ViralMBD

ViralMBD identifies viral fragments in methyl-CpG binding domain (MBD) affinity purification sequencing (MBD-seq) data to detect methylated viral sequences relevant to epigenetics and cancer research.

Key Features:

• Viral detection methodology: Maps non-reference alignable reads from paired-end MBD-seq data to a comprehensive set of viral reference genomes.
• Detected virus range: Identifies viral sequences including phages, adenoviruses, herpesviridae, and human papillomavirus (HPV).
• Application to cervical samples: Validated on 92 cervical tissue and cell line samples covering primary carcinomas, CIN1, CIN2/3, normal tissue, and controls with emphasis on HPV detection.
• Statistical analysis: Reports significant differences in viral load or methylation between normal and carcinoma/CIN2/3 samples with adjusted p-values <10^-5.
• Validation of results: PCR-based assays independently validated 71% of detections and the tool's capacity to distinguish fragments from different HPV types.

Scientific Applications:

• Epigenetics research: Enables identification of methylated viral sequences to study viral effects on host epigenetic modifications.
• Cancer development studies: Supports investigation of viruses such as HPV in cervical cancer progression and lesion grade comparisons.
• Cost-effective analysis: Extracts viral information from otherwise unmapped MBD-seq reads to provide additional biological insight without separate sequencing assays.

Methodology:

Maps unmapped or non-uniquely mapped paired-end MBD-seq reads to a comprehensive viral reference genome set using reference-based alignment of non-reference alignable reads.