Evolving techniques for gene fusion detection in soft tissue tumours

Histopathology

Volumn 64, Issue 1, 2014, Pages 151-162

  Mertens, Fredrik ^a   Tayebwa, Johnbosco ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Gene fusion; Next generation sequencing; Sarcoma; Soft tissue

Indexed keywords

BCR ABL PROTEIN; DNA; GENOMIC DNA; MESSENGER RNA; MYC PROTEIN; POLYADENYLIC ACID; RNA; STAT6 PROTEIN; TRANSCRIPTION FACTOR PAX3; TRANSCRIPTOME;

BURKITT LYMPHOMA; CARCINOGENESIS; CHONDROSARCOMA; CHROMOSOME ABERRATION; CHROMOSOME ANALYSIS; CHROMOSOME BANDING PATTERN; CHROMOSOME REARRANGEMENT; CHROMOSOME TRANSLOCATION; CHRONIC MYELOID LEUKEMIA; CYTOGENETICS; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; GENE FUSION; GENE SEQUENCE; HUMAN; IN VITRO STUDY; KARYOTYPE; MOLECULAR GENETICS; NEXT GENERATION SEQUENCING; NONHUMAN; ONCOGENE C MYC; ONCOGENE MYC; PRIORITY JOURNAL; REGULATORY SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RHABDOMYOSARCOMA; RNA SEQUENCE; SERIAL ANALYSIS OF GENE EXPRESSION; SOFT TISSUE TUMOR; SOLITARY FIBROUS TUMOR; SOMATIC MUTATION; UPREGULATION;

GENE FUSION; NEXT-GENERATION SEQUENCING; SARCOMA; SOFT TISSUE;

GENE REARRANGEMENT; GENETIC TECHNIQUES; HUMANS; ONCOGENE PROTEINS, FUSION; SARCOMA;

EID: 84889635690     PISSN: 03090167     EISSN: 13652559     Source Type: Journal    
DOI: 10.1111/his.12272     Document Type: Review

References (61)

