London Calling 2023: (Epi)genotyping by low-pass sequencing using nanopore technologies

We proposed an (epi)genotype-by-sequencing using Oxford Nanopore sequencing as an alternative to SNP genotyping arrays in genomic selection and polygenic risk score estimation. Genotype-by-sequencing requires a low sequencing depth to be cost effective, which may increase the error at the genotype assignment. The latest nanopore chemistry (LSK114 and Q20+) achieved a modal basecalling accuracy of 99.55% and allowed estimating direct genomic value with an accuracy ranging between 0.79 and 0.99. Simultaneously, we were able to detect more than one million high reliable methylated sites, even at low sequencing depth.