Linked-read whole genome sequencing reveals undetected variants in autism spectrum disorder

Abstract Introduction: Autism Spectrum Disorder (ASD) is a neurodevelopmental condition with complex etiology. Although genetics play a key role in ASD, causative or predisposing genetic variants have been detected only in 30% of patients. Here, for the first time, linked-read whole genome sequencing of ASD patients is used to access disease associated regions unmappable by short-reads NGS. Materials and Methods: 10 children with ASD, including 3 couples of affected siblings, were enrolled and HMW DNA isolated from peripheral blood. DNA was submitted to 10Xgenomics microfluidics partitioning and barcoding, library preparation and Illumina WG-NGS. Data were analyzed through 10x Long Ranger pipelines to find SNVs, in/dels and larger structural variants in comparison to 1000 genomes, genome aggregation database and NHLBI-ESP populations. Genes affected by variants were compared with those already known to be associated with ASD (SFARI database, large-scale sequencing studies, bioinformatics predictions). Results: this approach successfully produced sequences up to 9mln bp in length. Among the detected variants, 405 were listed in SFARI, 43 confirmed bioinformatics predictions and 3,210 were new. Among the latter variants, 22 were homozygous in all the 3 couples of siblings. Conclusion: this powerful approach deciphered underlying genomic heterogeneity and missing variations in ASD. Further studies will be performed to validate the new ASD variants in a large size of samples and in public data. Data integration will be also performed to identify pathways and gene networks involved in the disorder to understand disease mechanisms and design target-driven treatment. Acknowledgements: EU project GEMMA (grant agreement No 825033).