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. 2010 May 13;5(5):e10612.
doi: 10.1371/journal.pone.0010612.

Second generation sequencing of the mesothelioma tumor genome

Affiliations

Second generation sequencing of the mesothelioma tumor genome

Raphael Bueno et al. PLoS One. .

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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Conflict of interest statement

Competing Interests: There are authors on this manuscript that work for three companies: Roche 454 Life Sciences, Inc., Synamatix Sdn Bhd and Excel Medical Ventures and according to PLOS One rules must be called Funder. Each of these companies provided work for this project as a subcontractor and was paid for it. None of these companies owns any IP, has any control or exerted any influence on this article other than scientific editorializing. Specifically, the authors contracted 454 (and then Roche-454) to perform some of the sequencing since at the time there was no 454 machine in Boston. The authors met with their staff and they helped in the experimental design, but the sequencing was paid for by the authors' institution and the company holds no IP or any other controls. Synamatix was contracted to help the authors perform bioinformatic analysis using their equipment as the authors did not at the time have the full computer capability. They were used as a service company and do not control any IP or data. One of the authors' long term collaborators, Steve Gullans, moved from academia to the venture company he founded, Excel. He participated as a paid scientific collaborator and consultant in a manner unrelated to his company. Like the case for the others, his company places no restrictions nor owns any IP. Given that as described above, all these companies provided paid for, subcontracted resources, not unlike a Core function, the authors included some of their employees as authors for some scientific contributions. Furthermore, all the final data analysis, processing and validation was done in the authors' academic institution. However, there is no competing interest nor are there any data sharing limitations. Thus the authors continue to adhere to PLOS one rules and regulations in full.

Figures

Figure 1
Figure 1. Sequence read mapping to the reference genome to display the Karyotype of the patient tumor and normal DNA by Illumina and Roche/454 sequencing and by CGH.
Figure 2
Figure 2. The read density of the long arm of chromosome 21 in tumor and normal with the validated rearrangements.

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References

    1. Vogelzang NJ, Rusthoven JJ, Symanowski J, Denham C, et al. Phase III study of pemetrexed in combination with cisplatin versus cisplatin alone in patients with malignant pleural mesothelioma. J Clin Oncol. 2003;21(14):2636–2644. - PubMed
    1. Sugarbaker DJ. Macroscopic complete resection: the goal of primary surgery in multimodality therapy for pleural mesothelioma. J Thorac Oncol. 2006;1(2):175–176. - PubMed
    1. Gordon GJ, Dong L, Yeap BY, Richards WG, et al. Four-gene expression ratio test for survival in patients undergoing surgery for mesothelioma. J Natl Cancer Inst. 2009;101(9):678–686. - PMC - PubMed
    1. Kindler HL. Malignant pleural mesothelioma. Curr Treat Options Oncol. 2000;1(4):313–326. - PubMed
    1. Krug LM. An overview of chemotherapy for mesothelioma. Hematol Oncol Clin North Am. 2005;19(6):1117–1136, vii. - PubMed

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