Comparison of Fluorescence In Situ Hybridization, Next-Generation Sequencing, and DNA Methylation Microarray for Copy...

Area of Science:

• Oncology
• Genetics
• Molecular Diagnostics

Background:

• Gene-level and chromosomal copy number variation (CNV) assessments are crucial for glioma diagnosis.
• Traditional fluorescence in situ hybridization (FISH) is commonly used, but newer methods like next-generation sequencing (NGS) and DNA methylation microarray (DMM) are emerging.
• Comparative performance and concordance of these CNV detection assays in gliomas are not well-established.

Purpose of the Study:

• To systematically compare the performance and concordance of FISH, NGS, and DMM for detecting key CNV parameters in gliomas.
• To identify factors associated with discrepancies between these diagnostic methods.
• To provide recommendations for integrated multiplatform assays in clinical glioma diagnosis.

Main Methods:

• Retrospective cohort study of 104 glioma patients.
• Systematic comparison of FISH, NGS, and DMM for 6 CNV parameters: EGFR, CDKN2A/B, 1p, 19q, chromosome 7, and chromosome 10.
• Statistical analysis to assess concordance and identify factors associated with discordant results.

Main Results:

• High consistency was observed between FISH, NGS, and DMM for epidermal growth factor receptor (EGFR) assessment.
• FISH showed lower concordance with NGS/DMM for other CNV parameters compared to NGS and DMM, which exhibited strong concordance.
• Discordant cases were significantly associated with high-grade gliomas (grade 3/4) and a high fraction of the genome altered, indicating higher malignancy and genomic instability.

Conclusions:

• NGS and DMM demonstrate superior concordance for CNV assessment in gliomas compared to conventional FISH.
• Discrepancies in CNV detection are linked to tumor grade and genomic instability.
• Integrated multiplatform assays are recommended for accurate clinical diagnosis and prognostication of gliomas.