Nordic Consensus Recommendations for Clinical Bioinformatics in Whole-Genome Sequencing Diagnostics
Developed by 13 clinical bioinformatics units in the Nordic Alliance for Clinical Genomics, these consensus recommendations cover the full WGS diagnostic pipeline: reference genome standards (hg38), structural variant calling with multiple tools, containerized reproducibility, ISO 15189-level quality management, and validation using GIAB truth sets. The guidelines address pipeline testing, sample identity verification through fingerprinting, and the diverse competencies required for clinical bioinformatics operations. This is a practical framework for laboratories scaling up NGS-based diagnostics.
The original study
Recommendations for bioinformatics in clinical practice.
- Authors
- Lavrichenko K, Engdal ES, Marvig RL, Jemt A, Vignes JM, Almusa H, et al.
- Journal
- Genome medicine
- Type
- Journal Article, Review
- PMID
- 41107899
Original abstract
BACKGROUND: Next-generation sequencing (NGS) is well established in clinical diagnostics, and whole-genome sequencing (WGS) is increasingly becoming the method of choice, as a result of lower prices and robust comprehensive data. While guidelines exist for variant interpretation and laboratory quality considerations, there remains a need for standardised bioinformatics practices to ensure clinical consensus, accuracy, reproducibility and comparability. METHODS: This article presents consensus recommendations developed by 13 clinical bioinformatics units participating in the Nordic Alliance for Clinical Genomics (NACG) by expert bioinformaticians working in clinical production. The recommendations are based on clinical practice and focus on analysis types, test and validation, standardisation and accreditation, as well as core competencies and technical management required for clinical bioinformatics operations. RESULTS: Key recommendations include adopting the hg38 genome build as reference, and a standard set of recommended analyses, including the use of multiple tools for structural variant (SV) calling and in-house data sets for filtering recurrent calls. Clinical bioinformatics in production should operate at standards similar to ISO 15189, utilising off-grid clinical-grade high-performance computing systems, standardised file formats and strict version control. Reproducibility should be ensured through containerised software environments. Pipelines must be documented and tested for accuracy and reproducibility, minimally covering unit, integration and end-to-end testing. Standard truth sets such as GIAB and SEQC2 for germline and somatic variant calling, respectively, should be supplemented by recall testing of real human samples that have been previously tested using a validated method. Data integrity must be verified using file hashing, while sample identity must be confirmed through fingerprinting and genetically inferred identification markers such as sex and relatedness. Finally, clinical bioinformatics should encompass diverse skills, including software development, data management, quality assurance and domain expertise in human genetics. CONCLUSIONS: These recommendations provide a consensus framework for standardising bioinformatics practices across clinical WGS applications and can serve as a practical guide to facilities that are new to large-scale sequencing-based diagnostics, or as a reference for those who already run high-volume clinical production using NGS.