Pan-cancer whole-genome analyses of metastatic solid tumours

[1]  S. Sleijfer,et al.  The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies , 2019, Nature Genetics.

[2]  S. Sleijfer,et al.  The Drug Rediscovery protocol facilitates the expanded use of existing anticancer drugs , 2019, Nature.

[3]  Lincoln D Stein,et al.  The International Cancer Genome Consortium Data Portal , 2019, Nature Biotechnology.

[4]  S. Morganella,et al.  A Compendium of Mutational Signatures of Environmental Agents , 2019, Cell.

[5]  Takafumi N. Yamaguchi,et al.  The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact , 2019, Nature Communications.

[6]  Johannes G. Reiter,et al.  Minimal functional driver gene heterogeneity among untreated metastases , 2018, Science.

[7]  N. Schultz,et al.  A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT) , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.

[8]  Marc Salit,et al.  Determining Performance Metrics for Targeted Next-Generation Sequencing Panels Using Reference Materials. , 2018, The Journal of molecular diagnostics : JMD.

[9]  J. Carpten,et al.  Abstract 437: Leveraging new methods in single-cell copy number analysis and clonotype detection to uncover and characterize hidden subclones within standard cell lines , 2018, Molecular and Cellular Biology / Genetics.

[10]  Christopher W. Whelan,et al.  Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing , 2018, Cell.

[11]  B. Taylor,et al.  Genome doubling shapes the evolution and prognosis of advanced cancers , 2018, Nature Genetics.

[12]  Jessica L. Davis,et al.  Larotrectinib for paediatric solid tumours harbouring NTRK gene fusions: phase 1 results from a multicentre, open-label, phase 1/2 study. , 2018, The Lancet. Oncology.

[13]  C. Sander,et al.  Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets , 2018, Nature Genetics.

[14]  J. Szustakowski,et al.  Nivolumab plus Ipilimumab in Lung Cancer with a High Tumor Mutational Burden , 2018, The New England journal of medicine.

[15]  Ashton C. Berger,et al.  Genomic and Functional Approaches to Understanding Cancer Aneuploidy. , 2018, Cancer cell.

[16]  Steven J. M. Jones,et al.  Comprehensive Characterization of Cancer Driver Genes and Mutations , 2018, Cell.

[17]  Steven J. M. Jones,et al.  Pathogenic Germline Variants in 10,389 Adult Cancers. , 2018, Cell.

[18]  Michael C. Heinold,et al.  The landscape of genomic alterations across childhood cancers , 2018, Nature.

[19]  Xin Zhou,et al.  Pan-cancer genome and transcriptome analyses of 1,699 pediatric leukemias and solid tumors , 2018, Nature.

[20]  Yu-Chih Liang,et al.  ZFP36L1 and ZFP36L2 inhibit cell proliferation in a cyclin D-dependent and p53-independent manner , 2018, Scientific Reports.

[21]  Astrid Gall,et al.  Ensembl 2018 , 2017, Nucleic Acids Res..

[22]  N. Socci,et al.  Accelerating Discovery of Functional Mutant Alleles in Cancer. , 2018, Cancer discovery.

[23]  Chuang Tan,et al.  Universal Patterns of Selection in Cancer and Somatic Tissues , 2018, Cell.

[24]  Mauricio O. Carneiro,et al.  Scaling accurate genetic variant discovery to tens of thousands of samples , 2017, bioRxiv.

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

[26]  G. Getz,et al.  The whole-genome panorama of cancer drivers , 2017, bioRxiv.

[27]  P. Stephens,et al.  Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers , 2017, Molecular Cancer Therapeutics.

[28]  T. E. Wilson,et al.  Fragile sites in cancer: more than meets the eye , 2017, Nature Reviews Cancer.

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

[30]  Johannes G. Reiter,et al.  Origins of lymphatic and distant metastases in human colorectal cancer , 2017, Science.

[31]  P. Lønning,et al.  Genomic Evolution of Breast Cancer Metastasis and Relapse , 2017, Cancer cell.

[32]  Robert J. Lonigro,et al.  Integrative Clinical Genomics of Metastatic Cancer , 2017, Nature.

[33]  M. Socinski,et al.  First‐Line Nivolumab in Stage IV or Recurrent Non–Small‐Cell Lung Cancer , 2017, The New England journal of medicine.

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

[35]  Moriah H Nissan,et al.  OncoKB: A Precision Oncology Knowledge Base. , 2017, JCO precision oncology.

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

[37]  Timothy L. Tickle,et al.  STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq , 2017, bioRxiv.

[38]  B. Taylor,et al.  Implementing Genome-Driven Oncology , 2017, Cell.

[39]  N. McGranahan,et al.  Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future , 2017, Cell.

[40]  Michael L. Gatza,et al.  Amplification of SOX4 promotes PI3K/Akt signaling in human breast cancer , 2017, Breast Cancer Research and Treatment.

[41]  M. Rubin,et al.  Non-coding genetic variation in cancer. , 2017, Current opinion in systems biology.

[42]  W. Chung,et al.  Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics , 2016, Genetics in Medicine.

[43]  Steven J. M. Jones,et al.  CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer , 2017, Nature Genetics.

[44]  Mingming Jia,et al.  COSMIC: somatic cancer genetics at high-resolution , 2016, Nucleic Acids Res..

[45]  S. Sleijfer,et al.  Implementation of a Multicenter Biobanking Collaboration for Next-Generation Sequencing-Based Biomarker Discovery Based on Fresh Frozen Pretreatment Tumor Tissue Biopsies. , 2017, The oncologist.

[46]  A. Hoischen,et al.  Reliable Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue Using Single Molecule Tags. , 2016, The Journal of molecular diagnostics : JMD.

