Context.—

Sarcomas are rare and highly heterogeneous mesenchymal tumors with deceptive morphologic features that pose a challenge for precise diagnostics. Chromosomal rearrangements generating pathognomonic gene fusions are useful diagnostic markers, traditionally tested using single-plex standard of care assays with limited diagnostic yield. NanoString nCounter technology has emerged as a robust solution with multiplexing capabilities.

Objective.—

To optimize NanoString effective coverage of specific entities and conduct a validation study to support its clinical implementation.

Design.—

We reconfigured a NanoString’s codeset by including a set of probes for detecting gene fusion variants of solitary fibrous tumors, low-grade fibromyxoid sarcomas/sclerosing epithelioid fibrosarcomas, and undifferentiated small round cell sarcomas, totaling 188 probes. A technical validation study was conducted with 96 retrospective samples. Additionally, 76 prospective samples were evaluated to assess the assay’s clinical performance.

Results.—

Both technical and clinical validation studies showed that NanoString’s codeset reached >88% sensitivity and 100% specificity, compared with standard of care methods, and superior diagnostic yield as a first-line test. Our design enabled the detection of almost all fusion variants of NGFI-A binding protein 2 (NAB2) with signal transducer and activator of transcription 6 (STAT6) in solitary fibrous tumors, as well as cAMP responsive element binding protein 3 like 1/2 (CREB3L1/2) rearrangements in all low-grade fibromyxoid sarcoma/sclerosing epithelioid fibrosarcoma cases. Identification of specific gene fusions of undifferentiated small round cell sarcoma was also improved, but additional strategies are necessary to attain full coverage.

Conclusions.—

The NanoString platform demonstrated good sensitivity, specificity, and superior diagnostic yield. It is a cost-effective assay with rapid turnaround time, low sample consumption, streamlined analysis, and easy customization. Therefore, it is a promising alternative first-line diagnostic tool for routine sarcoma testing.

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Author notes

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Salguero-Aranda and Perez equally contributed to this study.

This research was funded by Grupo Español de Investigación en Sarcomas and Fundación Mari Paz Jiménez Casado (IV Beca Trienal FMPJC_GEIS 2020) with assistance to Díaz-Martín; Instituto de Salud Carlos III (PI22/00325) with assistance to Díaz-Martín; Asociación Española Contra el Cáncer (ECAEC222952DEAL Estudios Clínicos AECC 2022) with assistance to de Álava; Junta de Andalucía (PI-0061-2020) with assistance to Salguero-Aranda and de Álava; Asociación Pablo Ugarte, Fundación María García Estrada, Fundación CRIS contra el cáncer; and FARO Niños con Cáncer. Salguero-Aranda was supported by the Instituto de Salud Carlos III (Sara Borrell postdoctoral program, 2022), Perez was supported by the Servicio Andaluz de Salud (Juan Rodés program), and Díaz-Martín was supported by Servicio Andaluz de Salud (Nicolás Monardes program, Consejería de Salud y Familias, Junta de Andalucía). de Álava’s laboratory is supported by the ISCIII-FEDER (PI23-1460) and CIBERONC (CB16/12/00361).

Competing Interests

The authors have no relevant financial interest in the products or companies described in this article.

Supplementary data