NCM 2023 Houston: Understanding normal patterns of human structural variation with nanopore sequencing

More than half of individuals with a suspected Mendelian condition remain without a precise molecular diagnosis after comprehensive clinical evaluation, limiting their ability to benefit from precision therapies or N-of-1 trials. One major obstacle is that traditional sequencing technologies (i.e. short-read genome sequencing [srGS]) cannot reliably identify and map structural variants (SVs; insertions, deletions, inversions, or repeat expansions larger than 50 bp). Consequently, there is a lack of understanding about the diversity of SVs in the human genome, making it difficult to filter for and prioritize candidate disease-causing variants. To address these limitations, the 1000 Genomes ONT Sequencing Consortium, building upon the 1000 Genomes Project, is using Oxford Nanopore Technologies’ long-read sequencing (LRS) platform to sequence 750 reportedly healthy individuals in an attempt to characterize normal genome-wide SV patterns and identify variants in challenging regions that are not effectively evaluated using srGS. Preliminary data from the first 250 genomes, sequenced to 30x coverage with an average read of 50 kbp, demonstrate the potential of this approach. Here we use both alignment and de novo assembly-based methods, resulting in contig N50 values exceeding 30 Mbp. With this data, we performed phased variant calling and SV calling, enabling us to filter and prioritize SVs in unresolved clinical cases. The generated dataset will be publicly available, encouraging collaborative efforts within the human genetics community to identify disease-causing variants among individuals sequenced with nanopore sequencing.