Gene test validation and verification

Use public, purchased or laboratory-developed reference samples

Assay validation contains truth sets from major reference providers, including several germline and somatic from Genome in a Bottle, AcroMetrix, Horizon Discovery, and SeraCare. Laboratory-developed ddPCR or Sanger-validated samples can also be made privately available for use.

Sequence the sample and perform the secondary analysis to generate the variant calls

Upload BED file and reference VCF to assay validation

For verifying an assay, sequence the sample according to standard procedure and perform the concordance analysis to monitor the sensitivity (recall) and precision. For validation use a combination of coverage analysis using sample quality control and concordance analysis to optimise read depth and test performance. The system can work separately on technical and clinical targets provided as BED files.

Upload variants from secondary analysis to assay validation and run validation

For concordance analysis the BED file and the VCF file are required, but if the BAM and FASTQ are uploaded as well, the full spectrum of quality metrics will be available for further use in the workflow optimisation process.

Analyse and use sensitivity and precision as evidence for quality audits and accreditations

Analyse sensitivity, precision and F-score, as well as limit of detection (depending on reference material) and obtain a full report on poorly covered regions. Store the reports as evidence of consistent quality for possible audits, accreditation or participation in external quality assessments, such as those run by EMQN, GenQA, or CAP