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- Title
A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
- Authors
Asmann, Yan W; Hossain, Asif; Necela, Brian M; Middha, Sumit; Kalari, Krishna R; Sun, Zhifu; Chai, High-Seng; Williamson, David W; Radisky, Derek; Schroth, Gary P; Kocher, Jean-Pierre A; Perez, Edith A; Thompson, E Aubrey
- Abstract
SnowShoes-FTD, developed for fusion transcript detection in paired-end mRNA-Seq data, employs multiple steps of false positive filtering to nominate fusion transcripts with near 100% confidence. Unique features include: (i) identification of multiple fusion isoforms from two gene partners; (ii) prediction of genomic rearrangements; (iii) identification of exon fusion boundaries; (iv) generation of a 5'-3' fusion spanning sequence for PCR validation; and (v) prediction of the protein sequences, including frame shift and amino acid insertions. We applied SnowShoes-FTD to identify 50 fusion candidates in 22 breast cancer and 9 non-transformed cell lines. Five additional fusion candidates with two isoforms were confirmed. In all, 30 of 55 fusion candidates had in-frame protein products. No fusion transcripts were detected in non-transformed cells. Consideration of the possible functions of a subset of predicted fusion proteins suggests several potentially important functions in transformation, including a possible new mechanism for overexpression of ERBB2 in a HER-positive cell line. The source code of SnowShoes-FTD is provided in two formats: one configured to run on the Sun Grid Engine for parallelization, and the other formatted to run on a single LINUX node. Executables in PERL are available for download from our web site: http://mayoresearch.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.
- Publication
Nucleic acids research, 2011, Vol 39, Issue 15, pe100
- ISSN
1362-4962
- Publication type
Journal Article
- DOI
10.1093/nar/gkr362