Tonight I watched Fritz Sedlazeck from The Baylor College of Medicine Human Genome Sequencing Center present at the Nanopore Community Meeting 2022 on “Rapid structural variant calling across AllOfUs using Oxford Nanopore sequencing.” Sedlazeck spoke about structural variations (SV) that are 50bp+ genomic alterations. Long read sequencing SV calling improves detection. Sedlazeck and team created Sniffles2 to call SVs. Sniffles2 compared to other callers was the fastest in identifying challenging medical genes. Sedlazeck’s team is now focusing on full SV genotyping to scale up to the population level. The system they developed can perform population VCF in 65 seconds compared to ~36 CPU hours for the previous tool. Sedlazeck took 1002 genomes sequenced with Nanopore and used Sniffles2 to identify SVs in 2 hours. AllofUs is a large study targeting millions of human genomes. They have done around 70 samples with Q10+ and ~20kb N50 with 2-3% error rate. They are creating new pipelines for STR calling and CNV calling. They are developing tools to detect somatic SVs with Sniffles2 in complex samples. Sedlazeck also explained they collaborated on deep long read sequencing (>55x) of regional brain sample to learn about rare neurodegenerative disorders. It also sounded like the group is developing other long-read sequencing tool that could be useful!
