Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures

[1]  Benjamin J. Raphael,et al.  Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes , 2020, Cell.

[2]  Aung Ko Win,et al.  Evaluating the utility of tumour mutational signatures for identifying hereditary colorectal cancer and polyposis syndrome carriers , 2019, Gut.

[3]  A. Gonzalez-Perez,et al.  A compendium of mutational cancer driver genes , 2020, Nature Reviews Cancer.

[4]  Richard T. Barfield,et al.  Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival , 2020, Nature Communications.

[5]  Jaime Fern'andez del R'io,et al.  Array programming with NumPy , 2020, Nature.

[6]  An integrated analysis of lymphocytic reaction, tumour molecular characteristics and patient survival in colorectal cancer , 2020, British Journal of Cancer.

[7]  Benjamin J. Raphael,et al.  Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig , 2020, Nature Communications.

[8]  F. McCormick Sticking it to KRAS: Covalent Inhibitors Enter the Clinic. , 2020, Cancer cell.

[9]  Joel Nothman,et al.  SciPy 1.0-Fundamental Algorithms for Scientific Computing in Python , 2019, ArXiv.

[10]  Ryan L. Collins,et al.  The mutational constraint spectrum quantified from variation in 141,456 humans , 2020, Nature.

[11]  Romina Royo,et al.  A practical guide for mutational signature analysis in hematological malignancies , 2019, Nature Communications.

[12]  Judith E Grolleman,et al.  Somatic mutational signatures in polyposis and colorectal cancer. , 2019, Molecular aspects of medicine.

[13]  Isidro Cortés-Ciriano,et al.  Detecting the mutational signature of homologous recombination deficiency in clinical samples , 2019, Nature Genetics.

[14]  W. Foulkes,et al.  Mutational Signature Analysis Reveals NTHL1 Deficiency to Cause a Multi-tumor Phenotype. , 2019, Cancer cell.

[15]  Gregory M. Cooper,et al.  CADD: predicting the deleteriousness of variants throughout the human genome , 2018, Nucleic Acids Res..

[16]  Ville Mustonen,et al.  The repertoire of mutational signatures in human cancer , 2018, Nature.

[17]  Christopher T. Saunders,et al.  Strelka2: fast and accurate calling of germline and somatic variants , 2018, Nature Methods.

[18]  T. Walsh,et al.  Using Somatic Mutations from Tumors to Classify Variants in Mismatch Repair Genes. , 2018, American journal of human genetics.

[19]  Aung Ko Win,et al.  Cohort Profile: The Colon Cancer Family Registry Cohort (CCFRC). , 2018, International journal of epidemiology.

[20]  Chunlei Liu,et al.  ClinVar: improving access to variant interpretations and supporting evidence , 2017, Nucleic Acids Res..

[21]  K. Cole,et al.  Comprehensive Analysis of Hypermutation in Human Cancer , 2017, Cell.

[22]  Edwin Cuppen,et al.  MutationalPatterns: comprehensive genome-wide analysis of mutational processes , 2016, Genome Medicine.

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

[24]  Michael P. Schroeder,et al.  Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations , 2017, Genome Medicine.

[25]  L. Alexandrov,et al.  Mutational signature analysis identifies MUTYH deficiency in colorectal cancers and adrenocortical carcinomas , 2017, The Journal of pathology.

[26]  Teresa M. Przytycka,et al.  Detecting presence of mutational signatures in cancer with confidence , 2017, bioRxiv.

[27]  A. Giuliani,et al.  A Specific Mutational Signature Associated with DNA 8-Oxoguanine Persistence in MUTYH-defective Colorectal Cancer , 2017, EBioMedicine.

[28]  Donavan T. Cheng,et al.  Mutational Landscape of Metastatic Cancer Revealed from Prospective Clinical Sequencing of 10,000 Patients , 2017, Nature Medicine.

[29]  E. Birney,et al.  HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures , 2017, Nature Medicine.

[30]  Shivashankar H. Nagaraj,et al.  Whole-genome landscape of pancreatic neuroendocrine tumours , 2017, Nature.

[31]  M. Kloor,et al.  No association of CpG island methylator phenotype and colorectal cancer survival: population-based study , 2016, British Journal of Cancer.

[32]  Trevor Hastie,et al.  REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. , 2016, American journal of human genetics.

