virID

virID identifies microbial-associated reads in metagenomic and RNA-seq datasets to detect known and novel viral sequences and assess microbial associations in diseases such as blastic plasmacytoid dendritic cell neoplasm (BPDCN).

Key Features:

• Microbial Read Identification: Processes unassigned reads from initial analyses such as GATK-PathSeq to detect microbial-associated sequences.
• Sensitivity and Specificity: Demonstrated detection of known oncogenic viruses including Merkel cell polyomavirus, human papillomavirus, and Kaposi's sarcoma herpesvirus across cancer datasets.
• Blind Testing Capability: Operates in blinded analyses to enable unbiased identification of microbial sequences.
• Input Data Types: Applied to RNA sequencing data from skin and bone marrow samples and to control datasets including cutaneous T-cell lymphoma (CTCL) and normal skin.

Scientific Applications:

• BPDCN microbial association investigation: Used to investigate potential associations between microorganisms and blastic plasmacytoid dendritic cell neoplasm (BPDCN).
• Viral detection in cancer cohorts: Identified known viruses such as Merkel cell polyomavirus in Merkel cell carcinoma, human papillomavirus in head and neck squamous cell carcinoma, and Kaposi's sarcoma herpesvirus in Kaposi's sarcoma.
• Comparative analysis with controls: Applied to RNA-seq from BPDCN and control samples including CTCL and normal skin to compare microbial content across sample types.

Methodology:

Initial analysis with GATK-PathSeq to identify known microbial sequences, followed by processing of unassigned reads with virID to uncover remaining microbial associations, including known and novel viral entities.