TargetQC: A targeted quality control framework for clinical genomic testing.

Assessment of exon-level, gene-level and pathogenic-site coverage together with variant detection accuracy, over user-defined gene sets and thresholds

TargetQC is a quality control framework for clinical sequencing, configurable through user-defined gene sets, coverage thresholds and variant sets. It assesses exon and gene coverage, identifies regions meeting predefined coverage thresholds, evaluates variant detection accuracy and measures sequencing quality at pathogenic variant sites. It was applied to the reference sample NA12878 and to 665 clinical samples across five exome sequencing platforms and one genome sequencing platform. Two exome platforms achieved the most complete coverage of OMIM coding regions in NA12878, two others the highest coverage compliance in clinical samples, and one exome platform together with genome sequencing the highest variant detection accuracy.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

The merit here is moving quality control away from global figures — mean depth, percentage of bases above a threshold — toward the regions that actually decide a report: OMIM exons and known pathogenic sites. That is the right level of analysis for a laboratory selecting or changing a capture kit, and the framework is generic enough to be re-run on an in-house gene list. Two reservations: the platforms are anonymized, which makes the result impossible to act on, and the framework measures coverage, not final diagnostic yield.

Analysis by Dr Thibaut Benquey