This article is part of a special issue on exome sequencing.

Open Access Research

First somatic mutation of E2F1 in a critical DNA binding residue discovered in well-differentiated papillary mesothelioma of the peritoneum

Willie Yu123, Waraporn Chan-On12, Melissa Teo4, Choon Kiat Ong12, Ioana Cutcutache5, George E Allen12, Bernice Wong12, Swe Swe Myint12, Kiat Hon Lim6, P Mathijs Voorhoeve78, Steve Rozen5, Khee Chee Soo4, Patrick Tan10119* and Bin Tean Teh1122*

Author Affiliations

1 NCCS-VARI Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore

2 Laboratory of Cancer Therapeutics, Division of Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore

3 National University of Singapore Graduate School for Integrative Sciences and Engineering, 28 Medical Drive, 117456, Singapore

4 Department of Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore

5 Division of Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore

6 Department of Pathology, Singapore General Hospital - Pathology Building, Outram Road, 169608, Singapore

7 Laboratory of Molecular Tumor Genetics, Division of Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore

8 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive - Blk MD7 #02-03, 117597, Singapore

9 Cancer Science Institute of Singapore, National University of Singapore, 5 Lower Kent Ridge Road, 119074, Singapore

10 Laboratory of Genomic Oncology, Division of Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore

11 Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore

12 Laboratory of Cancer Genetics, Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA

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Genome Biology 2011, 12:R96  doi:10.1186/gb-2011-12-9-r96

Published: 28 September 2011

Additional files

Additional file 1:

Sequencing coverage at CDKN2A, RASSF1A and NF2. Each graph shows the exons (brown box) and introns (brown line) as defined by ENSEMBL, the chromosome and chromosomal coordinates of the gene, the actual capture region as defined by Agilent SureSelect Human All Exon Kit v1.01 (gray box with green outlines or green lines if the capture region is very small relative to the distance between exons), and three plots showing sequencing depth versus chromosomal coordinates for the tumor, the normal sample and the cell line.

Format: PPTX Size: 124KB Download file

Open Data

Additional file 2:

Full candidate somatic mutation set with validation using Sanger sequencing. Full data set containing computationally predicted somatic single nucleotide alterations with a quality by depth of at least three. The data set was also validated using Sanger sequencing.

Format: XLSX Size: 13KB Download file

Open Data

Additional file 3:

Sanger sequencing validation of E2F1, PPFIBP2 and TRAF7 for tumor, normal and cell line samples. Heterozygous mutation (red arrow) on E2F1, PPFIBP2, and TRAF7 presented in the tumor and cell line compared to the normal sample.

Format: PPTX Size: 127KB Download file

Open Data

Additional file 4:

Relative expression of E2F1 wild type or E2F1 mutant after co-transfection with EGFP in MSTO-211H and NCI-H28 cells. E2F1 levels were normalized to EGFP levels in each condition. Similar levels of transcripts of the R166H mutant and wild type E2F1 were observed.

Format: PPTX Size: 78KB Download file

Open Data

Additional file 5:

Schematic for detection of somatic single nucleotide variants in high-throughput sequencing data. Flowchart describing computational detection of somatic single nucleotide variants in exome sequencing data.

Format: PPTX Size: 66KB Download file

Open Data