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Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing

Qi Zhao1, Ewen F Kirkness2, Otavia L Caballero1, Pedro A Galante3, Raphael B Parmigiani3, Lee Edsall4, Samantha Kuan4, Zhen Ye4, Samuel Levy5, Ana Tereza R Vasconcelos6, Bing Ren4, Sandro J de Souza3, Anamaria A Camargo3, Andrew JG Simpson1* and Robert L Strausberg1*

Author Affiliations

1 Ludwig Collaborative Group, Department of Neurosurgery, Johns Hopkins University, 1550 Orleans Street, Baltimore, MD 21231, USA

2 J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

3 Ludwig Institute for Cancer Research, São Paulo Branch at Hospital Alemão Oswaldo Cruz, Rua João Julião 245, 01323-903 São Paulo, Brazil

4 Ludwig Institute for Cancer Research, San Diego Branch, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA

5 Scripps Translational Science Institute, 3344 North Torrey Pines Court, La Jolla, CA 92037, USA

6 Laboratório Nacional de Computação Científica, Laboratório de Bioinformática, Av. Getúlio Vargas 333, Petrópolis, RJ 25651-075, Brazil

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Genome Biology 2010, 11:R114  doi:10.1186/gb-2010-11-11-r114

Published: 25 November 2010

Additional files

Additional file 1:

Supplemental tables. Table S1: exome genotyping in HCC1954. Table S2: exome genotyping in HCC1954BL. Table S3: LOH genes in HCC1954. Table S4: LOH genes in HCC1954BL. Table S5: ASE genes in HCC1954. Table S6: ASE genes in HCC1954BL. Table S7: primers used in ASE events validation. Table S8: summary of putative tumor suppressor genes identified by LOH and ASE events.

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Additional file 2:

Supplemental figures. LOH events detected across each chromosome.

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