Brain cancer is one of the most challenging diseases in global medicine, mainly due to the high complexity involved in classifying tumor types. Clinicians rely on a combination of patient history, clinical symptoms, radiological imaging (such as MRI and CT scans), and histopathology. However, relying solely on traditional histopathology is no longer sufficient for accurate diagnosis. Molecular genetics testing now plays a crucial role in both the diagnosis and treatment planning for brain cancer, with its cost being minimal compared to the overall expenses of patient care.

In recent years, the combination of advanced DNA and epigenome analysis technologies, along with breakthroughs in bioinformatics, has become essential for helping physicians classify and diagnose brain tumors with greater precision. These methods focus on detecting multiple biomarkers, including mutations associated with brain cancer, copy number variation (CNV), and epigenome-level data, particularly abnormal DNA methylation patterns. All these indicators can be used effectively to diagnose and classify brain cancer patients.

Recently, the Siriraj Long-read Lab (Si-LoL), under the Siriraj Genomics Center at the Faculty of Medicine Siriraj Hospital, Mahidol University, created an innovation to assist pathologists in diagnosing brain cancer patients more accurately and rapidly. Furthermore, this method is more cost-effective compared to sending tissue samples abroad for testing. Supported by the Siriraj Excellent Innovation Center (SIEIC), the research team has filed a Patent Cooperation Treaty (PCT) application under the title, “Method for Brain Tumor Classification based on The Integrative Analysis of Multiple Biomarkers.”

The Integrative Analysis Innovation: For Maximum Accuracy

The core of this innovation is the process of extracting DNA from patient tumor samples—whether fresh tissue from the operating room, Formalin-Fixed Paraffin-Embedded (FFPE) samples, or cytology samples* (*supported by the team of Prof. Dr. Shanop Shuangshoti). The extracted DNA is then sequenced using Oxford Nanopore technology. The resulting data is simultaneously analyzed across multiple biomolecular dimensions:

1. Gene mutation: Examining specific, localized abnormalities in the genetic sequence.
2. Copy Number Variation (CNV): Gaining an overview of which genes are duplicated or deleted.
3. DNA methylation profiling: Studying the epigenome (or ‘above DNA’) level, which serves as a highly accurate biomarker for patient group classification.

Integrating data from these multiple biomarkers in a single test provides more comprehensive results than conventional methods that require separate tests. This approach effectively reduces time, lowers costs, and increases the accuracy of brain cancer classification.

Alignment with International Standards

The World Health Organization (WHO)’s latest revision of the CNS tumor classification now mandates the use of methylation profiling in diagnosis. The innovation developed at Siriraj directly addresses this global standard, providing pathologists with deeper insights to support decision-making for optimal treatment plans.

Real-World Implementation at Siriraj Hospital

Siriraj Hospital has already started providing this innovative service through the Advanced Lab Service (ALS) channel, managed by the Siriraj Specimen Management Center (SiSC). This service accepts tissue samples from patients—both Thai and international—across the country, ensuring broad access to the testing. This marks a crucial step, demonstrating how laboratory research can be tangibly translated into real-world applications to help patients.

Benefits for Patients and the Thai Healthcare System

This brain cancer diagnostic innovation, developed by Thai researchers, offers several key benefits:

• Patients gain access to faster, more accurate diagnoses at a lower cost, reducing the complexity and expense of sending tissue overseas.
• It supports more targeted treatment decisions.
• It upskills laboratory staff in the globally expanding field of sequencing technology.
• It elevates the capability of the Thai healthcare system to meet international standards.

Research Team and Funding Support

This achievement is the result of collaboration among various units within the Faculty of Medicine Siriraj Hospital:

• Brain Cancer Specialists: (Prof. Sith Sathornsumetee, Asst. Prof. Chottiwat Tansirisithikul, and the surgical team)
• Si-LoL Laboratory: (Miss Sopacha Arayamethakorn, Miss Pattaraporn Nimsamer, Miss Tantip Arigul, Miss Soravee Kaewkarn, Dr. Piroon Jenjaroenpun, and Dr. Thidathip Wongsurawat)
• Siriraj Genomics Center: (Mr. Ekkapong Roothumnong and Prof. Manop Pithukpakorn)
• Department of Pathology: (Assoc. Prof. Pornsuk Cheunsuchon and Assoc. Prof. Jantima Tanboon)
• Master’s Student (Master of Science in Medical Bioinformatics, Graduate School): (Mr. Wichayapat Thongratana)

The Brain Cancer Project has received continuous funding through the Genomics Thailand Project, driven by the Health Systems Research Institute (HSRI) in collaboration with the Ministry of Public Health (MoPH) and the Ministry of Higher Education, Science, Research and Innovation (MHESI). The project also received support from the Siriraj Foundation for the international PCT patent application.

For the 2026 fiscal year, the project has received renewed funding through the Genomics Thailand Project to promote the use of the innovation alongside continuous development, in collaboration with five other institutions.

Conclusion

The innovation for brain cancer classification using the integrative analysis of multiple biomarkers represents a significant leap forward for the Thai medical sector. It demonstrates that fundamental research and the application of bioinformatics technology can lead to genuine, transformative improvements in patient care.