Long Read Genome Sequencing Elucidates Diverse Functional Consequences of Structural and Repeat Variation in Autism

Long-read whole genome sequencing (LR-WGS) technologies enhance the discovery of structural variants (SVs) and tandem repeats (TRs). Application of LR-WGS has potential to identify novel risk factors that contribute to autism spectrum disorder (ASD). We performed LR-WGS on 243 individuals from 63 ASD families and generated an integrated call set combining long- and short-read data. LR-WGS increased detection of gene-disrupting SVs and TRs by 29% and 38%, respectively, and enabled identification of novel exonic de novo germline and somatic SVs that were not detected previously with short read WGS. We observed complex SV patterns, including a previously undescribed class of nested duplication-deletion (DUP-DEL) events. Joint analysis of phased TRs and methylation data revealed that hypermethylation of expanded FMR1 alleles (≥35 CGG repeats) in females occurs independently of X chromosome inactivation. Rare SVs, TRs, and damaging SNVs together accounted for 6.2% (95% CI: 1.7-15%) of the heritability of ASD in this sample. These findings demonstrate how LR-WGS can resolve complex genetic variation and its functional consequences and regulatory effects in a single assay.