ChildSeq-RNA: A next-generation sequencing-based diagnostic assay to identify known fusion transcripts in childhood sarcomas

Journal of Molecular Diagnostics

Volumn 16, Issue 3, 2014, Pages 361-370

  Qadir, Mohammed A ^a   Zhan, Shing H ^a   Kwok, Brian ^a   Bruestle, Jeremy ^b   Drees, Becky ^b   Popescu, Oana Eugenia ^c   Sorensen, Poul H ^a,d  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b Spiral Genetics Inc   (United States)

^c CHILDREN S AND WOMEN S HEALTH CENTRE OF BRITISH COLUMBIA   (Canada)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN EWS; TRANSCRIPTION FACTOR ETV6; TRANSCRIPTION FACTOR FKHR; TRANSCRIPTION FACTOR FLI 1; TRANSCRIPTION FACTOR PAX3; TRANSCRIPTION FACTOR PAX7; WT1 PROTEIN; ETV6-NTRK3 FUSION PROTEIN, HUMAN; EWSR1-FLI1 FUSION PROTEIN, HUMAN; ONCOPROTEIN; PAIRED BOX TRANSCRIPTION FACTOR; PAX3-FOXO1A FUSION PROTEIN, HUMAN; RNA;

ARTICLE; CHILD; CHILDHOOD CANCER; CONTROLLED STUDY; DESMOPLASTIC SMALL ROUND CELL TUMOR; ENTROPY; EWING SARCOMA; EXON; FIBROSARCOMA; GENE EXPRESSION; GENE FUSION; HUMAN; HUMAN CELL; MOLECULAR LIBRARY; PRIMARY TUMOR; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RHABDOMYOSARCOMA; RNA ANALYSIS; RNA SEQUENCE; SARCOMA; SARCOMA CELL; EVALUATION STUDY; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; TUMOR CELL LINE;

CELL LINE, TUMOR; CHILD; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; ONCOGENE FUSION; ONCOGENE PROTEINS, FUSION; PAIRED BOX TRANSCRIPTION FACTORS; RNA; SARCOMA; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, RNA;

EID: 84898805213     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2014.01.002     Document Type: Article

References (46)

