{"entity":{"id":"ngs-bioinformatics-software","kind":"technology","name":"Clinical NGS bioinformatics and variant interpretation","aka":[],"tldr":"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.","status":"established","asOf":"2026-09-08","links":[{"label":"ClinicalTrials.gov NCT03155620: NCI-COG Pediatric MATCH (APEC1621)","url":"https://clinicaltrials.gov/study/NCT03155620"}],"tags":["supporting"],"related":["oncokb","civic","cbioportal"],"cancers":[],"sections":["diagnostics","ai-computation"],"technologies":["cgp","wes-wgs","ai-trial-matching","genomics-cloud-platforms"],"targets":[],"drugs":[],"companies":["sophia-genetics","qiagen","velsera","illumina"],"institutions":[],"pathways":[],"terms":[],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":[],"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"]},"route":"/technologies/ngs-bioinformatics-software/","neighbours":{"collection":[{"id":"cbioportal","kind":"collection","name":"cBioPortal for Cancer Genomics","route":"/collections/cbioportal/"},{"id":"civic","kind":"collection","name":"CIViC","route":"/collections/civic/"},{"id":"oncokb","kind":"collection","name":"OncoKB","route":"/collections/oncokb/"}],"section":[{"id":"ai-computation","kind":"section","name":"AI & Computation","route":"/fronts/ai-computation/"},{"id":"diagnostics","kind":"section","name":"Diagnostics & Biomarkers","route":"/fronts/diagnostics/"}],"technology":[{"id":"ai-trial-matching","kind":"technology","name":"AI trial matching & clinical decision support","route":"/technologies/ai-trial-matching/"},{"id":"variant-knowledgebases","kind":"technology","name":"Cancer variant knowledgebases and molecular tumour boards","route":"/technologies/variant-knowledgebases/"},{"id":"cgp","kind":"technology","name":"Comprehensive genomic profiling","route":"/technologies/cgp/"},{"id":"genomics-cloud-platforms","kind":"technology","name":"Genomics cloud and secure research environments","route":"/technologies/genomics-cloud-platforms/"},{"id":"liquid-biopsy","kind":"technology","name":"Liquid biopsy (ctDNA)","route":"/technologies/liquid-biopsy/"},{"id":"mrd-testing","kind":"technology","name":"MRD / molecular residual disease testing","route":"/technologies/mrd-testing/"},{"id":"wes-wgs","kind":"technology","name":"Whole-exome & whole-genome sequencing","route":"/technologies/wes-wgs/"}],"company":[{"id":"illumina","kind":"company","name":"Illumina","route":"/companies/illumina/"},{"id":"qiagen","kind":"company","name":"QIAGEN","route":"/companies/qiagen/"},{"id":"sophia-genetics","kind":"company","name":"SOPHiA GENETICS","route":"/companies/sophia-genetics/"},{"id":"velsera","kind":"company","name":"Velsera (Seven Bridges and Pierian)","route":"/companies/velsera/"}],"paper":[{"id":"paper-yaeger-metastatic-colorectal-genomic-landscape-cancer-cell-2018","kind":"paper","name":"Clinical sequencing defines the genomic landscape of metastatic colorectal cancer","route":"/key-papers/paper-yaeger-metastatic-colorectal-genomic-landscape-cancer-cell-2018/"}],"cancer":[{"id":"cmml","kind":"cancer","name":"Chronic myelomonocytic leukaemia and MDS/MPN overlap neoplasms","route":"/cancers/cmml/"}],"trial":[{"id":"pediatric-match","kind":"trial","name":"NCI-COG Pediatric MATCH (APEC1621)","route":"/trials/pediatric-match/"},{"id":"nci-match","kind":"trial","name":"NCI-MATCH (EAY131)","route":"/trials/nci-match/"}],"term":[{"id":"star-salmon","kind":"term","name":"STAR and Salmon (RNA-seq alignment and quantification)","route":"/terms/star-salmon/"},{"id":"variant-calling","kind":"term","name":"Variant calling","route":"/terms/variant-calling/"}]}}