Molecular Diagnosis in Ewing Family Tumors

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Molecular Diagnosis in Ewing Family Tumors Gabriella Gamberi, Stefania Cocchi, Stefania Benini, Giovanna Magagnoli, Luca Morandi, Jennifer Kreshak, Marco Gambarotti, Piero Picci, Licciana Zanella, Marco Alberghini The Journal of Molecular Diagnostics Volume 13, Issue 3, Pages 313-324 (May 2011) DOI: 10.1016/j.jmoldx.2011.01.004 Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Algorithm showing the protocol used in our laboratory to evaluate the presence of gene rearrangements in tumors with presumptive diagnosis of EFT. FISH, fluorescence in situ hybridization; LSI, locus-specific identifier (probe); FFPET, formalin-fixed paraffin-embedded tissue. The Journal of Molecular Diagnostics 2011 13, 313-324DOI: (10.1016/j.jmoldx.2011.01.004) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 RT-PCR for detection of EWSR1-FLI1 transcript (A) and EWSR1-ERG transcript (B) in the same patient. Lane pt1 is the RT-PCR product obtained from patient's tumor RNA. In A, the band corresponds to a type 2 EWSR1-FLI1 fusion transcript; in B, no band is present, denoting a negative result for the EWSR1-ERG fusion. Lane C is the t(11;22) positive control; the band represents type 1 fusion. Lanes marked neg are negative controls, and the size marker (lane L) is a 100-bp DNA ladder (Promega). The Journal of Molecular Diagnostics 2011 13, 313-324DOI: (10.1016/j.jmoldx.2011.01.004) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Sequence analysis of an EWSR1-FLI1 fusion transcript at the breakpoint region, confirming the fusion of EWSR1 exon 10 to FLI1 exon 5 resulting in t(11;22) type 4. The Journal of Molecular Diagnostics 2011 13, 313-324DOI: (10.1016/j.jmoldx.2011.01.004) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 A: Negative FISH analysis of FUS showing two normal fusion signals. B: Positive FISH analysis of EWSR1 for the same patient; arrows indicate the normal fusion signal and split red and green signals, indicating a rearrangement of one copy of the EWSR1 region. The Journal of Molecular Diagnostics 2011 13, 313-324DOI: (10.1016/j.jmoldx.2011.01.004) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 5 The most prevalent types of exon breakpoints (indicated by boxed numbers) for the t(11;22) EWSR1-FLI1 translocation in EFT, with the number of positive cases identified in our series and the expected band size of the products, using primer pair EWS 22ex7-FLI1 11ex9. The Journal of Molecular Diagnostics 2011 13, 313-324DOI: (10.1016/j.jmoldx.2011.01.004) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 6 The most prevalent types of exon breakpoints (indicated by boxed numbers) for the t(21;22) EWSR1-ERG translocation in EFT, with the number of positive cases identified in our series and the expected band size of the products, using primer pair EWSB-ERGB. The Journal of Molecular Diagnostics 2011 13, 313-324DOI: (10.1016/j.jmoldx.2011.01.004) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 7 The most prevalent types of exon breakpoints (indicated by boxed numbers) for the rare translocations of EFT, with the expected band size of the products, using primer pair EWS 22ex7-FEV 2ex3. In the present study, we detected 1 case with t(2;22) EWSR1-FEV translocation. Translocations t(7;22), t(17;22), and t(20;22) are not yet routinely assessed in our laboratory. The Journal of Molecular Diagnostics 2011 13, 313-324DOI: (10.1016/j.jmoldx.2011.01.004) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 8 The types of exon breakpoints (indicated by boxed numbers) of the rare variants in which the gene FUS is involved. The translocations t(2;16) and t(16;21) are not yet routinely assessed in our laboratory. The Journal of Molecular Diagnostics 2011 13, 313-324DOI: (10.1016/j.jmoldx.2011.01.004) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 9 Schematic of results. EFT, Ewing sarcoma family tumors; FISH, fluorescence in situ hybridization; SRCT, small round-cell tumors; +, positive results; −, negative results. The Journal of Molecular Diagnostics 2011 13, 313-324DOI: (10.1016/j.jmoldx.2011.01.004) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions