Abstract
| Original language | English |
|---|---|
| Pages (from-to) | 489 |
| Number of pages | 11 |
| Journal | Front. Oncol. |
| Volume | 10 |
| DOIs | |
| Publication status | Published - 2020 |
Keywords
- anchored multiplex PCR
- fusion transcripts
- hybrid capture-based panel
- molecular diagnosis
- NGS
- sarcoma
- Article
- bioinformatics
- controlled study
- dermatofibrosarcoma protuberans
- fluorescence in situ hybridization
- gene expression
- gene sequence
- high throughput sequencing
- human
- human tissue
- major clinical study
- multiplex polymerase chain reaction
- neuroectoderm tumor
- real time polymerase chain reaction
- RNA extraction
- RNA sequence
Fingerprint Dive into the research topics of 'Next-Generation Sequencing Approaches for the Identification of Pathognomonic Fusion Transcripts in Sarcomas: The Experience of the Italian ACC Sarcoma Working Group: Frontiers in Oncology'. Together they form a unique fingerprint.
Cite this
- APA
- Standard
- Harvard
- Vancouver
- Author
- BIBTEX
- RIS
Next-Generation Sequencing Approaches for the Identification of Pathognomonic Fusion Transcripts in Sarcomas: The Experience of the Italian ACC Sarcoma Working Group : Frontiers in Oncology. / Racanelli, D.; Brenca, M.; Baldazzi, D.; Goeman, F.; Casini, B.; De Angelis, B.; Guercio, M.; Milano, G.M.; Tamborini, E.; Busico, A.; Dagrada, G.; Garofalo, C.; Caruso, C.; Brunello, A.; Pignochino, Y.; Berrino, E.; Grignani, G.; Scotlandi, K.; Parra, A.; Hattinger, C.M.; Ibrahim, T.; Mercatali, L.; De Vita, A.; Carriero, M.V.; Pallocca, M.; Loria, R.; Covello, R.; Sbaraglia, M.; Dei Tos, A.P.; Falcioni, R.; Maestro, R.
In: Front. Oncol., Vol. 10, 2020, p. 489.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Next-Generation Sequencing Approaches for the Identification of Pathognomonic Fusion Transcripts in Sarcomas: The Experience of the Italian ACC Sarcoma Working Group
T2 - Frontiers in Oncology
AU - Racanelli, D.
AU - Brenca, M.
AU - Baldazzi, D.
AU - Goeman, F.
AU - Casini, B.
AU - De Angelis, B.
AU - Guercio, M.
AU - Milano, G.M.
AU - Tamborini, E.
AU - Busico, A.
AU - Dagrada, G.
AU - Garofalo, C.
AU - Caruso, C.
AU - Brunello, A.
AU - Pignochino, Y.
AU - Berrino, E.
AU - Grignani, G.
AU - Scotlandi, K.
AU - Parra, A.
AU - Hattinger, C.M.
AU - Ibrahim, T.
AU - Mercatali, L.
AU - De Vita, A.
AU - Carriero, M.V.
AU - Pallocca, M.
AU - Loria, R.
AU - Covello, R.
AU - Sbaraglia, M.
AU - Dei Tos, A.P.
AU - Falcioni, R.
AU - Maestro, R.
N1 - Cited By :3 Export Date: 18 February 2021 Correspondence Address: Maestro, R.; Unit of Oncogenetics and Functional Oncogenomics, Italy; email: maestro@cro.it Funding details: American Ceramic Circle, ACC Funding text 1: For their suggestions and support, the authors are grateful to: Valentina Laquintana (Regina Elena National Cancer Institute, Rome); Sara Piccinin, Daniela Gasparotto, Kelly Fassetta, Beatrice Valenti (Centro di Riferimento Oncologico, CRO Aviano); Franco Locatelli, Simona Caruso, Ida Russo, Rita Alaggio, Rita De Vito, Emanuele Agolini, Martina Rinelli (Bambino Ges? Children's Hospital, IRCCS, Rome); Carolina Zamuner (Veneto Institute of Oncology, Padua, Italy); Massimo Serra, Laura Pazzaglia, Marco Gambarotti, Stefania Benini, Alberto Righi (Istituto Ortopedico Rizzoli, Bologna); Federica Pieri, Michela Tebaldi, Elisa Chiadini (Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori, Meldola). Special thanks for their work go to secretaries, preclinical, and clinical coordinators of the ACC sarcoma working group, the Italian Sarcoma Group (ISG), the Rizzoli and the CRO Aviano Institutes. Funding. This work was supported by the Ministry of Health and Alleanza Contro il Cancro (ACC). References: Fletcher, C.D.M., Bridge, J.A., Hogendoorn, P.C.W., Mertens, F., (2013) WHO Classification of Tumors of Soft Tissue and Bone, , International Agency for Research on Cancer; Schaefer, I.-M., Cote, G.M., Hornick, J.L., Contemporary sarcoma diagnosis, genetics, and genomics (2018) J Clin Oncol, 36, pp. 101-110. , 29220288; Sbaraglia, M., Dei Tos, A.P., The pathology of soft tissue sarcomas (2019) Radiol Med, 124, pp. 266-281. , 29948548; Mertens, F., Antonescu, C.R., Mitelman, F., Gene fusions in soft tissue tumors: recurrent and overlapping pathogenetic themes (2016) Genes Chromosomes Cancer, 55, pp. 291-310. , 26684580; Ugurel, S., Mentzel, T., Utikal, J., Helmbold, P., Mohr, P., Pföhler, C., Neoadjuvant imatinib in advanced primary or locally recurrent dermatofibrosarcoma protuberans: a multicenter phase II DeCOG trial with long-term follow-up (2014) Clin Cancer Res, 20, pp. 499-510. , 24173542; Schöffski, P., Sufliarsky, J., Gelderblom, H., Blay, J.-Y., Strauss, S.J., Stacchiotti, S., Crizotinib in patients with advanced, inoperable inflammatory myofibroblastic tumours with and without anaplastic lymphoma kinase gene alterations (European Organisation for Research and Treatment of Cancer 90101 CREATE): a multicentre, single-drug, prospective, non-randomised phase 2 trial (2018) Lancet Respir Med, 6, pp. 431-441. , 29669701; Laetsch, T.W., DuBois, S.G., Mascarenhas, L., Turpin, B., Federman, N., Albert, C.M., Larotrectinib for paediatric solid tumours harbouring NTRK gene fusions: phase 1 results from a multicentre, open-label, phase 1/2 study (2018) Lancet Oncol, 19, pp. 705-714. , 29606586; Doebele, R.C., Drilon, A., Paz-Ares, L., Siena, S., Shaw, A.T., Farago, A.F., Entrectinib in patients with advanced or metastatic NTRK fusion-positive solid tumours: integrated analysis of three phase 1–2 trials (2020) Lancet Oncol, 21, pp. 271-282. , 31838007; Solomon, J.P., Linkov, I., Rosado, A., Mullaney, K., Rosen, E.Y., Frosina, D., NTRK fusion detection across multiple assays and 33,997 cases: diagnostic implications and pitfalls (2020) Mod Pathol, 33, pp. 38-46. , 31375766; Brenca, M., Maestro, R., Massive parallel sequencing in sarcoma pathobiology: state of the art and perspectives (2015) Expert Rev Anticancer Ther, 15, pp. 1473-1488. , 26536249; Xiao, X., Garbutt, C.C., Hornicek, F., Guo, Z., Duan, Z., Advances in chromosomal translocations and fusion genes in sarcomas and potential therapeutic applications (2018) Cancer Treat Rev, 63, pp. 61-70. , 29247978; Pei, J., Zhao, X., Patchefsky, A.S., Flieder, D.B., Talarchek, J.N., Testa, J.R., Clinical application of RNA sequencing in sarcoma diagnosis: an institutional experience (2019) Medicine, 98, p. e16031. , 31232935; Dobin, A., Gingeras, T.R., Optimizing RNA-Seq Mapping with STAR (2016) Methods Mol Biol, 1415, pp. 245-262. , 27115637; Chen, X., Schulz-Trieglaff, O., Shaw, R., Barnes, B., Schlesinger, F., Källberg, M., Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications (2016) Bioinformatics, 32, pp. 1220-1222. , 26647377; Kim, B., Lee, H., Shin, S., Lee, S.-T., Choi, J.R., Clinical evaluation of massively parallel RNA sequencing for detecting recurrent gene fusions in hematologic malignancies (2019) J Mol Diagn, 21, pp. 163-170. , 30347268; Uhrig, S., (2019) Arriba - Fast and Accurate Gene Fusion Detection from RNA-Seq Data, , https://github.com/suhrig/arriba, Available online at; Haas, B.J., Dobin, A., Li, B., Stransky, N., Pochet, N., Regev, A., Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods (2019) Genome Biol, 20, p. 213. , 31639029; Melsted, P., Hateley, S., Joseph, I.C., Pimentel, H., Bray, N., Pachter, L., Fusion detection and quantification by pseudoalignment (2017) bioRxiv, p. 166322; Lam, S.W., Cleton-Jansen, A.-M., Cleven, A.H.G., Ruano, D., van Wezel, T., Szuhai, K., Molecular analysis of gene fusions in bone and soft tissue tumors by anchored multiplex PCR-based targeted next-generation sequencing (2018) J Mol Diagn, 20, pp. 653-663. , 30139549; Pierron, G., Tirode, F., Lucchesi, C., Reynaud, S., Ballet, S., Cohen-Gogo, S., A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion (2012) Nat Genet, 44, pp. 461-466. , 22387997; Panagopoulos, I., Thorsen, J., Gorunova, L., Haugom, L., Bjerkehagen, B., Davidson, B., Fusion of the ZC3H7B and BCOR genes in endometrial stromal sarcomas carrying an X;22-translocation (2013) Genes Chromosomes Cancer, 52, pp. 610-618. , 23580382; Specht, K., Zhang, L., Sung, Y.-S., Nucci, M., Dry, S., Vaiyapuri, S., Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas (2016) Am J Surg Pathol, 40, pp. 433-442. , 26752546; Yoshida, A., Arai, Y., Hama, N., Chikuta, H., Bando, Y., Nakano, S., Expanding the clinicopathologic and molecular spectrum of BCOR-associated sarcomas in adults (2020) Histopathology, 76, pp. 509-520. , 31647130; Urbini, M., Astolfi, A., Pantaleo, M.A., Serravalle, S., Dei Tos, A.P., Picci, P., HSPA8 as a novel fusion partner of NR4A3 in extraskeletal myxoid chondrosarcoma (2017) Genes Chromosomes Cancer, 56, pp. 582-586. , 28383167; Carter, C.S., East, E.G., McHugh, J.B., Biphenotypic sinonasal sarcoma: a review and update (2018) Arch Pathol Laboratory Med, 142, pp. 1196-1201. , 30281368; Bridge, J.A., Sumegi, J., Druta, M., Bui, M.M., Henderson-Jackson, E., Linos, K., Clinical, pathological, and genomic features of EWSR1-PATZ1 fusion sarcoma (2019) Mod Pathol, 32, pp. 1593-1604. , 31189996; Miettinen, M., Felisiak-Golabek, A., Luiña Contreras, A., Glod, J., Kaplan, R.N., Killian, J.K., New fusion sarcomas: histopathology and clinical significance of selected entities (2019) Hum Pathol, 86, pp. 57-65. , 30633925
PY - 2020
Y1 - 2020
N2 - This work describes the set-up of a shared platform among the laboratories of the Alleanza Contro il Cancro (ACC) Italian Research Network for the identification of fusion transcripts in sarcomas by using Next Generation Sequencing (NGS). Different NGS approaches, including anchored multiplex PCR and hybrid capture-based panels, were employed to profile a large set of sarcomas of different histotypes. The analysis confirmed the reliability of NGS RNA-based approaches in detecting sarcoma-specific rearrangements. Overall, the anchored multiplex PCR assay proved to be a fast and easy-to-analyze approach for routine diagnostics laboratories. © Copyright © 2020 Racanelli, Brenca, Baldazzi, Goeman, Casini, De Angelis, Guercio, Milano, Tamborini, Busico, Dagrada, Garofalo, Caruso, Brunello, Pignochino, Berrino, Grignani, Scotlandi, Parra, Hattinger, Ibrahim, Mercatali, De Vita, Carriero, Pallocca, Loria, Covello, Sbaraglia, Dei Tos, Falcioni and Maestro.
AB - This work describes the set-up of a shared platform among the laboratories of the Alleanza Contro il Cancro (ACC) Italian Research Network for the identification of fusion transcripts in sarcomas by using Next Generation Sequencing (NGS). Different NGS approaches, including anchored multiplex PCR and hybrid capture-based panels, were employed to profile a large set of sarcomas of different histotypes. The analysis confirmed the reliability of NGS RNA-based approaches in detecting sarcoma-specific rearrangements. Overall, the anchored multiplex PCR assay proved to be a fast and easy-to-analyze approach for routine diagnostics laboratories. © Copyright © 2020 Racanelli, Brenca, Baldazzi, Goeman, Casini, De Angelis, Guercio, Milano, Tamborini, Busico, Dagrada, Garofalo, Caruso, Brunello, Pignochino, Berrino, Grignani, Scotlandi, Parra, Hattinger, Ibrahim, Mercatali, De Vita, Carriero, Pallocca, Loria, Covello, Sbaraglia, Dei Tos, Falcioni and Maestro.
KW - anchored multiplex PCR
KW - fusion transcripts
KW - hybrid capture-based panel
KW - molecular diagnosis
KW - NGS
KW - sarcoma
KW - Article
KW - bioinformatics
KW - controlled study
KW - dermatofibrosarcoma protuberans
KW - fluorescence in situ hybridization
KW - gene expression
KW - gene sequence
KW - high throughput sequencing
KW - human
KW - human tissue
KW - major clinical study
KW - multiplex polymerase chain reaction
KW - neuroectoderm tumor
KW - real time polymerase chain reaction
KW - RNA extraction
KW - RNA sequence
U2 - 10.3389/fonc.2020.00489
DO - 10.3389/fonc.2020.00489
M3 - Article
VL - 10
SP - 489
JO - Front. Oncol.
JF - Front. Oncol.
SN - 2234-943X
ER -