ArticlePloS one2010
Second generation sequencing of the mesothelioma tumor genome.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 citations in OpenAlex.
- Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations.Nature genetics · 2016Pooled it
- The Rocky Road from Preclinical Findings to Successful Targeted Therapy in Pleural Mesothelioma.International journal of molecular sciences · 2022Review
- Establishment and validation of a novel immune-related prognostic signature in malignant pleural mesothelioma.Annals of translational medicine · 2022Article
- Extracellular Vesicle Enriched miR-625-3p Is Associated with Survival of Malignant Mesothelioma Patients.Journal of personalized medicine · 2021Article
- Aurora Kinase A as a Diagnostic and Prognostic Marker of Malignant Mesothelioma.Frontiers in oncology · 2021Article
- Malignant pleural mesothelioma: an update.Jornal brasileiro de pneumologia : publicacao oficial da Sociedade Brasileira de Pneumologia e Tisilogia · 2021Review
- Preclinical Models and Resources to Facilitate Basic Science Research on Malignant Mesothelioma - A Review.Frontiers in oncology · 2021Review
- Fluorescence in situ hybridization (FISH) provides estimates of minute and interstitial BAP1, CDKN2A, and NF2 gene deletions in peritoneal mesothelioma.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2020Article
- Genomics and Epigenetics of Malignant Mesothelioma.High-throughput · 2018Review
- Identification of novel therapeutic target genes and pathway in pancreatic cancer by integrative analysis.Medicine · 2017Article
- Metastatic triple-negative breast cancer patient withCold Spring Harbor molecular case studies · 2017Article
- Switching off malignant mesothelioma: exploiting the hypoxic microenvironment.Genes & cancer · 2016Review
- Whole exome and targeted deep sequencing identify genome-wide allelic loss and frequent SETDB1 mutations in malignant pleural mesotheliomas.Oncotarget · 2016Article
- Gender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma.Cancer research · 2016Article
- The somatic autosomal mutation matrix in cancer genomes.Human genetics · 2015Article
- BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma.Journal of translational medicine · 2015Article
- Malignant pleural mesothelioma: history, controversy and future of a manmade epidemic.European respiratory review : an official journal of the European Respiratory Society · 2015Review
- Gene expression of mesothelioma in vinylidene chloride-exposed F344/N rats reveal immune dysfunction, tissue damage, and inflammation pathways.Toxicologic pathology · 2015Article
- Personalized oncogenomics: clinical experience with malignant peritoneal mesothelioma using whole genome sequencing.PloS one · 2015Article
- MicroRNA and mRNA features of malignant pleural mesothelioma and benign asbestos-related pleural effusion.BioMed research international · 2015Article
Corrections and comments
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Authors and funding
16 authors at 3 institutions in 1 country.
Funding
Abstract
The current paradigm for elucidating the molecular etiology of cancers relies on the interrogation of small numbers of genes, which limits the scope of investigation. Emerging second-generation massively parallel DNA sequencing technologies have enabled more precise definition of the cancer genome on a global scale. We examined the genome of a human primary malignant pleural mesothelioma (MPM) tumor and matched normal tissue by using a combination of sequencing-by-synthesis and pyrosequencing methodologies to a 9.6X depth of coverage. Read density analysis uncovered significant aneuploidy and numerous rearrangements. Method-dependent informatics rules, which combined the results of different sequencing platforms, were developed to identify and validate candidate mutations of multiple types. Many more tumor-specific rearrangements than point mutations were uncovered at this depth of sequencing, resulting in novel, large-scale, inter- and intra-chromosomal deletions, inversions, and translocations. Nearly all candidate point mutations appeared to be previously unknown SNPs. Thirty tumor-specific fusions/translocations were independently validated with PCR and Sanger sequencing. Of these, 15 represented disrupted gene-encoding regions, including kinases, transcription factors, and growth factors. One large deletion in DPP10 resulted in altered transcription and expression of DPP10 transcripts in a set of 53 additional MPM tumors correlated with survival. Additionally, three point mutations were observed in the coding regions of NKX6-2, a transcription regulator, and NFRKB, a DNA-binding protein involved in modulating NFKB1. Several regions containing genes such as PCBD2 and DHFR, which are involved in growth factor signaling and nucleotide synthesis, respectively, were selectively amplified in the tumor. Second-generation sequencing uncovered all types of mutations in this MPM tumor, with DNA rearrangements representing the dominant type.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.