Constellation illuminates rare disease genetics

Abstract

Despite significant advances in genomic sequencing, the resolution of many rare disease cases is still hindered by variant detection limitations. Short reads struggle in homologous regions, and long reads remain costly and difficult to scale. Here, we present the first systematic evaluation of Illuminas Constellation sequencing technology for rare disease research. By fragmenting long DNA molecules directly on the flow cell surface, Constellation unlocks proximity information that enables long-range phasing and structural variant detection. Across 21 families, Constellation independently identified all known causative variants and resolved previously unsolved trios. It reliably resolved complex structural and copy number variants (e.g. impacting MECP2) and recovered haplotype phasing information across key disease impacting variants, all from low DNA input using existing Illumina infrastructure. These findings establish Constellation as a scalable, cost-efficient advance, closing critical diagnostic gaps and broadening access to long-range variant analysis in rare disease genomics.