Maximizing the Benefits of WES Data for Clinical Diagnosis of individuals with Differences/Variations of Sex Development

Abstract Variations of Sex Development (VSD) are conditions where genetic and anatomical features do not align with typical male or female characteristics, often due to sex chromosome differences, hormonal imbalances, or other genetic factors. Diagnosing the genetic etiology of VSD can be challenging due to the complex and variable nature of the condition. We developed a whole exome sequencing (WES) pipeline, demonstrating WES as an all-in-one genetic testing tool. It offers reliable karyotyping and SRY gene detection, potentially replacing costly and time-consuming karyotyping and FISH assays. Our pipeline tests all known and candidate VSD genes simultaneously, avoiding the need for single-gene tests. A customized filtering system, including a blacklist of variants from healthy controls, enhances variant detection. Among 171 subjects with a VSD diagnosis of unresolved etiology, our pipeline provided probable genetic diagnoses for 50 patients, identifying two chromosomal aberrations, one SRY translocation missed by initial FISH-assay, and 47 point mutations in known VSD genes, 18 of which are novel. Overall, WES consolidates multiple genetic tests into one, making it a more accessible and cost-effective diagnostic tool for clinics, usable by non-experts.