Low-cost rare variant detection for population scale genetic screening

Abstract

Genetic screening for rare pathogenic variants facilitates early detection and prevention of disease manifestations in medically actionable disorders, but sequencing costs limit widespread use. We introduce DoBSeq, a low-cost, high-throughput screening framework for detecting rare, single-nucleotide variants and indels. The framework includes: extraction of DNA from dried blood spots used in neonatal screening, automation of two-dimensional DNA pooling and library preparation, high-depth targeted sequencing using a 582-gene custom panel, and a probabilistic model to assign rare pathogenic variants to individuals. Benchmarked against whole-genome sequencing across 582 genes in a batch of 576 individuals, the framework detected 95% of all variants and recovered all clinically relevant pathogenic single-nucleotide variants in American College of Medical Genetics and Genomics (ACMG) actionable genes. Applied to 2304 anonymised blood donors, it yielded variant frequencies consistent with existing population estimates. At a sample cost of 29 USD, including 11 USD running costs, this framework provides a cost-efficient approach to population-level genetic screening.