Whole Exome Sequencing in Extended Families Identifies Shared and Unique Likely Gene-Disrupting Alterations

Background:  Autism spectrum disorders (ASDs) encompass a constellation of neurodevelopmental conditions and studies to date demonstrate that the underlying etiology is extremely heterogeneous. With the advent of whole exome sequencing (WES), studies have been implicating genes across many disorders. Thus far, autism exome studies have primarily focused either on simplex families to discover de novo alterations or consanguineous families that carry recessive mutations.

Objectives:  Our study performs exome sequencing in extended, multiplex families with affected cousin pairs to identify potential ASD genetic factors. Our initial analysis focused on identifying identical by descent (IBD) variants that could contribute to ASD risk. This study extends these results and combines the results with also more severe alterations which may not be shared across families.

Methods:  We performed WES on at least two affected cousins across 40 multiplex ASD families. A total of 164 individuals were captured with the Agilent SureSelect Human All Exon kit, sequenced on the Illumina HiSeq 2000, and the resulting data processed and annotated with BWA, GATK, and SeattleSeq. We have previously identified alterations that were inherited from a common ancestor and identical by descent. In this analysis, we focused on heterozygous alterations that were predicted to result in stop-gain or stop-loss mutation, or potentially interfere with splicing, collectively called “likely gene-disrupting” (LGD) variants. The LGD alterations that were both shared and unique within were evaluated families. We also determined whether any of these alterations fell within 142 ASD candidate genes; these included syndromic ASD genes and genes with relatively high confidence (as defined by the SFARI gene database).

Results:  Following exome sequencing, each extended family was identified to carry approximately 90,000 variants. When we filtered each of the families for potential LGD alterations, we decreased the variants of interest to a few hundred per family. We then culled the data to determine if our variants intersected any previously reported ASD candidate genes; we identified a unique a stop-gain alteration in NRXN3, a gene already identified in ASD patients with copy number variants. Furthermore, potential splicing alterations were recognized, including in the ASD candidate genes CC2D1A, a gene also connected to intellectual disabilities, as well as VPS13B, a gene first reported to cause Cohen syndrome and since linked to ASDs, developmental disorders, epilepsy, and intellectual disabilities.

Conclusions:  By studying these extended, multiplex families, we hope to reveal how inherited and unique alterations in may be acting in concert to result in ASDs.