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Article

Whole-Exome Sequencing Reveals Novel Candidate Driver Mutations and Potential Druggable Mutations in Patients with High-Risk Neuroblastoma

by
Natakorn Nokchan
1,2,
Praewa Suthapot
1,3,4,
Pongsakorn Choochuen
1,2,
Natthapon Khongcharoen
1,2,
Suradej Hongeng
3,
Usanarat Anurathapan
3,
Komwit Surachat
1,2,
Surasak Sangkhathat
1,2,5,* and
Thai Pediatric Cancer Atlas (TPCA) Consortium
†
1
Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
2
Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
3
Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
4
Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
5
Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
*
Author to whom correspondence should be addressed.
†
Membership of the Thai Pediatric Cancer Atlas (TPCA) Consortium is provided in Supplementary Material.
J. Pers. Med. 2024, 14(9), 950; https://doi.org/10.3390/jpm14090950
Submission received: 1 May 2024 / Revised: 26 August 2024 / Accepted: 6 September 2024 / Published: 8 September 2024
(This article belongs to the Section Omics/Informatics)
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Abstract

Neuroblastoma is the most prevalent solid tumor in early childhood, with a 5-year overall survival rate of 40–60% in high-risk cases. Therefore, the identification of novel biomarkers for the diagnosis, prognosis, and therapy of neuroblastoma is crucial for improving the clinical outcomes of these patients. In this study, we conducted the whole-exome sequencing of 48 freshly frozen tumor samples obtained from the Biobank. Somatic variants were identified and selected using a bioinformatics analysis pipeline. The mutational signatures were determined using the Mutalisk online tool. Cancer driver genes and druggable mutations were predicted using the Cancer Genome Interpreter. The most common mutational signature was single base substitution 5. MUC4, MUC16, and FLG were identified as the most frequently mutated genes. Using the Cancer Genome Interpreter, we identified five recurrent cancer driver mutations spanning MUC16, MUC4, ALK, and CTNND1, with the latter being novel and containing a missense mutation, R439C. We also identified 11 putative actionable mutations including NF1 Q1798*, Q2616*, and S636X, ALK F1174L and R1275Q, SETD2 P10L and Q1829E, BRCA1 R612S, NOTCH1 D1670V, ATR S1372L, and FGFR1 N577K. Our findings provide a comprehensive overview of the novel information relevant to the underlying molecular pathogenesis and therapeutic targets of neuroblastoma.
Keywords: neuroblastoma; tumor-only; whole-exome sequencing; somatic variants; mutational signatures; tumor mutational burden; cancer driver gene; druggable mutations neuroblastoma; tumor-only; whole-exome sequencing; somatic variants; mutational signatures; tumor mutational burden; cancer driver gene; druggable mutations

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MDPI and ACS Style

Nokchan, N.; Suthapot, P.; Choochuen, P.; Khongcharoen, N.; Hongeng, S.; Anurathapan, U.; Surachat, K.; Sangkhathat, S.; Thai Pediatric Cancer Atlas (TPCA) Consortium. Whole-Exome Sequencing Reveals Novel Candidate Driver Mutations and Potential Druggable Mutations in Patients with High-Risk Neuroblastoma. J. Pers. Med. 2024, 14, 950. https://doi.org/10.3390/jpm14090950

AMA Style

Nokchan N, Suthapot P, Choochuen P, Khongcharoen N, Hongeng S, Anurathapan U, Surachat K, Sangkhathat S, Thai Pediatric Cancer Atlas (TPCA) Consortium. Whole-Exome Sequencing Reveals Novel Candidate Driver Mutations and Potential Druggable Mutations in Patients with High-Risk Neuroblastoma. Journal of Personalized Medicine. 2024; 14(9):950. https://doi.org/10.3390/jpm14090950

Chicago/Turabian Style

Nokchan, Natakorn, Praewa Suthapot, Pongsakorn Choochuen, Natthapon Khongcharoen, Suradej Hongeng, Usanarat Anurathapan, Komwit Surachat, Surasak Sangkhathat, and Thai Pediatric Cancer Atlas (TPCA) Consortium. 2024. "Whole-Exome Sequencing Reveals Novel Candidate Driver Mutations and Potential Druggable Mutations in Patients with High-Risk Neuroblastoma" Journal of Personalized Medicine 14, no. 9: 950. https://doi.org/10.3390/jpm14090950

APA Style

Nokchan, N., Suthapot, P., Choochuen, P., Khongcharoen, N., Hongeng, S., Anurathapan, U., Surachat, K., Sangkhathat, S., & Thai Pediatric Cancer Atlas (TPCA) Consortium. (2024). Whole-Exome Sequencing Reveals Novel Candidate Driver Mutations and Potential Druggable Mutations in Patients with High-Risk Neuroblastoma. Journal of Personalized Medicine, 14(9), 950. https://doi.org/10.3390/jpm14090950

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