[47]  B. Leggett,et al.  RNF43 and ZNRF3 are commonly altered in serrated pathway colorectal tumorigenesis , 2016, Oncotarget.

[48]  F. Silvestris,et al.  NETs: organ-related epigenetic derangements and potential clinical applications , 2016, Oncotarget.

[49]  E. Ratner,et al.  SYD985, a Novel Duocarmycin-Based HER2-Targeting Antibody–Drug Conjugate, Shows Antitumor Activity in Uterine Serous Carcinoma with HER2/Neu Expression , 2016, Molecular Cancer Therapeutics.

[50]  A. Sablina,et al.  Loss of Chromosome 8p Governs Tumor Progression and Drug Response by Altering Lipid Metabolism. , 2016, Cancer cell.

[51]  Steven J. M. Jones,et al.  A somatic reference standard for cancer genome sequencing , 2016, Scientific Reports.

[52]  Xiaoyu Chen,et al.  Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications , 2016, Bioinform..

[53]  L. Wessels,et al.  OncoScape: Exploring the cancer aberration landscape by genomic data fusion , 2016, Scientific Reports.

[54]  Crispin J. Miller,et al.  Recurrent MLK4 Loss-of-Function Mutations Suppress JNK Signaling to Promote Colon Tumorigenesis. , 2016, Cancer research.

[55]  Ricardo Villamarín-Salomón,et al.  ClinVar: public archive of interpretations of clinically relevant variants , 2015, Nucleic Acids Res..

[56]  Hanlee P. Ji,et al.  Pan-cancer analysis of the extent and consequences of intratumor heterogeneity , 2015, Nature Medicine.

[57]  R. Kuick,et al.  The PIAS-like Coactivator Zmiz1 Is a Direct and Selective Cofactor of Notch1 in T Cell Development and Leukemia. , 2015, Immunity.

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

[59]  M. Nykter,et al.  The Evolutionary History of Lethal Metastatic Prostate Cancer , 2015, Nature.

[60]  Jindan Yu,et al.  Current perspectives on FOXA1 regulation of androgen receptor signaling and prostate cancer , 2015, Genes & diseases.

[61]  Gang Fu,et al.  Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data , 2014, Nucleic Acids Res..

[62]  Roman K. Thomas,et al.  Molecular Pathways: Targeting NRG1 Fusions in Lung Cancer , 2014, Clinical Cancer Research.

[63]  M. van de Rijn,et al.  Dystrophin Is a Tumor Suppressor in Human Cancers with Myogenic Programs , 2014, Nature Genetics.

[64]  S. Willems,et al.  p16INK4A and p14ARF Gene Promoter Hypermethylation as Prognostic Biomarker in Oral and Oropharyngeal Squamous Cell Carcinoma: A Review , 2014, Disease markers.

[65]  S. Elledge,et al.  Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome , 2013, Cell.

[66]  D. Haussler,et al.  The Somatic Genomic Landscape of Glioblastoma , 2013, Cell.

[67]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[68]  S. Gabriel,et al.  Pan-cancer patterns of somatic copy-number alteration , 2013, Nature Genetics.

[69]  C. Klein Selection and adaptation during metastatic cancer progression , 2013, Nature.

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

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

[72]  H. Aburatani,et al.  Integrated molecular analysis of clear-cell renal cell carcinoma , 2013, Nature Genetics.

[73]  D. Busam,et al.  SMAD2, SMAD3 and SMAD4 mutations in colorectal cancer. , 2013, Cancer research.

[74]  A. Børresen-Dale,et al.  Copynumber: Efficient algorithms for single- and multi-track copy number segmentation , 2012, BMC Genomics.

[75]  Melissa E. Ko,et al.  CDX2 is an amplified lineage-survival oncogene in colorectal cancer , 2012, Proceedings of the National Academy of Sciences.

[76]  Steven J. M. Jones,et al.  Comprehensive genomic characterization of squamous cell lung cancers , 2012, Nature.

[77]  Wendy S. W. Wong,et al.  Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs , 2012, Bioinform..

[78]  A. McKenna,et al.  Absolute quantification of somatic DNA alterations in human cancer , 2012, Nature Biotechnology.

[79]  Syed Haider,et al.  International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data , 2011, Database J. Biol. Databases Curation.

[80]  G. Getz,et al.  GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers , 2011, Genome Biology.

[81]  C. Perou,et al.  Allele-specific copy number analysis of tumors , 2010, Proceedings of the National Academy of Sciences.

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

[83]  Elias Campo Guerri,et al.  International network of cancer genome projects , 2010, Nature.

[84]  Gary D Bader,et al.  International network of cancer genome projects , 2010, Nature.

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

[86]  L. Senelick It (review) , 2008 .

[87]  S. Nee More than meets the eye , 2004, Nature.

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

[89]  J. Gebert,et al.  Can APC mutation analysis contribute to therapeutic decisions in familial adenomatous polyposis? Experience from 680 FAP families , 2001, Gut.

[90]  S. Bull,et al.  Tumor microsatellite instability and clinical outcome in young patients with colorectal cancer. , 2000, The New England journal of medicine.

[91]  M. Krečmerová,et al.  Lipases as Tools in the Synthesis of Prodrugs from Racemic 9-(2,3-Dihydroxypropyl)adenine , 2012, Molecules.

[92]  F. Waldman,et al.  Y chromosome loss detected by FISH in bladder cancer. , 1995, Cancer genetics and cytogenetics.

[93]  S. Hunter,et al.  Y chromosome loss in esophageal carcinoma: An in situ hybridization study , 1993, Genes, chromosomes & cancer.

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