Submitted by thm2008 on November 4, 2015 - 7:41am
| Title | FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. |
| Publication Type | Journal Article |
| Year of Publication | 2010 |
| Authors | Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB |
| Journal | Genome Biol |
| Volume | 11 |
| Issue | 10 |
| Pagination | R104 |
| Date Published | 2010 |
| ISSN | 1474-760X |
| Keywords | Base Sequence, Cell Line, Tumor, Computational Biology, Expressed Sequence Tags, Gene Expression Profiling, Gene Fusion, Gene Rearrangement, Humans, Male, Molecular Sequence Data, Neoplasms, Prostatic Neoplasms, Reverse Transcriptase Polymerase Chain Reaction, RNA, Neoplasm, Sequence Analysis, RNA |
| Abstract | We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements. |
| DOI | 10.1186/gb-2010-11-10-r104 |
| Alternate Journal | Genome Biol. |
| PubMed ID | 20964841 |
| PubMed Central ID | PMC3218660 |
| Grant List | 5R44HG004237 / HG / NHGRI NIH HHS / United States R01CA125612 / CA / NCI NIH HHS / United States RR19895 / RR / NCRR NIH HHS / United States |