1. Boveri T. Zur frage der entstehung maligner tumoren. Jena: Gustav Fisher Verlag, 1914.
2. Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature 2009; 458; 719-724.
3. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW. Cancer genome landscapes. Science 2013; 339; 1546-1558.
4. Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat. Rev. Cancer 2007; 7; 233-245.
5. Straessler KM, Jones KB, Hu H et al. Modeling clear cell sarcomagenesis in the mouse: cell of origin differentiation state impacts tumor characteristics. Cancer Cell 2013; 23; 215-227.
6. Druker BJ. Translation of the Philadelphia chromosome into therapy for CML. Blood 2008; 112; 4808-4817.
7. Mano H. ALKoma: a cancer subtype with a shared target. Cancer Discov. 2012; 2; 495-502.
8. Gisselsson D. Cytogenetic methods. In Heim S, Mitelman F, eds. Cancer cytogenetics, 3rd edn. Hoboken, NJ: Wiley-Blackwell, 2009; 9-16.
9. Mitelman F, Johansson B, Mertens F. Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat. Genet. 2004; 36; 331-334.
10. Mitelman F, Johansson B, Mertens F eds. Mitelman database of chromosome aberrations and gene fusions in cancer (2013). http://cgap.nci.nih.gov/Chromosomes/Mitelman (accessed 30 May 2013).
11. Albertson DG, Pinkel D. Genomic microarrays in human genetic disease and cancer. Hum. Mol. Genet. 2003; 12; R145-R152.
12. Sinclair PB, Nacheva EP, Leversha M et al. Large deletions at the t(9;22) breakpoint are common and may identify a poor-prognosis subgroup of patients with chronic myeloid leukemia. Blood 2000; 95; 738-744.
13. Tomlins SA, Rhodes DR, Perner S et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005; 310; 644-648.
14. Wang L, Motoi T, Khanin R et al. Identification of a novel, recurrent HEY1-NCOA2 fusion in mesenchymal chondrosarcoma based on a genome-wide screen of exon-level expression data. Genes Chromosom. Cancer 2012; 51; 127-139.
15. Lovf M, Thomassen GOS, Bakken AC et al. Fusion gene microarray reveals cancer type-specificity among fusion genes. Genes Chromosomes Cancer 2011; 50; 348-357.
16. Shendure J, Ji H. Next-generation DNA sequencing. Nat. Biotechnol. 2008; 26; 1135-1145.
17. Fullwood MJ, Wei C-L, Liu ET, Ruan Y. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009; 19; 521-532.
18. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009; 10; 57-63.
19. Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 2011; 12; 87-98.
20. Sanger F, Air GM, Barrell BG et al. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 1977; 265; 687-695.
21. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA 1977; 74; 5463-5467.
22. Margulies M, Egholm M, Altman WE et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437; 376-380.
23. Shendure J, Porreca GJ, Reppas NB et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005; 309; 1728-1732.
24. Mardis ER. The $1, 000 genome, the $100, 000 analysis? Genome Med. 2010; 2; 84.
25. Volik S, Zhao S, Chin K et al. End-sequence profiling: sequence-based analysis of aberrant genomes. Proc. Natl Acad. Sci. USA 2003; 100; 7696-7701.
26. Volik S, Raphael BJ, Huang G et al. Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res. 2006; 16; 394-404.
27. Fonseca NA, Rung J, Brazma A, Marioni JC. Tools for mapping high-throughput sequencing data. Bioinformatics 2012; 28; 3169-3177.
28. Carrara M, Beccuti M, Lazzarato F et al. State-of-the-art fusion-finder algorithms sensitivity and specificity. Biomed. Res. Int. 2013; 2013; 340620.
29. Ruan Y, Ooi HS, Choo SW et al. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res. 2007; 17; 828-838.
30. Raphael BJ, Volik S, Yu P et al. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol. 2008; 9; R59.
31. Campbell PJ, Stephens PJ, Pleasance ED et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet. 2008; 40; 722-729.
32. Maher CA, Kumar-Sinha C, Cao X et al. Transcriptome sequencing to detect gene fusions in cancer. Nature 2009; 458; 97-101.
33. Maher CA, Palanisamy N, Brenner JC et al. Chimeric transcript discovery by paired-end transcriptome sequencing. Proc. Natl Acad. Sci. USA 2009; 106; 12353-12358.
34. Stephens PJ, McBride DJ, Lin M-L et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 2009; 462; 1005-1010.
35. Asmann YW, Necela BM, Kalari KR et al. Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer. Cancer Res. 2012; 72; 1921-1928.
36. Banerji S, Cibulskis K, Rangel-Escareno C et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature 2012; 486; 405-409.
37. Bass AJ, Lawrence MS, Brace LE et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat. Genet. 2011; 43; 964-968.
38. Imielinski M, Berger AH, Hammerman PS et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 2012; 150; 1107-1120.
39. Mohajeri A, Tayebwa J, Collin A et al. Comprehensive genetic analysis identifies a pathognomonic NAB2/STAT6 fusion gene, non-random secondary genomic imbalances, and a characteristic gene expression profile in solitary fibrous tumor. Genes Chromosomes Cancer 2013; 52; 873-886.
40. Ågerstam H, Lilljebjörn H, Lassen C et al. Fusion gene-mediated truncation of RUNX1 as a potential mechanism underlying disease progression in the 8p11 myeloproliferative syndrome. Genes Chromosomes Cancer 2007; 46; 635-643.
41. Akiva P, Toporik A, Edelheit S et al. Transcription-mediated gene fusion in the human genome. Genome Res. 2006; 16; 30-36.
42. Nacu S, Yuan W, Kan Z et al. Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med. Genomics 2011; 4; 11.
43. Gingeras TR. Implications of chimaeric non-co-linear transcripts. Nature 2009; 461; 206-211.
44. Zaphiropoulos PG. Trans-splicing in higher eukaryotes: implications for cancer development? Front. Genet. 2011; 2; 1-4.
45. Li H, Wang J, Mor G, Sklar J. A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science 2008; 321; 1357-1361.
46. Rickman DS, Pflueger D, Moss B et al. SLC45A3-ELK4 is a novel and frequent erythroblast transformation-specific fusion transcript in prostate cancer. Cancer Res. 2009; 69; 2734-2738.
47. Panagopoulos I. Absence of the JAZF1/SUZ12 chimeric transcript in the immortalized non-neoplastic endometrial stromal cell line T HESCs. Oncol. Lett. 2010; 1; 947-950.
48. Mandahl N, Mertens F. Soft tissue tumors. In Heim S, Mitelman F eds. Cancer cytogenetics, 3rd edn. Hoboken, NJ: Wiley-Blackwell, 2009; 675-711.
49. Delattre O, Zucman J, Plougastel B et al. Gene fusion with an ETS DNA-binding domain caused by chromosome translocation in human tumours. Nature 1992; 359; 162-165.
50. Wachtel M, Dettling M, Koscielniak E et al. Gene expression signatures identify rhabdomyosarcoma subtypes and detect a novel t(2;2)(q35;p23) translocation fusing PAX3 to NCOA1. Cancer Res. 2004; 64; 5539-5545.
51. McPherson A, Hormozdiari F, Zayed A et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput. Biol. 2011; 7; e1001138.
52. Taylor BS, DeCarolis PL, Angeles CV et al. Frequent alterations and epigenetic silencing of differentiation pathway genes in structurally rearranged liposarcomas. Cancer Discov. 2011; 1; 587-597.
53. Lee C-H, Ou W-B, Marino-Enriquez A et al. 14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma. Proc. Natl Acad. Sci. USA 2012; 109; 929-934.
54. Nyquist KB, Panagopoulos I, Thorsen J et al. Whole-transcriptome sequencing identifies novel IRF2BP2-CDX1 fusion gene brought about by translocation t(1;5)(q42;q32) in mesenchymal chondrosarcoma. PLoS ONE 2012; 7; e49705.
55. Pierron G, Tirode F, Lucchesi C et al. A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion. Nat. Genet. 2012; 44; 461-466.
56. Antonescu CR, Le Loarer F, Mosquera J-M et al. Novel YAP1-TFE3 fusion defines a distinct subset of epithelioid hemangioendothelioma. Genes Chromosom. Cancer 2013; 52; 775-784.
57. Chmielecki J, Crago AM, Rosenberg M et al. Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors. Nat. Genet. 2013; 45; 131-132.
58. Mosquera JM, Sboner A, Zhang L et al. Recurrent NCOA2 gene rearrangements in congenital/infantile spindle cell rhabdomyosarcoma. Genes Chromosomes Cancer 2013; 52; 538-550.
59. Panagopoulos I, Thorsen J, Gorunova L et al. Fusion of the ZC3H7B and BCOR genes in endometrial stromal sarcomas carrying an X;22-translocation. Genes Chromosomes Cancer 2013; 52; 610-618.
60. Robinson DR, Wu Y-M, Kalyana-Sundaram S et al. Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing. Nat. Genet. 2013; 45; 180-185.
61. Panagopoulos I, Thorsen J, Gorunova L et al. RNA sequencing identifies fusion of the EWSR1 and YY1 genes in mesothelioma with t(14;22)(q32;q12). Genes Chromosomes Cancer 2013; 52; 733-740.