Fig. 1

Genomic analysis pipeline of discordant twins for type 1 narcolepsy. Genomes of discordant twins for type 1 narcolepsy were sequenced, and the resulting reads processed for quality control. Good quality reads were then mapped against the human genome reference GRCh38. A new quality control over each assembly was carried out, and the variant calling step was conducted using three independent tools. After that, the consensus between variant call was determined for each twin: in the unaffected one, this resulted in a total of 5,257,409 variants, whereas in the affected twin, 5,310,227 variants. Unique variants were: 104,041 variants in the unaffected twin, and 156,863 variants in the affected twin, and classified as divergent variations in monozygotic twins (DVMTs). Only these 260,904 DVMTs were functionally annotated and filtered to prioritize SNVs with potential clinical relevance. Non-disruptive variants that might change protein effectiveness, or variants assumed to have high (disruptive) impact in the protein, probably causing protein truncation, loss of function or triggering nonsense mediated decay were included in a further enrichment analysis to provide insights about biological processes, cellular components and molecular functions of these DVMTs. Additionally, mitochondrial haplogroups, as well as the typing for the HLA alleles of each twin were determined. The parentheses highlight the tools used for each step