A New Integrated Genetic and Transcriptomic Approach for Investigating DUX4 and DUX4C

The double homeobox 4 gene (DUX4) and its centromeric paralogue, DUX4C, reside in the subtelomeric region of chromosome 4 and have been implicated in facioscapulohumeral muscular dystrophy (FSHD) and cancers. We combined genomic and transcriptomic analyses using both short- and long-read sequencing technologies. This integrative framework aimed to: (i) delineate the major haplotypes of DUX4C and DUX4T through systematic analysis of publicly available short-read datasets and prior literature; (ii) reconstruct complete haplotype sequences using long-read whole-genome (LWGS) data to generate a haplotype-resolved reference suitable for accurate genotyping from short-read whole-genome (SWGS) data, while also evaluating the genetic relationship between DUX4C and DUX4T; and (iii) characterize transcript diversity using long-read RNA sequencing to develop an expanded transcript reference.