NGS BED File QC & Intronic Variant Coverage Review
Resonance Genomics provides research-use-only NGS BED file QC and computational review of existing sequencing target intervals. Our workflow identifies potential gaps in the representation of coding, splice-adjacent, and selected intronic or deep-intronic loci. This independent assessment helps laboratories determine whether specified genomic regions of interest are included in their target BED files and identify candidates for further assay evaluation or capture-design refinement. The scope of each review is agreed upon before analysis.
Review workflows are organized relative to MANE Select and MANE Plus Clinical transcript frameworks where applicable.
Workflow Features
- Research-use-only review of existing NGS target BED intervals against specified coding, splice-adjacent, and intronic loci
- Identification of selected intronic and deep-intronic variants that fall outside supplied target intervals
- MANE Select and MANE Plus Clinical transcript-aware coordinate organization, where applicable
- Configurable exon-padding and splice-region assessment (e.g., ±10–20 bp)
- Identification of potential target-region gaps for laboratory review and optional capture-design refinement
- Structured tabular summaries of included and excluded loci, with reference assembly and coordinate information
- Assembly-specific review using GRCh37 or GRCh38 reference coordinates, as supported by the agreed project workflow
Why This Matters
Targeted NGS panels and exome capture designs are commonly organized around coding exons and selected splice-adjacent regions. However, disease-associated variants may also occur deeper within introns, outside conventional target intervals. As evidence for additional intronic variants emerges, laboratories may benefit from periodically reviewing whether their existing BED files include selected loci relevant to their research or assay scope.
An independent, coordinate-based review can identify candidate gaps between defined genomic regions of interest and the target intervals represented in a laboratory’s BED file. These findings can support decisions about further coverage investigation, potential target-region refinement, or assay development, while preserving the laboratory’s established validation and interpretation processes. Inclusion of a locus in a BED file does not itself establish adequate sequencing depth, capture efficiency, or reliable variant detection.
Structured Review Outputs
- Summary of coding, splice-adjacent, and selected intronic loci evaluated within the agreed review scope
- Identification of specified genomic loci represented within or outside the supplied BED target intervals
- Candidate coverage-gap report highlighting regions for further laboratory investigation
- Reference assembly, genomic coordinates, and transcript annotations where applicable
- Optional recommendations for target-region refinement or additional capture-design review
- Structured tabular results suitable for independent review by the laboratory’s scientific team
Research Use Statement
Resonance Genomics provides this computational workflow for research use only (RUO) and laboratory evaluation. BED-file interval comparisons and proposed target-region refinements do not establish sequencing depth, capture efficiency, analytical sensitivity, or clinical assay performance. All findings and recommendations require independent laboratory review and, where applicable, assay validation. Outputs are not intended for diagnostic reporting, independent clinical decision-making, or final clinical interpretation.
Discuss Workflow
Laboratories interested in reviewing existing NGS target BED files, assessing selected intronic or deep-intronic loci, or exploring capture-design refinement are welcome to contact Resonance Genomics. We can discuss the research objectives, reference assembly, available input information, proposed deliverables, and appropriate data-sharing arrangements before agreeing on the scope of an evaluation. Please do not submit patient-identifiable genomic data or confidential BED files through the general inquiry form.