al.  Transcription factor PROX1 induces colon cancer progression by promoting the transition from benign to highly dysplastic phenotype. , 2008, Cancer cell.

[57]  G. Parmigiani,et al.  Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses , 2008, Science.

[58]  A. Visel,et al.  Ultraconservation identifies a small subset of extremely constrained developmental enhancers , 2008, Nature Genetics.

[59]  David I. Wilson,et al.  Separation of the PROX1 gene from upstream conserved elements in a complex inversion/translocation patient with hypoplastic left heart , 2009, European Journal of Human Genetics.

[60]  Justin C. Fay,et al.  Quantification of rare allelic variants from pooled genomic DNA , 2009, Nature Methods.

[61]  P. Radice,et al.  SNPs in ultraconserved elements and familial breast cancer risk. , 2009, Carcinogenesis.