The many logistical and technical challenges associated with sample and data handling in largescale genotyping studies can increase the risk of sample misidentification, which may compromise subsequent analyses. However, the standard quality assurance methods typical for large genotyping arrays can often be further utilized to identify and recover problematic samples. This article emphasizes the importance of identifying and correcting underlying sample misidentification rather than simply excluding known discrepancies, which may potentially include undetected issues. Lastly, we provide a screening protocol to complement standard quality assessments as a guideline for identifying mismatched samples and a tool for assessing the most common causes of sample misidentification. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.
Keywords: GWAS; genotyping; quality control; sample misidentification; screening protocol.
© 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.