Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity

[1]  L. Fernandez-Cuesta,et al.  A molecular phenotypic map of malignant pleural mesothelioma , 2022, bioRxiv.

[2]  J. Pearson,et al.  Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma , 2022, Genome medicine.

[3]  Erik N. Bergstrom,et al.  Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA , 2022, Nature.

[4]  C. Steele,et al.  Signatures of copy number alterations in human cancer , 2021, Nature.

[5]  C. Swanton,et al.  Cancer evolution: Darwin and beyond , 2021, The EMBO journal.

[6]  J. Ngeow,et al.  Homologous recombination deficiency: cancer predispositions and treatment implications. , 2021, The oncologist.

[7]  R. Kurzrock,et al.  Missing the target in cancer therapy , 2021, Nature Cancer.

[8]  A. Jager,et al.  Homologous Recombination Deficiency Testing for BRCA-Like Tumors: The Road to Clinical Validation , 2021, Cancers.

[9]  P. Robson,et al.  Patterns of transcription factor programs and immune pathway activation define four major subtypes of SCLC with distinct therapeutic vulnerabilities. , 2021, Cancer cell.

[10]  H. Pass,et al.  Asbestos-induced chronic inflammation in malignant pleural mesothelioma and related therapeutic approaches—a narrative review , 2021, Precision cancer medicine.

[11]  L. Fernandez-Cuesta,et al.  Challenges in lung and thoracic pathology: molecular advances in the classification of pleural mesotheliomas , 2021, Virchows Archiv.

[12]  Joshua D. Campbell,et al.  Whole genome doubling confers unique genetic vulnerabilities on tumor cells , 2020, Nature.

[13]  W. Curran,et al.  YAP1 Expression in Small Cell Lung Cancer Defines a Distinct Subtype with T-cell Inflamed Phenotype. , 2020, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

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

[15]  F. Hirsch,et al.  Neuroendocrine subtypes of small cell lung cancer differ in terms of immune microenvironment and checkpoint molecule distribution , 2020, Molecular oncology.

[16]  J. Marioni,et al.  MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data , 2020, Genome Biology.

[17]  Angela E. Leek,et al.  Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution , 2020, Nature Genetics.

[18]  U. Alon,et al.  Tumour heterogeneity and the evolutionary trade-offs of cancer , 2020, Nature Reviews Cancer.

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

[20]  S. Armato,et al.  EURACAN/IASLC proposals for updating the histologic classification of pleural mesothelioma: towards a more multidisciplinary approach. , 2020, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[21]  Uri Alon,et al.  Tumor diversity and the trade-off between universal cancer tasks , 2019, Nature Communications.

[22]  N. Girard,et al.  Redefining malignant pleural mesothelioma types as a continuum uncovers immune-vascular interactions , 2019, EBioMedicine.

[23]  G. Wainrib,et al.  Deep learning-based classification of mesothelioma improves prediction of patient outcome , 2019, Nature Medicine.

[24]  F. Galateau-Sallé,et al.  Mesothelioma: Scientific clues for prevention, diagnosis, and therapy , 2019, CA: a cancer journal for clinicians.

[25]  Aurélie A G Gabriel,et al.  Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids , 2019, Nature Communications.

[26]  N. Le Stang,et al.  MTAP immunohistochemistry is an accurate and reproducible surrogate for CDKN2A fluorescence in situ hybridization in diagnosis of malignant pleural mesothelioma , 2019, Modern Pathology.

[27]  J. Zucman‐Rossi,et al.  Dissecting heterogeneity in malignant pleural mesothelioma through histo-molecular gradients for clinical applications , 2019, Nature Communications.

[28]  Sarah H. Johnson,et al.  Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma , 2019, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[29]  Lisle E Mose,et al.  Improved indel detection in DNA and RNA via realignment with ABRA2 , 2019, Bioinform..

[30]  E. Gazzano,et al.  Epithelial to Mesenchymal Transition in Human Mesothelial Cells Exposed to Asbestos Fibers: Role of TGF-β as Mediator of Malignant Mesothelioma Development or Metastasis via EMT Event , 2019, International journal of molecular sciences.

