Autism Genetics: homozygosity mapping and functional validation

Autism spectrum disorders (ASDs) affect 1% or more of American children.  ASDs are characterized by defects in social behavior, including language delay, abnormal social interactions, and repetitive or stereotyped interests or behaviors.  ASDs show a large genetic component, with estimates of heritability as high as 60-90%.  However, the extreme heterogeneity of ASD is a persistent hurdle to gene discovery, and known genetic causes account for less than 15% of diagnoses.

Although high throughput sequencing (HTS) methods allow systematic analysis of genetic variation across the entire exome, or even the entire genome, the interpretation of this data faces analytical challenges that have by no means been solved.  The use of consanguineous pedigrees, in which parents share ancestry, allows the identification of candidate genes that can then be analyzed more broadly in nonconsanguineous families.  Consanguineous families 1] reduce the heterogeneity of ASD, 2] simplify HTS analysis and validation, and 3] provide genetic linkage evidence to support the validity of specific mutations in a single family. Preliminary data confirms that HTS in such pedigrees can efficiently identify, in an unbiased fashion, recessive genetic causes of ASD relevant to both consanguineous and nonconsanguineous cohorts of patients. 

This study will seek to enroll consanguineous families diagnosed with ASD, perform homozygosity mapping to locate regions of the genome likely to harbor the mutation that causes their ASD, and perform whole genome sequencing (WGS) on the affected individuals to identify candidate variants.  Further, linkage and whole exome sequencing data that was generated on consanguineous families from previous studies will continue to be analyzed.  This study will expand on the previous work by 1] Generating WGS data on normal controls to identify common alleles within Middle Eastern populations thus allowing swifter, more sensitive and ultimately cheaper analysis in this and many other Middle Eastern WGS studies; 2] Generating relatively high throughput methods of functionally validating strong candidate genes discovered through WGS using yeast models, transformed somatic cell lines, and other model systems; and 3] Using RNAi to generate mouse models of candidate genes discovered in this study, and an ongoing neuronal activity-dependent gene study, to examine the effects of removing the genes on dendrite and dendritic spine morphology and synaptic activity.

Recent studies suggest that, despite the high level of heterogeneity, there are common biochemical pathways associated with ASD.  The findings from this study will be instrumental in the identification of the genes that make up these pathways, and provide potential pharmaceutical targets for the treatment of ASD.