Next-generation sequencing (NGS) technologies are transforming regulated drug development by enabling high-resolution analysis for applications such as gene editing, adventitious agent detection, and sequence confirmation. However, integrating NGS into GMP and GLP workflows introduces significant challenges related to data integrity and compliance with 21 CFR Part 11. These regulations require strict controls over electronic records, including secure audit trails, validated software, and traceable data handling. This whitepaper outlines a practical framework for implementing NGS workflows that meet regulatory expectations, drawing on Avance Biosciences’ extensive experience in designing compliant, fit-for-purpose sequencing solutions for FDA submissions.