Long-read nanopore sequencing reveals novel common genetic structural variants in Prader-Willi syndrome and associated psychosis

Abstract

Prader-Willi syndrome (PWS) is associated with severe hyperphagia, a specific behavioral phenotype and a high risk for developing psychotic episodes. Despite intense research, how genes within the PWS locus contribute to the phenotype remains elusive. In this study, we sequenced the whole genomes of 20 individuals with PWS using long-read nanopore sequencing by Oxford Nanopore Technologies (ONT). We demonstrate that ONT sequencing can resolve the PWS locus by determining the genetic subtype of PWS. Furthermore, we identified several novel structural variants (SV, >30bp) common in all PWS individuals. We are the first to show that the opioid system and the nociceptin/orphanin FQ system may be affected in PWS due to SVs in OPRM1 and OPRL1. Furthermore, we demonstrate that individuals with PWS, especially those with psychosis, exhibit a high burden of SVs in loci with known associations with bipolar disorder, schizophrenia and autism spectrum disorder. Our results challenge the current hypothesis that the PWS phenotype can be mainly explained by the loss of paternally expressed genes on chr15q11.2-13.