Thyroid Cancer Diagnosis via DNA Methylation Analysis
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Solution Overview
Problem
Current diagnostic methods for thyroid cancer, particularly for distinguishing between benign and malignant thyroid tumors and predicting metastasis and recurrence, are inadequate due to limited genome coverage and inability to accurately diagnose encapsulated follicular variant papillary carcinomas before surgery.
Innovation Solution
A method and composition for analyzing the methylation level of specific CpG sites in genomic DNA using the Infinium MethylationEPIC BeadChip technique, targeting genes such as MICAL2, LURAP1L-AS1, PKM2, LTBP1, MMP7, EIF4E, DIAPH1, and LOC100507487, to determine thyroid cancer diagnosis and prognosis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If the Infinium HumanMethylation450 BeadChip platform is used for DNA methylation analysis, then the cost is reduced and sample processing is simplified, but the genome coverage is limited and enhancer regions are not covered
Solution Approach 1:
The patent transitions from the 450K platform to the EPIC platform, changing the technical parameter of genome coverage while maintaining the bead chip methodology. This parameter change enables comprehensive coverage of enhancer regions and over 850,000 CpG sites, resolving the contradiction between ease of manufacture and measurement precision by adopting a more advanced platform that maintains operational simplicity while dramatically improving coverage
2Ease of operation
If fine needle aspiration cytology or core needle biopsy is used for pre-surgical diagnosis, then the diagnostic procedure is non-invasive or minimally invasive, but the ability to accurately differentiate thyroid tumors is insufficient
Solution Approach 1:
The patent introduces DNA methylation analysis as an intermediary diagnostic tool that bridges the gap between minimally invasive sampling and accurate diagnosis. By analyzing methylation patterns in DNA obtained from fine needle aspiration or biopsy samples, the method enables precise tumor classification without requiring more invasive procedures, thus resolving the contradiction between ease of operation and measurement precision
Solution Approach 2:
The patent replaces histological examination (mechanical/optical analysis of tissue structure) with molecular analysis of DNA methylation patterns. This substitution enables accurate pre-surgical diagnosis using minimally invasive samples, as methylation analysis can be performed on DNA extracted from cytology or biopsy specimens, eliminating the need for surgical intervention for diagnostic purposes
3Measurement precision
If surgical intervention is performed for all encapsulated thyroid tumors to ensure accurate diagnosis, then the diagnostic accuracy is improved, but the loss of time and increased patient burden occur
Solution Approach 1:
The patent performs preliminary DNA methylation analysis on samples obtained before surgery (via fine needle aspiration or core needle biopsy) to accurately classify thyroid tumors. This preliminary diagnostic action enables differentiation of benign from malignant tumors pre-surgically, allowing clinicians to avoid unnecessary surgical interventions for benign cases and plan appropriate treatment for malignant cases, thereby reducing overall diagnostic time and patient burden while maintaining high diagnostic accuracy
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Enables accurate and cost-effective diagnosis of thyroid cancer and prediction of recurrence rates by identifying hypermethylated or hypomethylated CpG sites, improving pre-surgical diagnosis and prognosis assessment.
Implementation Method 1
DNA methylation is the most well-known epigenetic modification, occurring from the addition of a methyl group to the 5'-position of a cytosine of cytosine-guanine dinucleotides CpG)
Data Source
AI summary
A method for analyzing the methylation level of a specific CpG site in genomic DNA and a composition suitable to use in the method are provided. The method and composition can provide information useful for diagnosing thyroid cancer or determining the prognosis of patients with thyroid cancer. By using the method and the composition, thyroid cancer can be easily and accurately diagnosed from biological samples at a low cost.