Mining for viral fragments in methylation enriched sequencing data.

Area of Science:

• Genomics
• Virology
• Epigenetics

Background:

• Next-generation sequencing (NGS) generates excess data, with up to 30% of fragments in methyl-CpG binding domain (MBD) sequencing being unmappable.
• Viruses are implicated in epigenetics and cancer development, necessitating their detection in biological samples.

Purpose of the Study:

• To develop and evaluate a methodology for identifying viruses in unmapped paired-end MBD-seq data.
• To investigate the presence and prevalence of viruses, particularly HPV, in cervical cancer and precancerous samples.

Main Methods:

• Mapping unmapped reads from MBD-seq data to a comprehensive viral genome database.
• Analyzing viral detection rates and fragment mapping counts in relation to sample type (carcinoma, CIN, normal).
• Validating viral detections using PCR-based assays.

Main Results:

• The methodology successfully identified various viruses, including HPV, in 92 cervical samples.
• HPV was detected in 95% of carcinomas, 100% of CIN2/3, both CIN1 samples, and 55% of normal samples.
• Significant differences in HPV fragment mapping were observed between normal and malignant/precancerous cervical samples, indicating varying viral loads and methylation.

Conclusions:

• The proposed method effectively identifies methylated viral sequences in MBD-seq data at low additional cost.
• This approach provides valuable insights into viral presence, concentration, and types, despite limitations in a priori viral genome knowledge.
• The findings highlight the potential of repurposing unmapped sequencing data for viral discovery in epigenetics and cancer research.