Supplementary Tables S1-S8, Figures S1-S4 from Whole-Exome Sequencing Reveals Frequent Genetic Alterations in BAP1, NF2, CDKN2A, and CUL1 in Malignant Pleural Mesothelioma

Guo, Guangwu; Chmielecki, Juliann; Goparaju, Chandra; Heguy, Adriana; Dolgalev, Igor; Carbone, Michele; Seepo, Sara; Meyerson, Matthew; Pass, Harvey I.

doi:10.1158/0008-5472.22408272.v1

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Supplementary Tables S1-S8, Figures S1-S4 from Whole-Exome Sequencing Reveals Frequent Genetic Alterations in BAP1, NF2, CDKN2A, and CUL1 in Malignant Pleural Mesothelioma

journal contribution

posted on 2023-03-30, 23:32 authored by Guangwu Guo, Juliann Chmielecki, Chandra Goparaju, Adriana Heguy, Igor Dolgalev, Michele Carbone, Sara Seepo, Matthew Meyerson, Harvey I. Pass

Supplementary Tables S1-S8, Figures S1-S4. Table S1. Clinical characteristics of the 22 MPM patients. Table S2. Primer sequences of PIK3C2B, RDX, and TAOK1 for validation experiment. Table S3. A list of all somatic mutations detected in 22 MPMs (shown in separate excel file). Table S4. The average mutation rates of different cancer types in previously reported cancer genome studies. Table S5. Recurrently mutated genes that harbored much higher mutations than the background with significant threshold of P <0.01. Table S6. List of significant focal copy number alterations in the 22 MPMs (shown in separate excel file). Table S7. Pathways that are significantly enriched with genetic alterations in MPM. Table S8. Somatic mutations in the genes of Hippo signaling pathway(12) in MPMs. Figure S1. Spectrum of somatic point mutations identified in the 22 MPMs. Figure S2. Copy number alteration profiles of 22 MPMs using the whole exome sequencing data. Figure S3. Statistically significant focal deletions (blue) plotted along the genome for the MPM. Figure S4. A significant region of focal deletion at 9p21 containing CDKN2A/B and MIR31 (microRNA 31) in MPM rendered by the Integrative Genomics Viewer (IGV).

History

ARTICLE ABSTRACT

Malignant pleural mesothelioma (MPM) is an aggressive neoplasm associated with asbestos exposure. Although previous studies based on candidate gene approaches have identified important common somatic mutations in MPM, these studies have focused on small sets of genes and have provided a limited view of the genetic alterations underlying this disease. Here, we performed whole-exome sequencing on DNA from 22 MPMs and matched blood samples, and identified 517 somatic mutations across 490 mutated genes. Integrative analysis of mutations and somatic copy-number alterations revealed frequent genetic alterations in BAP1, NF2, CDKN2A, and CUL1. Our study presents the first unbiased view of the genomic basis of MPM. Cancer Res; 75(2); 264–9. ©2014 AACR.