Variant Prioritization for Neurodegeneration

DNA extraction and WES were performed as previously described by Chakrabarty et al. (2021 (link)) using the Ion Torrent platform (ThermoFisher Scientific, USA). Pre-processing and annotation of sequenced data were done with Torrent suite software (ThermoFisher Scientific, USA) and Ion Reporter software V5.18 (Thermo Fisher Scientific, USA), respectively. Cascade of filtration criteria such as minor allele frequency of < 1%, non-synonymous, homozygous and heterozygous mutations were included for the prioritization of variants. From each case’s data, the variants present in the pool of our in-house normal exome data were excluded. The remaining variants were further shortlisted when their coverage was > 10 × , present within the homopolymer region (< 4), absent in UCSC common SNP database and when the variants were expressed in brain. The UMD-Predictor tool associated with Variant Annotation and Filter Tool (VarAFT) software was employed for pathogenicity prediction (Desvignes et al. 2018 (link)). The homozygous and compound homozygous variants in genes previously associated with the neurodegenerative disorders were analyzed. Additionally, variants in the genes that encode the interacting partners of identified candidate genes or genes of the same protein class were also shortlisted.