Population genetic variation characterised through serial independent pool-seq: the Cyprus Genome Project

The Cyprus Genome Project characterizes the genetic landscape of the Cypriot population to address the lack of population-specific data in global repositories. We employed a serial independent pool-sequencing (pool-seq) strategy to sequence DNA from 10,000 healthy bone marrow donors, randomized into 10 independent biological replicates. This study design was selected to leverage specific operational and statistical advantages. Operationally, the method enables the processing of a large cohort that would be cost-prohibitive using individual sequencing. Statistically, the use of 10 independent biological replicates allowed for the differentiation of true low-frequency variants from sequencing artifacts. Furthermore, this design enabled the calculation of empirical confidence intervals for variant frequencies. We utilized both Whole Exome Sequencing and a targeted gene panel (813 genes) to maximize read depth and sensitivity. The study identified over 4 million variants, including > 100,000 variants absent from the gnomAD v4.1 and ClinVar databases. Validation against published clinical cohorts confirmed high concordance (r > 0.92). The results highlight significant differences between local and global allele frequencies, including pathogenic variants that are common in Cyprus but rare globally. The results, including an interactive genome map with full annotations from gnomAD v4.1 and ClinVar, are publicly accessible at www.cyprusgenome.org, with the aim of advancing healthcare and facilitating future clinical research.