Identification of new variants in patients with neurodegenerative disorders by whole genome sequencing data and development of a bioinformatic pipeline

We explored the missing heritability in a cohort of 140 patients affected by Neurodegenerative disorders (NDDs), including Amyotrophic Lateral Sclerosis (ALS), Frontotemporal dementia (FTD)) Parkinson disease (PD) and Spinocerebellar Ataxia (SCA). We performed Whole Genome Sequencing (WGS) after excluding pathogenic variants in the main disease-relevant causative genes and investigated 3 classes of potentially pathogenic variants: a)Coding/non-coding SNV/Indels in a panel of 696 genes involved in NODs. Using standard annotation, we identified pathogenic/likely pathogenic variants (ACMG) in genes causative of tare forms of each disease (N=15) and in gene causing a NND different from patient clinical presentation (N=15). In addition to the standard annotation we used SpliceAl, a deep leaming tool predicting an effect on splicing mechanism. We found 48 rare variants with a possible splicing Impact (ASTM 0.4). We performed in vitro studies for 9 variants (highest AS) and for 6 of them, we confirmed their role in splicing alteration. b)Genome-wide structural variants Using CNVkit, we identified a 15925 deletion (1.2Mb) in a PD case. Similar deletions has been associated with mild intellectual disability and dysmorphisms but never reported in PD. c)Genome wide Tandem Repeat (TR). Using literature (ExpansionHunter, GangSTR) and novel tools, we Identified 4 novel loci in ALS cohort with a possible TR expansion and replicated the results in larger independent cohorts from Italy (763 ALS, 1018 controls) and International Mine project (3121 ALS, 1217 controls). For 3 of them (FRA1DAC1, RFC1, HK1) the result was not replicated. For the last locus (TFG2) the preliminary data are promising since the TR was observed only in patient and in none controls (1/352 vs 0/292 in ITFG2). In conclusion, using a multilevel WGS data analysis we were able to find missed pathogenetic variants In genes associated with different NDDs, reinforcing the idea of a shared genetic cause among these diseases.