# Clinical NGS bioinformatics and variant interpretation

Source: https://onco.cc/technologies/ngs-bioinformatics-software/  
OnCo record `ngs-bioinformatics-software` (Technology). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

Software that turns raw sequencer output into a report of which mutations matter and which drugs they point to.

## Summary

Secondary analysis (alignment, variant calling: Illumina DRAGEN, Sentieon, GATK) and tertiary interpretation (Sophia Genetics DDM, QIAGEN QCI Interpret, PierianDx, Velsera/Seven Bridges, Genoox, Congenica) automate clinical reporting against knowledgebases such as OncoKB, CIViC, ClinVar, and COSMIC. Consistency of variant classification (AMP/ASCO/CAP tiers) across labs and the maintenance of curated knowledge are the quality issues; FDA has recognised OncoKB as a source for level-of-evidence claims.

## Fields

- Kind: Technology
- Status: established
- Last checked: 2026-09-08
- Tags: supporting
- Principle: Pipelines call and annotate variants, apply tumour-normal or panel-of-normals filtering, and match variants to curated evidence tiers to draft clinician reports.
- Strengths: Standardises interpretation; Rapid turnaround; Links to trials
- Limitations: Knowledgebase currency and disagreement; Complex variants (fusions, CNVs, MSI/TMB) need tuned pipelines; LDT and software-as-medical-device regulation evolving

## Sources

- ClinicalTrials.gov NCT03155620: NCI-COG Pediatric MATCH (APEC1621): https://clinicaltrials.gov/study/NCT03155620

## Connected records

- collections: [cBioPortal for Cancer Genomics](https://onco.cc/collections/cbioportal/), [CIViC](https://onco.cc/collections/civic/), [OncoKB](https://onco.cc/collections/oncokb/)
- fronts: [AI & Computation](https://onco.cc/fronts/ai-computation/), [Diagnostics & Biomarkers](https://onco.cc/fronts/diagnostics/)
- technologies: [AI trial matching & clinical decision support](https://onco.cc/technologies/ai-trial-matching/), [Cancer variant knowledgebases and molecular tumour boards](https://onco.cc/technologies/variant-knowledgebases/), [Comprehensive genomic profiling](https://onco.cc/technologies/cgp/), [Genomics cloud and secure research environments](https://onco.cc/technologies/genomics-cloud-platforms/), [Liquid biopsy (ctDNA)](https://onco.cc/technologies/liquid-biopsy/), [MRD / molecular residual disease testing](https://onco.cc/technologies/mrd-testing/), [Whole-exome & whole-genome sequencing](https://onco.cc/technologies/wes-wgs/)
- companies: [Illumina](https://onco.cc/companies/illumina/), [QIAGEN](https://onco.cc/companies/qiagen/), [SOPHiA GENETICS](https://onco.cc/companies/sophia-genetics/), [Velsera (Seven Bridges and Pierian)](https://onco.cc/companies/velsera/)
- key papers: [Clinical sequencing defines the genomic landscape of metastatic colorectal cancer](https://onco.cc/key-papers/paper-yaeger-metastatic-colorectal-genomic-landscape-cancer-cell-2018/)
- cancers: [Chronic myelomonocytic leukaemia and MDS/MPN overlap neoplasms](https://onco.cc/cancers/cmml/)
- trials: [NCI-COG Pediatric MATCH (APEC1621)](https://onco.cc/trials/pediatric-match/), [NCI-MATCH (EAY131)](https://onco.cc/trials/nci-match/)
- terms: [STAR and Salmon (RNA-seq alignment and quantification)](https://onco.cc/terms/star-salmon/), [Variant calling](https://onco.cc/terms/variant-calling/)

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