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

[32]  C. Cole,et al.  The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers , 2018, Nature Reviews Cancer.

[33]  J. Bressler,et al.  Clinical, Pathological, and Molecular Characteristics of CpG Island Methylator Phenotype in Colorectal Cancer: A Systematic Review and Meta-analysis , 2018, Translational oncology.

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

[35]  J. V. van Meerbeeck,et al.  Molecular analysis of an asbestos-exposed Belgian family with a high prevalence of mesothelioma , 2018, Familial Cancer.

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

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

[38]  H. Noushmehr,et al.  Glioma CpG island methylator phenotype (G-CIMP): biological and clinical implications. , 2018, Neuro-oncology.

[39]  Benjamin J. Raphael,et al.  The evolutionary history of 2,658 cancers , 2017, Nature.

[40]  Joel s. Brown,et al.  Classifying the evolutionary and ecological features of neoplasms , 2017, Nature Reviews Cancer.

[41]  D. Schrump,et al.  Targeting the epigenome in malignant pleural mesothelioma. , 2017, Translational lung cancer research.

[42]  Paolo Di Tommaso,et al.  Nextflow enables reproducible computational workflows , 2017, Nature Biotechnology.

[43]  Joachim Weischenfeldt,et al.  SvABA: genome-wide detection of structural variants and indels by local assembly , 2018, Genome research.

[44]  M. Zanetti.  Chromosomal chaos silences immune surveillance , 2017, Science.

[45]  F. Balloux,et al.  Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast , 2016, Nature Communications.

[46]  Peter A. Jones,et al.  Epigenetic Determinants of Cancer. , 2016, Cold Spring Harbor perspectives in biology.

[47]  Emanuel J. V. Gonçalves,et al.  A Landscape of Pharmacogenomic Interactions in Cancer , 2016, Cell.

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

[49]  S. Pastorino,et al.  Minimal asbestos exposure in germline BAP1 heterozygous mice is associated with deregulated inflammatory response and increased risk of mesothelioma , 2016, Oncogene.

[50]  N. Lazar,et al.  The ASA Statement on p-Values: Context, Process, and Purpose , 2016 .

[51]  Thomas D. Wu,et al.  Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations , 2016, Nature Genetics.

[52]  F. Galateau-Sallé,et al.  The 2015 World Health Organization Classification of Tumors of the Pleura: Advances since the 2004 Classification. , 2016, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[53]  Jean-Philippe Vert,et al.  Integrative DNA methylation and gene expression analysis to assess the universality of the CpG island methylator phenotype , 2015, Human Genomics.

[54]  Edwin Cuppen,et al.  Sambamba: fast processing of NGS alignment formats , 2015, Bioinform..

[55]  P. Laird,et al.  Association between molecular subtypes of colorectal cancer and patient survival. , 2015, Gastroenterology.

[56]  T. Nakajima,et al.  Identification of actionable mutations in malignant pleural mesothelioma. , 2014, Lung cancer.

[57]  Asma Ahmed,et al.  The ESAT-6 Protein of Mycobacterium tuberculosis Interacts with Beta-2-Microglobulin (β2M) Affecting Antigen Presentation Function of Macrophage , 2014, PLoS pathogens.

[58]  N. Friedman,et al.  Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells , 2014, Nature.

[59]  Ira M. Hall,et al.  SAMBLASTER: fast duplicate marking and structural variant read extraction , 2014, Bioinform..

[60]  Thomas Zichner,et al.  DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..

[61]  A. Viale,et al.  IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype , 2012, Nature.

[62]  D. Reinberg,et al.  The Polycomb complex PRC2 and its mark in life , 2011, Nature.

[63]  Xiao Zhang,et al.  Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis , 2010, BMC Bioinformatics.

[64]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[65]  R. Wilson,et al.  Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. , 2010, Cancer cell.

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

[67]  David Pellman,et al.  Cytokinesis failure generating tetraploids promotes tumorigenesis in p53-null cells , 2005, Nature.

[68]  Robert M. May,et al.  Ecological Strategies and Population Parameters , 1974, The American Naturalist.