A Framework for Bioinformatic Reporting in Prenatal Sequencing: Insights From a Systematic Review

ABSTRACT Genomic sequencing has become a key tool in the investigation of foetal anomalies, with a growing shift from targeted panels to exome and genome sequencing. These broader approaches generate significantly more data, underscoring the need for robust bioinformatics pipelines. However, practices vary widely between laboratories. This systematic review explores current differences in bioinformatics workflows, the transparency of reporting, and the clinical impact of these variations. Using a search strategy from a previous review of prenatal sequencing studies (2018–2022), we identified 89 new records. Combined with 65 from the earlier review, a total of 154 articles were included. Data extraction focused on bioinformatics pipeline details across all analytical stages, with attention to clinical relevance. We found that reporting of bioinformatics methods was frequently incomplete. Tool names and versions were often omitted, quality control steps were poorly described, and filtering strategies lacked reproducibility. These deficiencies in reporting hinder readers from fully interpreting the sequencing results and understanding the potential limitations. To address this, we propose a checklist of essential bioinformatics metrics to improve reporting standards and support reproducible, clinically meaningful analyses.