Volume 12 Supplement 1
A computational approach to identify transposable element insertions in cancer cells
© Silva et al; licensee BioMed Central Ltd. 2011
Published: 19 September 2011
Transposable elements (TEs) in the human genome may contribute to molecular evolution, hereditary diseases and cancer [1–3]. Therefore, analyzing the impact of TEs in the genome is necessary to better characterize genetic events related to tumorigenesis. Here, we used a computational approach to identify TE insertions in publicly available data for exome sequences in lymphoblastoid and breast tumor cells derived from the same patient.
A total of 29,340, sequences from the cell lines HCC1954 (18,365,271) and HCC1954BL (10,975,107) were used to investigate gene fusion with TEs (gfTEs) [4, 5]. The RepeatMasker and Burrows-Wheeler Alignment (BWA) tools were used to identify and to map gfTEs, respectively. We also used BEDTools to find overlaps between gfTEs and genome annotations. Human mRNAs and RepeatMasker tracks were downloaded in BED format from the GRCh37/ hg19 assembly. Repbase was used to filter the eukaryotic TEs.
Number of genes containing insertion of TEs from different families
We used a computational approach to identify putative cancer-specific gfTEs using human exome capture sequences. Interestingly, the total number of gfTEs was similar in normal and tumor cell lines, but the Gene Ontology analysis revealed an enrichment of insertions in genes encoding protein receptors and cell adhesion molecules. These results suggest that TEs could be contributing to cancer development.
- Cordaux R, Batzer MA: The impact of retrotransposons on human genome evolution. Nat Rev Genet. 2009, 10: 691-703. 10.1038/nrg2640.PubMedPubMed CentralView ArticleGoogle Scholar
- Callinan PA, Batzer MA: Retrotransposable elements and human disease. Genome Dyn. 2006, 1: 104-115.PubMedView ArticleGoogle Scholar
- Zhang W, Edwards A, Fan W, Deininger P, Zhang K: Alu distribution and mutation types of cancer genes. BMC Genomics. 2011, 12: 157-10.1186/1471-2164-12-157.PubMedPubMed CentralView ArticleGoogle Scholar
- Zhao Q, Kirkness EF, Caballero OL, Galante PA, Parmigiani RB, Edsall L, Kuan S, Ye Z, Levy S, Vasconcelos AT, Ren B, de Souza SJ, Camargo AA, Simpson AJ, Strausberg RL: Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing. Genome Biol. 2010, 11: R114-10.1186/gb-2010-11-11-r114.PubMedPubMed CentralView ArticleGoogle Scholar
- Galante PA, Parmigiani RB, Zhao Q, Caballero OL, de Souza JE, Navarro FC, Gerber AL, Nicolás MF, Salim AC, Silva AP, Edsall L, Devalle S, Almeida LG, Ye Z, Kuan S, Pinheiro DG, Tojal I, Pedigoni RG, de Sousa RG, Oliveira TY, de Paula MG, Ohno-Machado L, Kirkness EF, Levy S, da Silva WA, Vasconcelos AT, Ren B, Zago MA, Strausberg RL, Simpson AJ, de Souza SJ, Camargo AA: Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Res. 2011, 39: 6056-6068. 10.1093/nar/gkr221. doi: 10.1093/nar/gkr221PubMedPubMed CentralView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.