A methodological study on the process of prenatal optical genome mapping: focusing on cell culture and quality...

Optical genome mapping (OGM) has demonstrated significant potential in detecting structural variations (SVs) and has been comprehensively evaluated both retrospectively and prospectively in prenatal diagnosis. However, obtaining an adequate volume of amniotic fluid (AF) samples for OGM remains challenging due to the diverse detection techniques currently employed in prenatal diagnosis, which can limit the applicability of OGM in this setting. This study seeks to explore enhancements in cell culture techniques and quality control processes for prenatal samples when utilizing OGM in prenatal diagnosis.

OGM successfully analyzed 188 AF samples with a minimum input of 0.225 million cells for ultra-high-molecular-weight DNA extraction. The study provides a comprehensive overview of the mass of chorionic villus samples, the volume of AF used for cell culture, the duration of culture, and the cell yields obtained for OGM. It was demonstrated that reducing the number of cells used for DNA isolation may not significantly decrease DNA quality for OGM with optimal cell viability and may even yield better results than those achieved with recommended cell amounts. This suggests that the current QC standards may be overly stringent, and that variant analysis remains feasible for some samples that do not meet these criteria. Based on the variant data analysis of these samples, standards appropriate for prenatal samples were summarized.

The findings of this study indicate that a reduced volume of AF sample or a shortened cell culture duration can be achieved in prenatal OGM, thereby enhancing the feasibility of employing OGM in prenatal diagnosis and potentially benefiting patients. Furthermore, data QC metrics suitable for prenatal samples may be more tolerant than previously recommended, necessitating further investigation with larger cohorts to establish specific QC standards for prenatal samples.