Nanopanel2

Nanopanel2 calls somatic variants from Oxford Nanopore panel sequencing basecalled FAST5 files and phases amplicon variants to produce VCF/TSV variant calls and haplotype maps for clinical and diagnostic analysis of disease-relevant genomic regions.

Key Features:

• Input format: Operates directly on basecalled FAST5 files from Oxford Nanopore Technologies sequencing platforms.
• Output formats: Generates Variant Call Format (VCF) and Tab-Separated Values (TSV) files with variant calls and statistics, and produces haplotype map TSV and PDF files.
• Phasing/haplotype mapping: Performs direct phasing of amplicon variants and reports haplotype distributions for variants that pass quality filters.
• Algorithms and filters: Applies algorithms based on allele probability distributions combined with multiple filtering strategies to distinguish true positives from false positives.
• Sensitivity: Detects single nucleotide variants (SNVs) down to approximately 1% variant allele frequency and insertions/deletions (INDELs) down to approximately 5% variant allele frequency.
• False-positive rate: Maintains a low rate of low-frequency false-positive calls, approximately one per kilobase of amplicon.
• Long-read advantage: Leverages long-read Nanopore panel sequencing to enable direct phasing and detection of co-occurring variants such as drug-resistance mutations.
• Operational performance: Reported to support rapid workflows with turnaround under 48 hours and sequencing costs around $10 per sample.

Scientific Applications:

• Somatic variant calling: Calling somatic variants in Nanopore panel sequencing data for disease-relevant genomic regions.
• Clinical decision-making and diagnostics: Supporting clinical decision-making and genomic diagnostics through sensitive detection and phasing of clinically relevant variants.
• Drug-resistance analysis: Detecting and phasing co-occurring variants, including drug-resistance mutations, that are challenging for short-read sequencing.
• Haplotype distribution analysis: Generating haplotype maps to analyze variant co-occurrence and distributions within amplicons.

Methodology:

Operates on basecalled FAST5 files from Oxford Nanopore, applies algorithms using allele probability distributions and multiple filtering strategies to call and phase amplicon SNVs and INDELs, and outputs VCF, TSV, and haplotype map TSV/PDF files.