Objective: Autosomal recessive microcephaly (AR-MC) is a highly heterogeneous group of disorders. Despite recent advances in genetic analysis of AR-MC, it is estimated that many causative genes are yet to be identified. In this study, we performed whole-exome (WE) sequencing of consanguineous pedigrees with AR-MC in order to identify its novel causative genes.

Methods: DNA samples from one or two affected individuals from 40 families with AR-MC were subjected to WE sequencing on Illumina HiSeq, and the results were annotated with ANNOVAR.  Identified homozygous variants were filtered for their: 1] predicted effect on the protein product, 2] occurrence in public databases or other exomes sequenced in our lab, and 3] presence in a block of homozygosity within the family.

Results: We identified likely pathogenic mutations in known AR-MC genes in eight pedigrees (ASPM, WDR62, TRAPPC9, TUBGCP6, PNKP, AP4M1, ASNS). In six additional pedigrees, likely pathogenic mutations in genes not previously associated with human diseases emerged. These include two genes encoding centrosomal proteins, two genes encoding enzymes in amino acid metabolism and one gene encoding a synaptic protein. In total, we identified candidate pathogenic mutations in 14/40 pedigrees (35%).

Conclusions: This study confirms the highly heterogeneous nature of AR-MC, and highlights novel biological pathways involved in pathogenesis of AR-MC. WE sequencing proved efficient in identifying mutations in known and novel AR-MC genes in consanguineous pedigrees, and holds great promise for its clinical application in outbred populations as well.