Publications

Background: 

Genetic heterogeneity underpinning Autism Spectrum Disorders (ASD) makes it challenging to decipher the neurological mechanisms underlying its development. There is a strong genetic basis for ASD and adds to the risk and disease burden. De novo mutations (DNMs) identified in large exome sequencing studies have identified several new candidate genes and hinted at a revised model of causation. Utilizing an Indian familial dataset, this study looked at DNMs to uncover genetic risk factors for ASD using whole exome sequencing (WES), functional enrichment, and genetic network analyses of discovered variants. Methods: The study included 14 autistic male children and their biological parents. Children diagnosed as ASD by expert clinicians using INDT-ASD (INCLEN Diagnostic Tool for Autism Spectrum Disorder) employing ICD Criteria. The genomic DNA extracted from 14 trio samples (total of 42) was utilized for library preparation and sequenced on Illumina HiSeq series to generate 2 × 150bp sequence reads at 80 - 100X coverage. VarScan and Genome Analysis Tool Kit (GATK) were implemented to identify potential DNMs in the family datasets which were aligned to the reference genome build GRCh38. Deleterious DNMs were identified by applying stringent parameters. Functional enrichment analysis was performed on the filtered deleterious variants to identify their role in neurodevelopmental processes. Results: The Analysis revealed DNMs were predominantly missense variants along with few frameshift, stop gain and splice site variants that were found to alter protein functions. we identified 6 missense mutations DEAF1(p.R224W), KCNC1(p.T241M), ZSWIM4(p.P558L), SZT2(p.G1787R), ADCY1(p.L101R), RRS1(p.L257H), 1 splicing variant BRSK2(exon11:c.978-1G>C) and 1 splice donor variant TSC2 (rs137854209) in genes that were earlier reported as causal for ASD. Our data also reports 2 high impact frame shift mutations in genes like INO80E (p.P170X) and SPG7(p.R13RX) that have not hitherto been reported. Interestingly, further pathway analysis of these variants revealed their significant implications in neuron differentiation, neuron projection morphogenesis, axonogenesis and axon development (p ≤ 0.05). A very interesting finding was that the genes DEAF, CHSY1, ZSWIM4, PCSK5 had a significant immune function correlation revealing that there are several molecular cross talks that need to be explored to understand the genetic burdens on Autism. We compared our results with SFARI and denovo-db and found only partial overlap suggesting that it could be due to the genetic difference between population. Owing to a small sample size, extensive analysis was not possible, but increasing sample size and further exploration to clinical correlates like SRS scores and VABS scores are underway. Discussion: To best of our knowledge, this is the first study that has explored the DNMs in ASD children of Indian origin by WES. Our small sample-sized trios study hints at possible variations in the genetic burden in Indian samples. This ongoing study intends to validate in larger sample sets. Before further investigations with functional model studies.