1. S.L. Cohn Diagnosis and classification of the small round-cell tumors of childhood Am J Pathol 155 1999 11 15
2. J.M. Meis-Kindblom, G. Stenman, and L.G. Kindblom Differential diagnosis of small round cell tumors Semin Diagn Pathol 13 1996 213 241
3. Z. Pohar-Marinsek Difficulties in diagnosing small round cell tumours of childhood from fine needle aspiration cytology samples Cytopathology 19 2008 67 79
4. A. Aurias, C. Rimbaut, D. Buffe, J. Dubousset, and A. Mazabraud Translocation of chromosome 22 in Ewing's sarcoma C R Seances Acad Sci III 296 1983 1105 1107
5. O. Delattre, J. Zucman, B. Plougastel, C. Desmaze, T. Melot, M. Peter, H. Kovar, I. Joubert, P. de Jong, G. Rouleau, A. Aurias, and G. Thomas Gene fusion with an ETS DNA-binding domain caused by chromosome translocation in human tumours Nature 359 1992 162 165
6. O. Delattre, J. Zucman, T. Melot, X.S. Garau, J.M. Zucker, G.M. Lenoir, P.F. Ambros, D. Sheer, C. Turc-Carel, T.J. Triche, A. Aurias, and G. Thomas The Ewing family of tumors: a subgroup of small-round-cell tumors defined by specific chimeric transcripts N Engl J Med 331 1994 294 299
7. M. Peter, J. Couturier, H. Pacquement, J. Michon, G. Thomas, H. Magdelenat, and O. Delattre A new member of the ETS family fused to EWS in Ewing tumors Oncogene 14 1997 1159 1164
8. P.H. Sorensen, S.L. Lessnick, D. Lopez-Terrada, X.F. Liu, T.J. Triche, and C.T. Denny A second Ewing's sarcoma translocation, t(21;22), fuses the EWS gene to another ETS-family transcription factor, ERG Nat Genet 6 1994 146 151
9. F.G. Barr, N. Galili, J. Holick, J.A. Biegel, and G. Rovera Rearrangement of the PAX3 paired box gene in the paediatric solid tumour alveolar rhabdomyosarcoma Nat Genet 3 1993 113 117
10. R.J. Davis, C.M. D'Cruz, M.A. Lovell, J.A. Biegel, and F.G. Barr Fusion of PAX7 to FKHR by the variant t(1;13)(p36;q14) translocation in alveolar rhabdomyosarcoma Cancer Res 54 1994 2869 2872
11. N. Galili, R.J. Davis, W.J. Fredericks, S. Mukhopadhyay, F.J. Rauscher 3rd, B.S. Emanuel, G. Rovera, and F.G. Barr Fusion of a fork head domain gene to PAX3 in the solid tumour alveolar rhabdomyosarcoma Nat Genet 5 1993 230 235
12. W.L. Gerald, J. Rosai, and M. Ladanyi Characterization of the genomic breakpoint and chimeric transcripts in the EWS-WT1 gene fusion of desmoplastic small round cell tumor Proc Natl Acad Sci U S A 92 1995 1028 1032
13. M. Ladanyi, and W. Gerald Fusion of the EWS and WT1 genes in the desmoplastic small round cell tumor Cancer Res 54 1994 2837 2840
14. S.R. Knezevich, D.E. McFadden, W. Tao, J.F. Lim, and P.H. Sorensen A novel ETV6-NTRK3 gene fusion in congenital fibrosarcoma Nat Genet 18 1998 184 187
15. S. Jain, R. Xu, V.G. Prieto, and P. Lee Molecular classification of soft tissue sarcomas and its clinical applications Int J Clin Exp Pathol 3 2010 416 428
16. J.L. Ordóñez, D. Osuna, D.J. García-Domínguez, A.T. Amaral, A.P. Otero-Motta, C. Mackintosh, M.V. Sevillano, M.V. Barbado, T. Hernández, and E. de Alava The clinical relevance of molecular genetics in soft tissue sarcomas Adv Anat Pathol 17 2010 162 181
17. O. Slater, and J. Shipley Clinical relevance of molecular genetics to paediatric sarcomas J Clin Pathol 60 2007 1187 1194
18. F.G. Barr, J. Chatten, C.M. D'Cruz, A.E. Wilson, L.E. Nauta, L.M. Nycum, J.A. Biegel, and R.B. Womer Molecular assays for chromosomal translocations in the diagnosis of pediatric soft tissue sarcomas JAMA 273 1995 553 557
19. I. Machado, R. Noguera, A. Pellin, J.A. Lopez-Guerrero, M. Piqueras, S. Navarro, and A. Llombart-Bosch Molecular diagnosis of Ewing sarcoma family of tumors: a comparative analysis of 560 cases with FISH and RT-PCR Diagn Mol Pathol 18 2009 189 199
20. J.R. Downing, D.R. Head, D.M. Parham, E.C. Douglass, M.G. Hulshof, M.P. Link, T.A. Motroni, H.E. Grier, A.M. Curcio-Brint, and D.N. Shapiro Detection of the (11;22)(q24;q12) translocation of Ewing's sarcoma and peripheral neuroectodermal tumor by reverse transcription polymerase chain reaction Am J Pathol 143 1993 1294 1300
21. P.H. Sorensen, X.F. Liu, O. Delattre, J.M. Rowland, C.A. Biggs, G. Thomas, and T.J. Triche Reverse transcriptase PCR amplification of EWS/FLI-1 fusion transcripts as a diagnostic test for peripheral primitive neuroectodermal tumors of childhood Diagn Mol Pathol 2 1993 147 157
