Autism spectrum disorder (ASD) is a complex neurodevelopmental condition, prevalence is 1:68. Although genetics plays a key role in ASD etiology, only 30% of patients exhibit ASD associated genetic variants that are detectable by CGH, GWAS and/or exome NGS approach and hundreds of genes have been involved. Here, we tested the hypothesis that variants in non-coding and/or NGS unmappable regions could be involved in ASD and detected by long-reads whole-genome sequencing (LR-WGS). This approach allows to probe previously unreadable genomic tracts and discover disease-associated phased loci across very long haplotype blocks. Thus, we performed LR-WGS, by 10XGenomics technology, on genomic DNA isolated from 10 children with ASD (7 males and 3 females, including 2 couples of male siblings and 1 couple of male-female siblings) followed by bioinformatics analysis performed by 10X-Long Ranger pipeline. All the sequences passed the QC test, and the longest phase block reached 9M bp in length. We first looked at large structural variants (SVs) detectable only by long-read approach. We found a total of 204 hetero- or homo-zygous large SVs (deletions, duplications, inversions and breakends), up to 30 per subject and affecting 52 distinct genomic regions of 10^5 bp in average within almost all chromosomes. Interestingly, each SV affected from 1 up to 10 subjects and 51 out of 53 SVs involved genes that have never been associated with autism (not listed in SFARI database). All genes were submitted to DAVID 6.8 and METASCAPE gene enrichment tools evidencing some pathways including that of immune response and olfactory transduction. These SVs will be validated on an independent set of DNA samples previously collected from children with ASD and healthy controls. Resulting data will be integrated with clinical data to find genotype-phenotype associations. Small variants will be analyzed and validated, too. In conclusion, LR-WGS successfully discovered 51 new gene variants in 10 patients with ASD that, if confirmed, could explain some pathogenetic mechanisms of the disorder and represent possible diagnostic biomarkers for patient stratification and personalized medicine approaches.
Linked read sequencing reveals new genetic variants in autism
Cupaioli FA;Di Nanni N;Pelucchi P;Cifola I;Milanesi L;Mezzelani A
2020
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition, prevalence is 1:68. Although genetics plays a key role in ASD etiology, only 30% of patients exhibit ASD associated genetic variants that are detectable by CGH, GWAS and/or exome NGS approach and hundreds of genes have been involved. Here, we tested the hypothesis that variants in non-coding and/or NGS unmappable regions could be involved in ASD and detected by long-reads whole-genome sequencing (LR-WGS). This approach allows to probe previously unreadable genomic tracts and discover disease-associated phased loci across very long haplotype blocks. Thus, we performed LR-WGS, by 10XGenomics technology, on genomic DNA isolated from 10 children with ASD (7 males and 3 females, including 2 couples of male siblings and 1 couple of male-female siblings) followed by bioinformatics analysis performed by 10X-Long Ranger pipeline. All the sequences passed the QC test, and the longest phase block reached 9M bp in length. We first looked at large structural variants (SVs) detectable only by long-read approach. We found a total of 204 hetero- or homo-zygous large SVs (deletions, duplications, inversions and breakends), up to 30 per subject and affecting 52 distinct genomic regions of 10^5 bp in average within almost all chromosomes. Interestingly, each SV affected from 1 up to 10 subjects and 51 out of 53 SVs involved genes that have never been associated with autism (not listed in SFARI database). All genes were submitted to DAVID 6.8 and METASCAPE gene enrichment tools evidencing some pathways including that of immune response and olfactory transduction. These SVs will be validated on an independent set of DNA samples previously collected from children with ASD and healthy controls. Resulting data will be integrated with clinical data to find genotype-phenotype associations. Small variants will be analyzed and validated, too. In conclusion, LR-WGS successfully discovered 51 new gene variants in 10 patients with ASD that, if confirmed, could explain some pathogenetic mechanisms of the disorder and represent possible diagnostic biomarkers for patient stratification and personalized medicine approaches.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
