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Software that turns raw sequencer output into a report of which mutations matter and which drugs they point to.
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.
Pipelines call and annotate variants, apply tumour-normal or panel-of-normals filtering, and match variants to curated evidence tiers to draft clinician reports.
Nothing recorded yet: a foundation, or a gap to fill.
Dependencies are what this technology cannot be delivered without: manufacturing steps, instruments, software, upstream methods. See its full chain on the map.
Query for this technology: (TITLE:"Clinical NGS bioinformatics and variant interpretation" OR ABSTRACT:"Clinical NGS bioinformatics and variant interpretation") AND (cancer OR tumor OR tumour OR oncology OR carcinoma OR lymphoma OR leukemia OR leukaemia OR myeloma OR sarcoma OR melanoma OR glioma). Results are unfiltered search hits about Clinical NGS bioinformatics and variant interpretation, not a curated reading list.
Shares Illumina, Whole-exome & whole-genome sequencing, Comprehensive genomic profiling, Liquid biopsy (ctDNA) and the tag supporting.
Shares QIAGEN, Liquid biopsy (ctDNA) and the tag supporting.
Shares Genomics cloud and secure research environments and the tag supporting.
Shares Genomics cloud and secure research environments, AI trial matching & clinical decision support, Comprehensive genomic profiling and the tag supporting.
Shares MRD / molecular residual disease testing, Comprehensive genomic profiling and the tag supporting.
Shares AI trial matching & clinical decision support and the tag supporting.
Shares Comprehensive genomic profiling and the tag supporting.
Shares MRD / molecular residual disease testing and the tag supporting.
Open-source projects that implement or serve this technology, from OnCo's own catalogue: licence and last activity as the repository reported them on the day of the fetch. Listing is not endorsement; check the licence before reuse and the validation before clinical use.
An all-in-one preprocessor for sequencing reads (quality control, trimming, UMI handling) used at the head of many cancer pipelines.
The Broad Institute's Genome Analysis Toolkit: variant discovery for germline and somatic DNA, including the Mutect2 somatic caller and copy-number tools most cancer pipelines start from.
A web platform for accessible, reproducible data analysis with thousands of tools, including full somatic variant and cancer workflows on public servers.
The community-standard Nextflow pipeline for bulk RNA sequencing: quality control, alignment or pseudo-alignment and gene counts, used across cancer transcriptomics.
A validated, community-built pipeline for variant calling, RNA-seq and small RNA analysis, with somatic tumour-normal workflows and ensemble calling.
Copy-number detection from targeted and exome sequencing, using both on-target and off-target reads.
A community Nextflow pipeline for germline and somatic variant calling on whole-genome and exome data, with tumour-normal pairs, several callers and annotation built in.
The Ensembl Variant Effect Predictor annotates variants with genes, consequences and population and clinical data; the annotation step in most somatic pipelines.
Commercial and regulated products that serve this technology. Each card says what is behind it: a regulator's database, the literature, a public body's list, or only the company's own words. Listing is not endorsement, and a clearance is a regulatory fact, not a clinical one.
Hardware-accelerated secondary analysis: alignment and variant calling on a field-programmable gate array, which is how many clinical laboratories keep up with their sequencers.
An interpretation platform that automates the first pass of variant prioritisation and drafts the evidence behind each call.
A case management and sign-out environment for molecular pathology, tracking a tumour case from sequencing run to signed report.
A variant interpretation and reporting platform that classifies findings against curated evidence and produces the clinical report a molecular tumour board reads.
Reimplementations of the standard variant calling pipelines, including the somatic ones, engineered to give the same answers much faster on ordinary hardware.
A cloud analysis and interpretation platform hospitals send their sequencing data to, with its own algorithms for variant calling and for scores such as homologous recombination deficiency.
