Establishing a nanopore sequencing facility for acute care in New Zealand

Abstract There are ~200 children in high dependency neonatal acute care in New Zealand at any one time, requiring a scalable distributed solution for acute care genomics. We have baselined an expandable acute care clinical pipeline based around the PromethION 2 Solo system with connection to Fabric GEM™. We have performed benchmarking using GA4GH benchmarking tools and Genome in a Bottle HG002 – HG007. Evaluating ~3.3x106 truth SNVs and ~500x103 indels at read depths of between 24–42x coverage identified SNV recalls = 0.992 ±0.001, precision = 0.997 ±0.0006, and F1 = 0.995 ±0.0008 over a minimum of two runs completed by different technicians and analysts. Indel identification approached recalls = 0.838 ±0.043, precision = 0.922 ±0.019, and F1 = 0.874 ±0.032 over the same runs. Subsequent analyses indicated that the observed variation in recall, precision, and F1 was largely limited to correct copies of falsely duplicated regions and areas of collapsed errors with clusters of CHM13 hets in GRCh38. Rarefaction analyses up to 80x coverage identified that SNV identification plateaus at ~20x coverage, while indel identification plateaus at ~40x coverage. Analyses of samples from Coriell CNVPANEL01 demonstrated that large-scale genomic variations can be reliably detected after ~2 M reads, equivalent to ~2 hr sequencing time. We present the preliminary results from the pipeline development phase, performed in parallel with established international accredited facilities available to New Zealand’s clinicians.

Biography Justin M. O’Sullivan, PhD, is a Professor and Director of the Liggins Institute at the University of Auckland in New Zealand. He has honorary appointments at the Garvan Institute of Medical Research, Australia, University of Southampton, UK, and A*STAR Singapore Institute for Clinical Sciences. Justin’s research group is currently focused on: establishing rapid genome sequencing for clinical care; understanding how disease-associated mutations in non-coding DNA affect gene regulatory networks and the pathways that underlie disease development; the role of the microbiome in brain and behaviour development; and the role of microbiome restoration in clinical care.