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

Area of Science:

• Genomic Medicine
• Bioinformatics
• Prenatal Diagnostics

Background:

• Genomic sequencing, including exome and genome sequencing, is increasingly used for fetal anomaly investigation.
• Broader sequencing approaches generate vast data, necessitating robust bioinformatics pipelines.
• Current laboratory practices for bioinformatics workflows exhibit significant variation.

Purpose of the Study:

• To systematically review current bioinformatics workflows in prenatal sequencing.
• To assess the transparency of reporting and clinical impact of variations in these workflows.
• To identify deficiencies in current reporting standards for bioinformatics methods.

Main Methods:

• Systematic review of prenatal sequencing studies (2018-2022) using a previous review's search strategy.
• Inclusion of 154 articles (89 new records + 65 from prior review).
• Data extraction focused on bioinformatics pipeline details and clinical relevance.

Main Results:

• Reporting of bioinformatics methods was frequently incomplete across studies.
• Omissions included tool names/versions, poorly described quality control, and non-reproducible filtering strategies.
• Deficiencies hinder interpretation of sequencing results and understanding of limitations.

Conclusions:

• Inconsistent reporting of bioinformatics methods in prenatal sequencing compromises reproducibility and clinical interpretation.
• A proposed checklist of essential bioinformatics metrics aims to improve reporting standards.
• Enhanced transparency is needed to support reproducible and clinically meaningful genomic analyses.