FusionCancer: A database of cancer fusion genes derived from RNA-seq data

Diagnostic Pathology

Volumn 10, Issue 1, 2015, Pages

  Wang, Yunjin ^a   Wu, Nan ^b   Liu, Jiaqi ^b   Wu, Zhihong ^b   Dong, Dong ^a  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b PEKING UNION MEDICAL COLLEGE HOSPITAL   (China)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

GENE FUSION; GENETIC DATABASE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; NEOPLASM;

DATABASES, GENETIC; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEOPLASMS; ONCOGENE FUSION; RNA;

EID: 84937883258     PISSN: None     EISSN: 17461596     Source Type: Journal    
DOI: 10.1186/s13000-015-0310-4     Document Type: Article

References (21)

1. Edwards PA. Fusion genes and chromosome translocations in the common epithelial cancers. J Pathol. 2010;220:244-54.
2. Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer. 2007;7:233-45.
3. Shyr D, Liu Q. Next generation sequencing in cancer research and clinical application. Biological procedures online. 2013;15:4.
4. Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, Ishikawa S, et al. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature. 2007;448:561-6.
5. Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science. 2005;310:644-8.
6. Robinson DR, Kalyana-Sundaram S, Wu YM, Shankar S, Cao X, Ateeq B, et al. Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer. Nat Med. 2011;17:1646-51.
7. Williams SV, Hurst CD, Knowles MA. Oncogenic FGFR3 gene fusions in bladder cancer. Hum Mol Genet. 2013;22:795-803.
8. Chung GT, Lung RW, Hui AB, Yip KY, Woo JK, Chow C, et al. Identification of a recurrent transforming UBR5-ZNF423 fusion gene in EBV-associated nasopharyngeal carcinoma. J Pathol. 2013;231:158-67.
9. Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, Kleivi K, et al. Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol. 2011;12:R6.
10. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, et al. Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009;458:97-101.
11. Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, et al. Chimeric transcript discovery by paired-end transcriptome sequencing. Proceedings of the National Academy of Sciences of the United States of America 2009;106:12353-12358.
12. Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W. FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics. 2011;27:1922-8.
13. Iyer MK, Chinnaiyan AM, Maher CA. ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011;27:2903-4.
14. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
15. Jia W, Qiu K, He M, Song P, Zhou Q, Zhou F, et al. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biol. 2013;14:R12.
16. Kim N, Kim P, Nam S, Shin S, Lee S. ChimerDB - a knowledgebase for fusion sequences. Nucleic Acids Res. 2006;34:D21-4.
17. Kim DS, Huh JW, Kim HS. HYBRIDdb: a database of hybrid genes in the human genome. Bmc Genomics. 2007;8:128.
18. Kodama Y, Shumway M, Leinonen R, International Nucleotide Sequence Database, C. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res. 2012;40:D54-56.
19. Acland A, Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2014;42:D7-D17.
20. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011;39:D945-950.
21. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57-63.