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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Targeted DNA Sequencing for Tailored Therapies in Children with Extracranial Solid Tumors

by
Nataliya A. Andreeva
1,*,
Tatyana V. Shamanskaya
1,
Denis Y. Kachanov
1,
Nikolay V. Zhukov
1,
Nina V. Gegeliya
1,
Ruslan H. Abasov
1,
Natalia Y. Usman
1,
Anastasia V. Protsvetkina
1,
Dmitry M. Konovalov
1,
Dmitry V. Litvinov
1,
Natalia V. Myakova
1,
Nikolay S. Grachev
1,
Galina A. Novichkova
1 and
Alexander E. Druy
1,2
1
Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117198, Russia
2
Research Institute of Medical Cell Technologies, Yekaterinburg 620026, Russia
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2025, 26(23), 11463; https://doi.org/10.3390/ijms262311463
Submission received: 17 October 2025 / Revised: 18 November 2025 / Accepted: 25 November 2025 / Published: 26 November 2025
(This article belongs to the Section Molecular Oncology)
Versions Notes

Abstract

Next-generation sequencing (NGS) is instrumental for clinical decisions on molecularly targeted therapy (TT). In pediatric oncology, TT is a relatively rare choice administered chiefly on a tumor-agnostic basis. The investigation enrolled 304 pediatric patients with extracranial solid tumors that were diagnosed and treated in 2018–2023. Tumor DNA was sequenced using a customized QiaSeq panel (Qiagen, Hilden, Germany) of genes known to be relevant for pediatric solid tumors, including ALK, BRAF, BRCA1/2, EGFR, FGFR1, KIT, MAP2K1/2, NF1, PDGFRA/B, PIK3CA, PTEN, PTPN11, RAS family genes, etc. The assay allowed detection of nucleotide substitutions and small insertions/deletions, as well as gene copy number alterations. TT sensitivity predictors were identified in 120/304 cases (39.5%): Tier II in 83 patients, Tier IB in 32 patients (almost always ALK in neuroblastoma, n = 31) and Tier IA in 5 patients: BRAF p.V600E (n = 3) and NF1 aberrations (n = 2). TT commenced in 21/304 cases (6.9%), often first-line or as a first relapse therapy (14/21 cases), combined with chemotherapy (TT-CT) in 13 cases. The median of TT duration was 10.9 (range 0.8–43.5) months for single-mode and 12.3 (0.3–61.5) months for TT-CT. Clinical benefit rate was achieved in 14/21 patients (66.7%). At the time of writing, nine patients (42.8%) have no progression and are still on treatment for 30.4 months (range 10.3–40.5) after the start of TT. The median time to the best response to TT was 6 (range 0.8–12.3) months. The tolerance was generally good: the therapy was discontinued for toxicity in only one case. The study provides a TT-focused prospective analysis still rare in pediatric oncology. The outcomes indicate satisfactory tolerance and promising efficacy of TT, prompting an update of current treatment standards for several pediatric cancers.
Keywords: precision treatment; targeted treatment; molecular therapy; NGS; DNA sequencing; children; neuroblastoma precision treatment; targeted treatment; molecular therapy; NGS; DNA sequencing; children; neuroblastoma

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MDPI and ACS Style

Andreeva, N.A.; Shamanskaya, T.V.; Kachanov, D.Y.; Zhukov, N.V.; Gegeliya, N.V.; Abasov, R.H.; Usman, N.Y.; Protsvetkina, A.V.; Konovalov, D.M.; Litvinov, D.V.; et al. Targeted DNA Sequencing for Tailored Therapies in Children with Extracranial Solid Tumors. Int. J. Mol. Sci. 2025, 26, 11463. https://doi.org/10.3390/ijms262311463

AMA Style

Andreeva NA, Shamanskaya TV, Kachanov DY, Zhukov NV, Gegeliya NV, Abasov RH, Usman NY, Protsvetkina AV, Konovalov DM, Litvinov DV, et al. Targeted DNA Sequencing for Tailored Therapies in Children with Extracranial Solid Tumors. International Journal of Molecular Sciences. 2025; 26(23):11463. https://doi.org/10.3390/ijms262311463

Chicago/Turabian Style

Andreeva, Nataliya A., Tatyana V. Shamanskaya, Denis Y. Kachanov, Nikolay V. Zhukov, Nina V. Gegeliya, Ruslan H. Abasov, Natalia Y. Usman, Anastasia V. Protsvetkina, Dmitry M. Konovalov, Dmitry V. Litvinov, and et al. 2025. "Targeted DNA Sequencing for Tailored Therapies in Children with Extracranial Solid Tumors" International Journal of Molecular Sciences 26, no. 23: 11463. https://doi.org/10.3390/ijms262311463

APA Style

Andreeva, N. A., Shamanskaya, T. V., Kachanov, D. Y., Zhukov, N. V., Gegeliya, N. V., Abasov, R. H., Usman, N. Y., Protsvetkina, A. V., Konovalov, D. M., Litvinov, D. V., Myakova, N. V., Grachev, N. S., Novichkova, G. A., & Druy, A. E. (2025). Targeted DNA Sequencing for Tailored Therapies in Children with Extracranial Solid Tumors. International Journal of Molecular Sciences, 26(23), 11463. https://doi.org/10.3390/ijms262311463

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