Genome Sequencing and Comprehensive Rare Variant Analysis of 465 Families with Neurodevelopmental Disorders

Abstract

PurposeDespite significant progress in unravelling the genetic causes of neurodevelopmental disorders (NDDs), a substantial proportion of individuals with NDDs remain without a genetic diagnosis following microarray and/or exome sequencing. Here we aimed to assess the power of short-read genome sequencing (GS), complemented with long-read GS, to identify causal variants in NDD participants from the NIHR BioResource project. MethodsShort-read GS was conducted on 692 individuals (489 affected and 203 unaffected relatives) from 465 families. Additionally, long-read GS was performed on five affected individuals who had structural variants (SVs) in technically challenging regions, complex SVs, or required distal variant phasing. ResultsCausal variants were identified in 36% affected individuals (177/489) and a further 26% (129/489) had a variant of uncertain significance, after multiple rounds of re-analysis. Among all reported variants, 88% (333/380) were SNVs/indels, and the remainder were structural variants (SVs), non-coding, and mitochondrial variants. Furthermore, long-read GS facilitated resolution of challenging SVs and invalidated variants of difficult interpretation from short-read GS. ConclusionThis study demonstrates the value of short-read GS, complemented with long-reads, to investigate the genetic causes of NDDs. GS provides a comprehensive and unbiased method to identify all types of variants throughout the nuclear and mitochondrial genome in NDD individuals.