22. R.S. Bridge, V. Rajaram, L.P. Dehner, J.D. Pfeifer, and A. Perry Molecular diagnosis of Ewing sarcoma/primitive neuroectodermal tumor in routinely processed tissue: a comparison of two FISH strategies and RT-PCR in malignant round cell tumors Mod Pathol 19 2006 1 8
23. X. Qian, L. Jin, B.M. Shearer, R.P. Ketterling, S.M. Jalal, and R.V. Lloyd Molecular diagnosis of Ewing's sarcoma/primitive neuroectodermal tumor in formalin-fixed paraffin-embedded tissues by RT-PCR and fluorescence in situ hybridization Diagn Mol Pathol 14 2005 23 28
24. A. Gnirke, A. Melnikov, J. Maguire, P. Rogov, E.M. LeProust, W. Brockman, T. Fennell, G. Giannoukos, S. Fisher, C. Russ, S. Gabriel, D.B. Jaffe, E.S. Lander, and C. Nusbaum Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing Nat Biotechnol 27 2009 182 189
25. L. Mamanova, A.J. Coffey, C.E. Scott, I. Kozarewa, E.H. Turner, A. Kumar, E. Howard, J. Shendure, and D.J. Turner Target-enrichment strategies for next-generation sequencing Nat Methods 7 2010 111 118
26. A. Mortazavi, B.A. Williams, K. Mccue, L. Schaeffer, and B. Wold Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat Methods 5 2008 621 628
27. Z. Wang, M. Gerstein, and M. Snyder RNA-Seq: a revolutionary tool for transcriptomics Nat Rev Genet 10 2009 57 63
28. S. Batra, C.P. Reynolds, and B.J. Maurer Fenretinide cytotoxicity for Ewing's sarcoma and primitive neuroectodermal tumor cell lines is decreased by hypoxia and synergistically enhanced by ceramide modulators Cancer Res 64 2004 5415 5424
29. J.L. Biedler, L. Helson, and B.A. Spengler Morphology and growth, tumorigenicity, and cytogenetics of human neuroblastoma cells in continuous culture Cancer Res 33 1973 2643 2652
30. M.G. Brattain, W.D. Fine, F.M. Khaled, J. Thompson, and D.E. Brattain Heterogeneity of malignant cells from a human colonic carcinoma Cancer Res 41 1981 1751 1756
31. T. Dunn, L. Praissman, N. Hagag, and M.V. Viola ERG gene is translocated in an Ewing's sarcoma cell line Cancer Genet Cytogenet 76 1994 19 22
32. T. Koressaar, and M. Remm Enhancements and modifications of primer design program Primer3 Bioinformatics 23 2007 1289 1291
33. A. Untergrasser, I. Cutcutache, T. Koressaar, J. Ye, B.C. Faircloth, M. Remm, and S.G. Rozen Primer3: new capabilities and interfaces Nucleic Acids Res 40 2012 e115
34. P.Y. Muller, H. Janovjak, A.R. Miserez, and Z. Dobbie Processing of gene expression data generated by quantitative real-time RT-PCR Biotechniques 32 2002 1372 1378
35. T.F. Smith, and M.S. Waterman Identification of common molecular subsequences J Mol Biol 147 1981 195 197
36. A. Agresti, and D.B. Hitchcock Bayesian inference for categorical data analysis Stat Methods Appl 14 2005 297 330
37. C.E. Shannon A mathematical theory of communication Bell Syst Tech J 27 1948 379 423
38. W.R. Pearson, and D.J. Lipman Improved tools for biological sequence comparison Proc Natl Acad Sci U S A 85 1988 2444 2448
39. S.A. Forbes, N. Bindal, S. Bamford, C. Cole, C.Y. Kok, D. Beare, M. Jia, R. Shepherd, K. Leung, A. Menzies, J.W. Teague, P.J. Campbell, M.R. Stratton, and P.A. Futreal COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer Nucleic Acids Res 39 2011 D945 D950
40. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin 1000 Genome Project Data Processing Subgroup The sequence alignment/map (SAM) format and SAMtools Bioinformatics 25 2009 2078 2079
41. A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
42. R.D. Morin, M. Mendez-Lago, A.J. Mungall, R. Goya, K.L. Mungall, and R.D. Corbett et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma Nature 476 2011 298 303
43. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler Transform Bioinformatics 25 2009 1754 1760
44. J.Z. Levin, M.F. Berger, X. Adiconis, P. Rogov, A. Melnikov, T. Fennell, C. Nusbaum, L.A. Garraway, and A. Gnirke Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts Genome Biol 10 2009 R115
45. Q. Wang, J. Xia, P. Jia, W. Pao, and Z. Zhao Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives Brief Bioinform 14 2013 506 519
46. R.T. Sweeney, B. Zhang, S.X. Zhu, S. Varma, K.S. Smith, S.B. Montgomery, M. van de Rijn, J. Zehnder, and R.B. West Desktop transcriptome sequencing from archival tissue to identify clinically relevant translocations Am J Surg Pathol 37 2013 796 803