Autism spectrum disorder trios from consanguineous populations are enriched for rare biallelic variants, identifying 32 new candidate genes

Abstract

Autism spectrum disorder (ASD) is a severe neurodevelopmental disorder that affects about 1 in 55 children worldwide and imposes enormous economic and socioemotional burden on families and communities. Genetic studies of ASD have identified de novo copy number variants (CNVs) and point mutations that contribute significantly to the genetic architecture of ASD, but the majority of these studies were conducted in outbred populations, which are not ideal for detecting autosomal recessive (AR) inheritance. However, several studies have investigated ASD genetics in consanguineous populations and point towards AR as an under-appreciated source of ASD variants. Here, we used trio whole exome sequencing (WES) to look for rare variants for ASD in 115 proband-mother-father trios from populations with high rates of consanguinity, namely Pakistan, Iran, and Saudi Arabia. In total, we report 87 candidate sequence variants, with 57% biallelic, 21% autosomal dominant/de novo, and the rest X-linked. 52% of the variants were loss of function (LoF) or putative LoF (splice site, stop loss) and 47% non-synonymous. Our analysis indicates an enrichment of previously identified and candidate AR genes. These include variants in genes previously reported for AR ASD and/or intellectual disability (ID), such as AGA, ASL, ASPA, BTN3A2, CC2D1A, DEAF1, HTRA2, KIF16B, LINS1, MADD, MED25, MTHFR, RSRC1, TECPR2, VPS13B, ZNF335, and 32 previously unreported candidates, including 15 LoF or splice variants, in genes such as DAGLA, EFCAB8, ENPP6, FAXDC2, ILDR2, PKD1L1, SCN10A, and SLC36A1. We also identified candidate biallelic exonic loss CNVs a number of trios, implicating genes including DNAH7, and DHRS4/DHRS4L2.

Heterozygous De Novo Truncating Mutation of Nucleolin in an ASD Individual Disrupts Its Nucleolar Localization

“…The mutation (chr2:232320177_232320177delC; NM_005381.3:c.1991delG; p.Gly664Glufs*70) was identified by the Whole-Exome Sequencing (WES) of a set of ASD trios, as described elsewhere [ 16 , 17 ], and after verification, using Sanger sequencing, in the ASD individual and both biological parents, this mutation turned out as de novo ( Figure 1 A). The Gly664Glufs*70 mutation is not present in the gnomAD control database v2.1.1 (251,378 alleles, including 208,110 from the non-neuro subset).…”

“…For details on the DNA library preparation and sequencing, as well as the sequence alignment and analysis pipeline, see [ 15 ]. The comparison of proband and parental exome sequence variants for the identification of de novo variants was performed as described in Harripaul et al (MedRxiv and Ph.D. thesis) [ 16 , 17 ].…”

Biallelic Loss of Function Mutation in Sodium Channel Gene SCN10A in an Autism Spectrum Disorder Trio from Pakistan

“…The CNV calling was performed using Illumina Genome Suite/CNVpartition. Whole Exome Sequencing (WES) was performed on the DNA of the proband as well as both parents, using the Thruplex DNA-Seq (Rubicon Genomics, Ann Arbor, MI, USA) Library Preparation Kit with the Agilent SureSelect V5 Exome Capture kit, as described in Harripaul et al, submitted [ 5 ]. Sequencing was performed by The Centre for Applied Genomics ( ).…”

“…Sequencing was performed by The Centre for Applied Genomics ( ). Annotation and variant prioritization was performed as described in Harripaul et al, submitted [ 5 ], searching for potentially damaging homozygous variants, de novo heterozygous variants, and X-linked hemizygous variants. Variants of interest were confirmed initially through examining the WES reads using Integrated Genomic Viewer (IGV; ) [ 8 ], and then through Sanger sequencing in parents and proband ( ).…”

“…Heterozygous mutations, mainly missense, in other voltage-gated sodium channel genes are believed to cause developmental epileptic encephalopathies ( SCN1A : MIM 182389; SCN2A : MIM 182390; SCN3A : MIM 182391; SCN8A: MIM 600702). In several reported instances, de novo loss of function mutations in SCN2A have been reported for ASD [ 5 , 6 , 7 ]. Interestingly, biallelic mutations in some of these genes cause quite distinct disorders.…”