Motor neuron disease (MND) is a devastating and fatal neurodegenerative disease caused by the death of motor neurons. The only proven cause of MND are gene mutations, yet two-thirds of MND families still have an unidentified genetic cause.This project investigates a multi-faceted family, without a known causal gene mutation, consisting of two MND patients, one of which is a monozygotic twin with an unaffected co-twin. We aimed to identify and investigate inherited genetic variation between the pair of affected patients, and somatic variation between the disease-discordant co-twins using both short-read and long-read whole-genome sequencing (WGS) data.
To identify putative inherited disease-causing genetic variants, single nucleotide variants (SNVs), small insertion and deletions (indels), as well as structural variants (SVs) were interrogated. Affected-only shared variant analysis filtered SNVs for protein-altering variants that were absent or extremely rare from several large control databases (AC≤5). For SVs, Manta, Lumpy, MetaSV and Duphold tools were used to call and filter for candidate SVs. Reciprocal Overlap Annotator and AnnotSV generated an annotated list of shared and/or overlapping SVs between the two MND patients. For somatic variation that may potentially influence disease onset in the disease-discordant monozygotic twins, Mutect2 and VarScan2 identified genetic variants that differed between the twins.
Shared variant analysis identified 14 putative causal SNVs and indels (validated by Sanger sequencing) and 6 candidate SVs (3 were validated by Samplot visualisation and Pacbio HiFi sequencing data). Somatic variant analysis identified 9 potential ‘protective’ genetic SNVs (i.e. present in the unaffected co-twin only).
Leveraging short-read and long-read WGS in a unique Australian MND family comprising inherited MND and disease-discordant monozygotic twins, we have identified both putative disease-causal genetic variation and disease-modifying genetic variation. Since SVs have been largely understudied in MND, their discovery could form part of the current unidentified genetic causes of MND.