Genetic diagnosis of facioscapulohumeral muscular dystrophy type 1 using rare-variant linkage analysis and long-read genome sequencing.

Facioscapulohumeral dystrophy type 1 (FSHD1) is a progressive, debilitating skeletal myopathy that requires a multimodal approach for complete molecular characterization of pathogenic genotypes. Here, we report genomic analyses of a family with suspected FSHD1. We first performed short-read genome sequencing, followed by parametric linkage analysis using rare variants to map the disease locus to a single 1.7 Mb interval on chromosome 4q35.2 with a logarithm of the odds score of 3.2. We then used ultra-long-read genome sequencing as a single molecular test to genotype a pathogenic FSHD allele containing a 4qA permissive haplotype and 5 KpnI repeat units at the D4Z4 locus. These results demonstrate that genome-wide rare variant-based linkage analysis is a powerful tool for mapping disease loci in families, and ultra-long-read genome sequencing is capable of genotyping pathogenic FSHD1 alleles.