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Germline BAP1 mutations predispose to malignant mesothelioma

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TLDR
A BAP1-related cancer syndrome is identified that is characterized by mesothelioma and uveal melanoma, and it is hypothesized that other cancers may also be involved and that mesot helioma predominates upon asbestos exposure.
Abstract
Because only a small fraction of asbestos-exposed individuals develop malignant mesothelioma, and because mesothelioma clustering is observed in some families, we searched for genetic predisposing factors. We discovered germline mutations in the gene encoding BRCA1 associated protein-1 (BAP1) in two families with a high incidence of mesothelioma, and we observed somatic alterations affecting BAP1 in familial mesotheliomas, indicating biallelic inactivation. In addition to mesothelioma, some BAP1 mutation carriers developed uveal melanoma. We also found germline BAP1 mutations in 2 of 26 sporadic mesotheliomas; both individuals with mutant BAP1 were previously diagnosed with uveal melanoma. We also observed somatic truncating BAP1 mutations and aberrant BAP1 expression in sporadic mesotheliomas without germline mutations. These results identify a BAP1-related cancer syndrome that is characterized by mesothelioma and uveal melanoma. We hypothesize that other cancers may also be involved and that mesothelioma predominates upon asbestos exposure. These findings will help to identify individuals at high risk of mesothelioma who could be targeted for early intervention.

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Interplay Between the Cancer Genome and Epigenome

TL;DR: The ways in which alterations in the genome and epigenome influence each other and cooperate to promote oncogenic transformation are explored.
Journal ArticleDOI

The role of mutations in epigenetic regulators in myeloid malignancies

TL;DR: Recent genetic and functional data implicating mutations in epigenetic modifiers, including tet methylcytosine dioxygenase 2 (TET2), isocitrate dehydrogenase 1 (IDH1), IDH2, additional sex combs-like 1 (ASXL1), enhancer of zeste homologue 2 (EZH2) and DNA methyltransferase 3A (DNMT3A) are discussed.
References
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Journal ArticleDOI

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

TL;DR: This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
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Principal components analysis corrects for stratification in genome-wide association studies

TL;DR: This work describes a method that enables explicit detection and correction of population stratification on a genome-wide scale and uses principal components analysis to explicitly model ancestry differences between cases and controls.
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A second generation human haplotype map of over 3.1 million SNPs

Kelly A. Frazer, +237 more
- 18 Oct 2007 - 
TL;DR: The Phase II HapMap is described, which characterizes over 3.1 million human single nucleotide polymorphisms genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed, and increased differentiation at non-synonymous, compared to synonymous, SNPs is demonstrated.
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Frequent Mutation of BAP1 in Metastasizing Uveal Melanomas

TL;DR: Exome capture coupled with massively parallel sequencing is used to search for metastasis-related mutations in highly metastatic uveal melanomas of the eye and implicate loss of BAP1 in uveAL melanoma metastasis and suggest that the BAP 1 pathway may be a valuable therapeutic target.
Journal ArticleDOI

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.

TL;DR: Birdsuite is presented, a four-stage analytical framework instantiated in software for deriving integrated and mutually consistent copy number and SNP genotypes that more accurately depict the underlying sequence of each individual, reducing the rate of apparent mendelian inconsistencies.
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