Gene Fusion Markup Language: A prototype for exchanging gene fusion data

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Kalyana Sundaram, Shanker ^a,b   Shanmugam, Achiraman ^b   Chinnaiyan, Arul M ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b BHARATHIDASAN UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED ANALYSIS; CUTTING EDGE TECHNOLOGY; DATA ACCESSIBILITY; DATA REPRESENTATIONS; FUNCTIONAL CHARACTERIZATION; MACHINE-READABLE FORMAT; NEXT-GENERATION SEQUENCING; STRUCTURAL VARIATIONS;

ELECTRONIC DATA INTERCHANGE; MARKUP LANGUAGES; QUERY PROCESSING;

DATA INTEGRATION;

ARTICLE; GENE FUSION; GENETIC DATABASE; GENETIC MARKER; GENETICS; HUMAN; INTERNET; LINGUISTICS; MALE; STANDARD;

DATABASES, GENETIC; GENE FUSION; GENETIC MARKERS; HUMANS; INTERNET; MALE; VOCABULARY, CONTROLLED;

MLCS; MLOWN;

EID: 84867426856     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-269     Document Type: Article

References (40)

1. Nowell PC. The minute chromosome (Phl) in chronic granulocytic leukemia. Blut 1962, 8:65-66.
2. de Klein A, van Kessel AG, Grosveld G, Bartram CR, Hagemeijer A, Bootsma D, Spurr NK, Heisterkamp N, Groffen J, Stephenson JR. A cellular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemia. Nature 1982, 300(5894):765-767.
3. Tomlins SA, Laxman B, Dhanasekaran SM, Helgeson BE, Cao X, Morris DS, Menon A, Jing X, Cao Q, Han B, et al. Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 2007, 448(7153):595-599.
4. Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005, 310(5748):644-648.
5. Palanisamy N, Ateeq B, Kalyana-Sundaram S, Pflueger D, Ramnarayanan K, Shankar S, Han B, Cao Q, Cao X, Suleman K, et al. Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med 2010, 16(7):793-798.
6. Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin PC, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, et al. Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res 2011, 21(1):56-67.
7. Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, Ishikawa S, Fujiwara S, Watanabe H, Kurashina K, Hatanaka H, et al. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature 2007, 448(7153):561-566.
8. Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, Sougnez C, Voet D, Saksena G, Sivachenko A, et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet 2011, 43(10):964-968.
9. Salzman J, Marinelli RJ, Wang PL, Green AE, Nielsen JS, Nelson BH, Drescher CW, Brown PO. ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma. PLoS Biol 2011, 9(9):e1001156.
10. Morozova O, Marra MA. From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors. Biochem Cell Biol 2008, 86(2):81-91.
11. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11(1):31-46.
12. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 2008, 40(6):722-729.
13. Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, et al. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res 2009, 19(2):167-177.
14. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 2011, 39(Database issue):D945-D950.
15. Huret JL, Dessen P, Bernheim A. Atlas of genetics and cytogenetics in oncology and haematology, year 2003. Nucleic Acids Res 2003, 31(1):272-274.
16. Mitelman F, Johansson B, Mertens F. Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat Genet 2004, 36(4):331-334.
17. Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW. Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res 2006, 115(3-4):205-214.
18. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29(4):365-371.
19. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, et al. The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data. Nat Biotechnol 2004, 22(2):177-183.
20. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19(4):524-531.
21. Burgoon LD. The need for standards, not guidelines, in biological data reporting and sharing. Nat Biotech 2006, 24(11):1369-1373.
22. Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, et al. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res 2011, 39(15):e100.
23. Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, Kleivi K, Rye IH, Nyberg S, Wolf M, Borresen-Dale AL, et al. Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol 2011, 12(1):R6.
24. Ge HY, Liu KJ, Juan T, Fang F, Newman M, Hoeck W. FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics 2011, 27(14):1922-1928.
25. Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics 2011, 27(8):1068-1075.
26. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM. Transcriptome sequencing to detect gene fusions in cancer. Nature 2009, 458(7234):97-101.
27. McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol 2011, 7(5):e1001138.
28. Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, et al. FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol 2010, 11(10):R104.
29. Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L. Challenges and standards in integrating surveys of structural variation. Nat Genet 2007, 39(7 Suppl):S7-S15.
30. Kalas M, Puntervoll P, Joseph A, Bartaseviciute E, Topfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, et al. BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics 2010, 26(18):i540-i546.
31. Beisvag V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, et al. Contributions of the EMERALD project to assessing and improving microarray data quality. Biotechniques 2011, 50(1):27-31.
32. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008, 26(5):541-547.
33. Kottmann R, Gray T, Murphy S, Kagan L, Kravitz S, Lombardot T, Field D, Glockner FO. A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). OMICS 2008, 12(2):115-121.
34. Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tarraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, et al. The European nucleotide archive. Nucleic Acids Res 2011, 39(Database issue):D28-D31.
35. Shumway M, Cochrane G, Sugawara H. Archiving next generation sequencing data. Nucleic Acids Res 2010, 38(Database issue):D870-D871.
36. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol 2011, 29(5):415-420.
37. Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K. A standard variation file format for human genome sequences. Genome Biol 2010, 11(8):R88.
38. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2012, 40(Database issue):D13-D25.
39. Kim P, Yoon S, Kim N, Lee S, Ko M, Lee H, Kang H, Kim J. ChimerDB 2.0--a knowledgebase for fusion genes updated. Nucleic Acids Res 2010, 38(Database issue):D81-D85.
40. Nakaya J, Kimura M, Hiroi K, Ido K, Yang W, Tanaka H. Genomic Sequence Variation Markup Language (GSVML). Int J Med Inform 2010, 79(2):130-142.