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Genome Wide Variant Analysis of families with Autism Spectrum Disorder (ASD) using an Integrative Bioinformatics Pipeline

Introduction. Autism spectrum disorders (ASD) are a group of developmental disabilities that affect social interaction, communication and are characterized by repetitive behaviors. There is now a large body of evidence that suggests a complex role of genetics in ASD, in which many different loci are involved. Although many current population scale studies have been demonstrably useful, these studies generally focus on analyzing a limited part of the genome or use a limited set of bioinformatics tools. These limitations make it difficult to see the complete and panoramic picture of each ASD case. To address this problem, here we describe an integrative bioinformatics pipeline used to get a more complete and reliable set of candidate ASD-variants for validation and further functional analysis. Results. The resulting set of candidate variants include three small heterozygous CNVs (~22, ~36 and ~50 Kb). All of the CNVs were only found by ERDS, and despite the fact that the K21 pedigree had microarray data, PennCNV did not detect any CNV in those regions. A heterozygous de novo nonsense mutation in MYBBP1A was found in one of the quads (K21) located within exon 1, and a second de novo variant was also among the final results from another quad (SSC_2), this time a missense mutation in LAMB3, which also has not yet been observed in any other ASD proband.