Deciphering the role of germline complex de novo structural variations in rare disorders

De novo structural variants (dnSVs) have emerged as crucial genetic factors in the context of rare disorders. However, these variations often go undiagnosed in routine genetic screening practices. To shed light on their significance in rare disease, we conducted a comprehensive analysis of the largest cohort of parent-offspring whole-genome sequencing data from the UK 100,000 Genomes Project. Our study encompassed a vast cohort of 12,568 families, including 13,702 offspring affected by rare genetic diseases. We identified a total of 1,872 dnSVs, revealing that approximately 12% of the probands harboured at least one dnSV, of which 9% were identified as likely pathogenic in affected probands (151/1696). Advanced parents' age was found to be associated with an increased chance of having dnSVs in probands. We discovered 148 clustered breakpoints resulting from a single event. 60% of these complex dnSVs were classified into 9 major SV types, and could be observed in multiple individuals, while the remaining 40% were private events and had not been previously reported. We found 12% of pathogenic dnSVs are complex SVs, emphasising the critical importance of thoroughly examining and considering complex dnSVs in the context of rare disorders. Furthermore, we discovered an enrichment of maternal dnSVs at subtelometric, early-replicating regions of chromosome 16, suggesting possible sex-specific mechanisms in generation of dnSVs. This study sheds light on the extent of diversity of dnSVs in the germline and their contribution to rare genetic disorders.