title: Second generation sequencing of the mesothelioma tumor genome.
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.
authors.affiliation: The International Mesothelioma Program, Brigham and Women's Hospital, Boston, Massachusetts, United States of America.
authors.forename: Raphael
authors.initials: R
authors.lastname: Bueno
authors.forename: Assunta
authors.initials: A
authors.lastname: De Rienzo
authors.forename: Lingsheng
authors.initials: L
authors.lastname: Dong
authors.forename: Gavin J
authors.initials: GJ
authors.lastname: Gordon
authors.forename: Colin F
authors.initials: CF
authors.lastname: Hercus
authors.forename: William G
authors.initials: WG
authors.lastname: Richards
authors.forename: Roderick V
authors.initials: RV
authors.lastname: Jensen
authors.forename: Arif
authors.initials: A
authors.lastname: Anwar
authors.forename: Gautam
authors.initials: G
authors.lastname: Maulik
authors.forename: Lucian R
authors.initials: LR
authors.lastname: Chirieac
authors.forename: Kim-Fong
authors.initials: KF
authors.lastname: Ho
authors.forename: Bruce E
authors.initials: BE
authors.lastname: Taillon
authors.forename: Cynthia L
authors.initials: CL
authors.lastname: Turcotte
authors.forename: Robert G
authors.initials: RG
authors.lastname: Hercus
authors.forename: Steven R
authors.initials: SR
authors.lastname: Gullans
authors.forename: David J
authors.initials: DJ
authors.lastname: Sugarbaker
mesh_terms: D002869:Chromosome Aberrations; D002874:Chromosome Mapping; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic; D015321:Gene Rearrangement / Q000235:genetics; D052138:Genes, Neoplasm / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics; D007621:Karyotyping; D008654:Mesothelioma / Q000235:genetics*; D010997:Pleural Neoplasms / Q000235:genetics*; D017354:Point Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012015:Reference Standards; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004273:DNA, Neoplasm