[33]  P. Lenz,et al.  The Prostate, Lung, Colorectal and Ovarian Cancer (PLCO) Screening Trial Pathology Tissue Resource , 2016, Cancer Epidemiology, Biomarkers & Prevention.

[34]  W. Willett,et al.  Origin, Methods, and Evolution of the Three Nurses' Health Studies. , 2016, American journal of public health.

[35]  B. Taylor,et al.  deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution , 2016, Genome Biology.

[36]  O. Hofmann,et al.  VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research , 2016, Nucleic acids research.

[37]  B. Teh,et al.  MSIseq: Software for Assessing Microsatellite Instability from Catalogs of Somatic Mutations , 2015, Scientific Reports.

[38]  C. Ishioka,et al.  Functional Complementation Assay for 47 MUTYH Variants in a MutY-Disrupted Escherichia Coli Strain , 2015, Human mutation.

[39]  J. Shendure,et al.  A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer , 2015, Nature Genetics.

[40]  S. Thibodeau,et al.  Establishment of the Cancer Prevention Study II Nutrition Cohort Colorectal Tissue Repository , 2014, Cancer Epidemiology, Biomarkers & Prevention.

[41]  Aung Ko Win,et al.  Risk of colorectal cancer for carriers of mutations in MUTYH, with and without a family history of cancer. , 2014, Gastroenterology.

[42]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[43]  Christian Stock,et al.  Reduced risk of colorectal cancer up to 10 years after screening, surveillance, or diagnostic colonoscopy. , 2014, Gastroenterology.

[44]  J. Cerhan,et al.  Associations between Cigarette Smoking, Hormone Therapy, and Folate Intake with Incident Colorectal Cancer by TP53 Protein Expression Level in a Population-Based Cohort of Older Women , 2013, Cancer Epidemiology, Biomarkers & Prevention.

[45]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[46]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[47]  M. Stratton,et al.  Deciphering Signatures of Mutational Processes Operative in Human Cancer , 2013, Cell reports.

[48]  Steven Gallinger,et al.  A Multifactorial Likelihood Model for MMR Gene Variant Classification Incorporating Probabilities Based on Sequence Bioinformatics and Tumor Characteristics: A Report from the Colon Cancer Family Registry , 2013, Human mutation.

[49]  Aung Ko Win,et al.  Risk of Metachronous Colon Cancer Following Surgery for Rectal Cancer in Mismatch Repair Gene Mutation Carriers , 2013, Annals of Surgical Oncology.

[50]  Aung Ko Win,et al.  Risks of primary extracolonic cancers following colorectal cancer in lynch syndrome. , 2012, Journal of the National Cancer Institute.

[51]  Amarda Shehu,et al.  Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules , 2012, Adv. Artif. Intell..

[52]  A. Baierl,et al.  MNS16A tandem repeats minisatellite of human telomerase gene: a risk factor for colorectal cancer. , 2011, Carcinogenesis.

[53]  Sandra D Fights,et al.  Nurses' Health Study. , 2011, Medsurg nursing : official journal of the Academy of Medical-Surgical Nurses.

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

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

[56]  R. Bristow,et al.  Characterization of mutant MUTYH proteins associated with familial colorectal cancer. , 2008, Gastroenterology.

[57]  John D Potter,et al.  Colon Cancer Family Registry: An International Resource for Studies of the Genetic Epidemiology of Colon Cancer , 2007, Cancer Epidemiology Biomarkers & Prevention.

[58]  Yan Liu,et al.  Risk factors for prostate cancer incidence and progression in the health professionals follow‐up study , 2007, International journal of cancer.

[59]  J. Gisbert,et al.  Identification of MYH mutation carriers in colorectal cancer: a multicenter, case-control, population-based study. , 2007, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

[60]  Garnet L Anderson,et al.  The Women's Health Initiative recruitment methods and results. , 2003, Annals of epidemiology.

[61]  Alison L. Livingston,et al.  Inherited variants of MYH associated with somatic G:C→T:A mutations in colorectal tumors , 2002, Nature Genetics.

[62]  D. English,et al.  The Melbourne Collaborative Cohort Study. , 2002, IARC scientific publications.

[63]  M. Thun,et al.  The American Cancer Society Cancer Prevention Study II Nutrition Cohort: rationale, study design, and baseline characteristics. , 2002, Cancer.

[64]  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.

[65]  J. Potter,et al.  Increased incidence of carcinoma of the breast associated with abdominal adiposity in postmenopausal women. , 1990, American journal of epidemiology.