Comparative Performance of Methylation Array and Bisulfite Sequencing in Ovarian Tissue Samples and Cervical Swabs

IntroductionDNA methylation has emerged as a promising tool for the early detection of ovarian cancer. Consequently, accurate and cost-effective methods for detecting DNA methylation are essential. Although the Infinium Methylation Array provides broad coverage, its high cost limits clinical utility. Bisulfite Sequencing (BS) represents a potential alternative for biomarker validation and diagnostic assay development, provided it can reliably reproduce array-based methylation profiles. This study aims to assess the concordance between BS and Infinium Methylation Array data in ovarian cancer tissues and cervical swabs.MethodsDNA from 55 ovarian cancer tissues and 25 cervical swabs underwent bisulfite conversion and was analyzed using the Infinium Methylation Array and a custom BS panel. We compared the results, focusing on overall methylation levels, Spearman correlation between beta values, and Bland-Altman analysis. We also assessed whether sample clustering patterns by diagnosis were consistent across methods.ResultsMethylation profiles generated by bisulfite sequencing were consistent with those obtained using the Infinium Methylation Array. We observed strong sample-wise correlation between platforms, particularly in ovarian tissue samples. Agreement was slightly lower in cervical swabs, likely due to reduced DNA quality. Diagnostic clustering patterns were broadly preserved across both methods.ConclusionOur results show that BS can reliably replicate results from the Infinium Methylation Array and presents a cost-effective option for analyzing larger sample sets. Moreover, our work may serve as a best-practice guide, as it highlights key challenges associated with working with sequencing library preparation.