eVIDENCE

eVIDENCE enhances detection of low-frequency variants in cell-free DNA (cfDNA) to improve identification of circulating tumor DNA (ctDNA) and support mutation-level analysis in cancer genomics.

Key Features:

• Variant filtering workflow: Implements a specialized filtering workflow for candidate variants from molecular-barcoded targeted sequencing data, including support for ThruPLEX tag-seq (Takara Bio).
• Sequencing data processing: Processes BAM files by removing barcode and stem sequences to generate a refined BAM for downstream analysis.
• Candidate variant detection: Employs Conner software to detect candidate variants from processed sequencing data.
• Low-frequency sensitivity: Detects single nucleotide variants (SNVs) and insertions/deletions (indels) with reported variant allele frequencies (VAFs) as low as 0.2%.
• Targeted panel integration: Integrates targeted sequencing data with a custom gene panel of approximately 80 genes relevant to hepatocellular carcinoma.

Scientific Applications:

• Cancer genomics (HCC): Applied to cfDNA from hepatocellular carcinoma patients, reducing an initial set of over 45,800 variants to 70 SNVs and 7 indels.
• Variant validation: Supported validation of 25 unbiasedly selected low-frequency variants, demonstrating specificity for true positives.
• Detection of viral integration and rearrangements: Facilitated detection of hepatitis B virus integration sites and genomic rearrangements in the TERT region from cfDNA.

Methodology:

Processes BAM files by removing barcode and stem sequences, performs initial variant calling (from molecular-barcoded targeted sequencing using ThruPLEX tag-seq), employs Conner for candidate detection, integrates data with a ~80-gene custom panel, and applies eVIDENCE's variant-filtering workflow.