{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T07:25:26Z","timestamp":1782285926210,"version":"3.54.5"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Next generation sequencing technology generates high-throughput data, which allows us to detect fusion genes at both transcript and genomic levels. To detect fusion genes, the current bioinformatics tools heavily rely on paired-end approaches and overlook the importance of reads that span fusion junctions. Thus there is a need to develop an efficient aligner to detect fusion events by accurate mapping of these junction-spanning single reads, particularly when the read gets longer with the improvement in sequencing technology.<\/jats:p>\n               <jats:p>Results: We present a novel method, FusionMap, which aligns fusion reads directly to the genome without prior knowledge of potential fusion regions. FusionMap can detect fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq studies and characterize fusion junctions at base-pair resolution. We showed that FusionMap achieved high sensitivity and specificity in fusion detection on two simulated RNA-Seq datasets, which contained 75 nt paired-end reads. FusionMap achieved substantially higher sensitivity and specificity than the paired-end approach when the inner distance between read pairs was small. Using FusionMap to characterize fusion genes in K562 chronic myeloid leukemia cell line, we further demonstrated its accuracy in fusion detection in both single-end RNA-Seq and gDNA-Seq datasets. These combined results show that FusionMap provides an accurate and systematic solution to detecting fusion events through junction-spanning reads.<\/jats:p>\n               <jats:p>Availability: FusionMap includes reference indexing, read filtering, fusion alignment and reporting in one package. The software is free for noncommercial use at (http:\/\/www.omicsoft.com\/fusionmap).<\/jats:p>\n               <jats:p>Contact: \u00a0ge@amgen.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr310","type":"journal-article","created":{"date-parts":[[2011,5,19]],"date-time":"2011-05-19T02:22:22Z","timestamp":1305771742000},"page":"1922-1928","source":"Crossref","is-referenced-by-count":236,"title":["FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution"],"prefix":"10.1093","volume":"27","author":[{"given":"Huanying","family":"Ge","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kejun","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Todd","family":"Juan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Newman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wolfgang","family":"Hoeck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,5,18]]},"reference":[{"key":"2023012712453072500_B1","doi-asserted-by":"crossref","first-page":"4570","DOI":"10.1093\/nar\/gkq211","article-title":"Detection of splice junctions from paired-end RNA-seq data by SpliceMap","volume":"38","author":"Au","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012712453072500_B2","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1101\/gr.103697.109","article-title":"Integrative analysis of the melanoma transcriptome","volume":"20","author":"Berger","year":"2010","journal-title":"Genome Res."},{"key":"2023012712453072500_B3","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature05874","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project","volume":"447","author":"Birney","year":"2007","journal-title":"Nature"},{"key":"2023012712453072500_B4","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/ng.128","article-title":"Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing","volume":"40","author":"Campbell","year":"2008","journal-title":"Nat. Genet."},{"key":"2023012712453072500_B5","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1002\/path.2632","article-title":"Fusion genes and chromosome translocations in the common epithelial cancers","volume":"220","author":"Edwards","year":"2009","journal-title":"J. Pathol."},{"key":"2023012712453072500_B6","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1101\/gr.080259.108","article-title":"A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome","volume":"19","author":"Hampton","year":"2009","journal-title":"Genome Res."},{"key":"2023012712453072500_B7","author":"Illumina","year":"2010","journal-title":"SBS sequencing Kit v5 reagent preparation guide."},{"key":"2023012712453072500_B8","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012712453072500_B9","doi-asserted-by":"crossref","first-page":"R115","DOI":"10.1186\/gb-2009-10-10-r115","article-title":"Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts","volume":"10","author":"Levin","year":"2009","journal-title":"Genome Biol."},{"key":"2023012712453072500_B10","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1126\/science.2408149","article-title":"Tyrosine kinase activity and transformation potency of bcr-abl oncogene products","volume":"247","author":"Lugo","year":"1990","journal-title":"Science"},{"key":"2023012712453072500_B11","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/nature07638","article-title":"Transcriptome sequencing to detect gene fusions in cancer","volume":"458","author":"Maher","year":"2009","journal-title":"Nature"},{"key":"2023012712453072500_B12","doi-asserted-by":"crossref","first-page":"12353","DOI":"10.1073\/pnas.0904720106","article-title":"Chimeric transcript discovery by paired-end transcriptome sequencing","volume":"106","author":"Maher","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012712453072500_B13","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/2524","article-title":"High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays","volume":"20","author":"Pinkel","year":"1998","journal-title":"Nat. Genet."},{"key":"2023012712453072500_B14","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1182\/blood-2008-03-144790","article-title":"Molecular biology of bcr-abl1-positive chronic myeloid leukemia","volume":"113","author":"Quintas-Cardama","year":"2009","journal-title":"Blood"},{"key":"2023012712453072500_B15","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.cell.2009.04.034","article-title":"Commonality but diversity in cancer gene fusions","volume":"137","author":"Rabbitts","year":"2009","journal-title":"Cell"},{"key":"2023012712453072500_B16","doi-asserted-by":"crossref","first-page":"D871","DOI":"10.1093\/nar\/gkq1017","article-title":"Encode whole-genome data in the ucsc genome browser (2011 update)","volume":"39","author":"Raney","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012712453072500_B17","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/nature05329","article-title":"Global variation in copy number in the human genome","volume":"444","author":"Redon","year":"2006","journal-title":"Nature"},{"key":"2023012712453072500_B18","doi-asserted-by":"crossref","first-page":"R104","DOI":"10.1186\/gb-2010-11-10-r104","article-title":"FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data","volume":"11","author":"Sboner","year":"2010","journal-title":"Genome Biol."},{"key":"2023012712453072500_B19","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1186\/gm191","article-title":"Detection of DNA fusion junctions for BCR-ABL translocations by Anchored ChromPET","volume":"2","author":"Shibata","year":"2010","journal-title":"Genome Med."},{"key":"2023012712453072500_B20","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1471-2164-10-22","article-title":"BioMart\u2013biological queries made easy","volume":"10","author":"Smedley","year":"2009","journal-title":"BMC Genomics"},{"key":"2023012712453072500_B21","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1126\/science.2237408","article-title":"Detection of bcr-abl fusion in chronic myelogeneous leukemia by in situ hybridization","volume":"250","author":"Tkachuk","year":"1990","journal-title":"Science"},{"key":"2023012712453072500_B22","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1126\/science.1117679","article-title":"Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer","volume":"310","author":"Tomlins","year":"2005","journal-title":"Science"},{"key":"2023012712453072500_B23","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012712453072500_B24","doi-asserted-by":"crossref","first-page":"e178","DOI":"10.1093\/nar\/gkq622","article-title":"MapSplice: accurate mapping of RNA-seq reads for splice junction discovery","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012712453072500_B25","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1093\/bioinformatics\/btq057","article-title":"Fast and SNP-tolerant detection of complex variants and splicing in short reads","volume":"26","author":"Wu","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/14\/1922\/48933307\/bioinformatics_27_14_1922.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/14\/1922\/48933307\/bioinformatics_27_14_1922.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:37:47Z","timestamp":1674826667000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/14\/1922\/194689"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,5,18]]},"references-count":25,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2011,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr310","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2011,7]]},"published":{"date-parts":[[2011,5,18]]}}}