Development and Clinical Validation of Molecular Subgrouping in Medulloblastoma by Targeted Methylation Sequencing

Srivastava, Shreya; Lingaiah, Raghavendra; Bhaisora, Kamlesh; Polavarapu, Naveen Kumar; Pal, Lily; Singh, Shalini; Rai, Neha

doi:10.31557/APJCP.2025.26.7.2569

Development and Clinical Validation of Molecular Subgrouping in Medulloblastoma by Targeted Methylation Sequencing

Document Type : Protocol

Authors

¹ Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, UP, India.

² Department of Neurosurgery, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, UP, India.

³ Department of Radiotherapy, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, UP, India.

10.31557/APJCP.2025.26.7.2569

Abstract

Background: The WHO classification of CNS tumors confers promising prognostic value to the molecular classification of medulloblastoma (MB). Next-generation sequencing (NGS) has been the primary method employed for molecular classification through transcriptomic, genomic, or methylation profiling. However, due to cost and infrastructural needs, particularly in developing countries, we propose a relatively simple, rapid, and economical Sanger sequencing-based targeted methylation sequencing method for MB classification and prognostication. Methods: Eleven epigenetic targets were amplified using optimized primers and bisulfite-converted DNA for Sanger sequencing. Chromas software was used for low-quality data trimming and NCBI’s Needleman Wunsch alignment tool was used for sequence alignment to reference. The developed method was applied to tissues from twelve cases of medulloblastoma.Results: Successful interpretation of methylation status in ten out of eleven targets was achieved which was sufficient for classification according to the latest WHO classification of Medulloblastoma tumors. Twelve medulloblastoma cases were classified into WNT (n=2), Group 3 (n=5), and Group 4 (n=5). Conclusion: The developed Sanger sequencing method is a cost-effective, in-house solution that can be used for molecular subgrouping of medulloblastoma. It offers an alternative to NGS, can be done on a case-to-case basis, and does not require high-end infrastructure, sample pooling, or extensive bioinformatics knowledge.

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