Cancer Science & Research
Open AccessDNA Extraction from Cervical Tumors for Molecular Diagnostics and FFPE Quality Control
Authors: Bernard Kafor, Charles Okolie.
Abstract
Cervical cancer molecular testing increasingly depends on the recovery of DNA that is not merely abundant, but analytically fit for the intended assay. This requirement is particularly important for formalin-fixed paraffin-embedded (FFPE) cervical specimens, which constitute the dominant archival material in histopathology laboratories but are affected by fixation-induced fragmentation, cross-linking, base modification, and variable tumor content. This narrative review examines the specimen, pre-analytical, extraction, and quality-control factors that determine the performance of genomic DNA from cervical tumors in human papillomavirus (HPV) genotyping, somatic variant analysis, DNA methylation assays, and next-generation sequencing (NGS). Fresh/frozen tissue provides the highest molecular integrity but is less available in routine practice, whereas FFPE tissue enables retrospective and clinically annotated studies when fixation, tumor enrichment, extraction chemistry, and DNA qualification are controlled. Silica membrane and magnetic bead workflows offer the greatest standardization for routine molecular laboratories; classical organic and salting- out methods remain useful in selected research or resource-constrained settings but require stronger control of purity, reproducibility, and hazardous reagents. Importantly, DNA concentration alone is an inadequate acceptance criterion for degraded specimens. A fit-for-purpose workflow should integrate pathological assessment of tumor fraction, fluorometric DNA quantification, purity assessment, and an amplifiability or fragment-quality metric matched to the downstream platform. For cervical cancer, this approach links histopathology to reliable detection of HPV-related and host genomic alterations while reducing false-negative results and sequencing artifacts. Implementation in low-resource settings should prioritize standardized fixation, tumor enrichment, validated extraction protocols, staged quality control, and targeted molecular assays before expansion to broader sequencing. Such an integrated workflow can improve the reproducibility and clinical interpretability of cervical cancer molecular diagnostics across diverse laboratory environments.
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