WYMM Tour: Christchurch

Clonal propagation underpins the consistency and typicity of elite grapevine cultivars, yet the narrow genetic diversity it preserves can constrain adaptive potential and increase vulnerability to emerging pest, disease, and climate pressures. Meeting these challenges requires new approaches to generate, detect, and characterise useful variation while retaining the identity and value of established cultivars.

Using Oxford Nanopore Technologies’ PromethION platform, we have generated telomere-to-telomere, phased diploid grapevine genome assemblies and developed analysis pipelines to detect a broad spectrum of molecular variation, including structural variation, somatic mutation, and epigenetic changes. These approaches resolve diversity that has, until recently, remained largely inaccessible within clonal lineages. Applied to a Sauvignon blanc clonal diversity collection, this is supporting the development and selection of elite germplasm with improved resilience in future production environments. Extensions of these genomics approaches are also being deployed in new breeding initiatives and to provide cost-effective clonal diagnostic assay to industry.

Klebsiella pneumoniae is a major cause of healthcare-associated infection and an important antimicrobial-resistance (AMR) threat. When multiple patients are identified in the same hospital, the immediate question is whether cases reflect transmission or a diverse background of unrelated introductions. We used prospective hospital-based nanopore sequencing to distinguish these possibilities and resolve how AMR determinants were organised across complete bacterial genomes.

During a 15-month surveillance pilot, K. pneumoniae clinical and screening isolates from Wellington Regional Hospital were sequenced on-site as part of a diagnostic laboratory workflow. Complete assemblies were analysed for lineage diversity, AMR and virulence determinants, plasmid content, and core-genome relatedness between cases.

After quality control, 121 high-quality genomes were retained, including 118 complete assemblies. Sequencing revealed a highly diverse K. pneumoniae population: 75 sequence types, with 68% represented by a single isolate. Recurrent lineages were investigated using whole-genome comparisons, but no clone showed evidence of sustained patient-to-patient transmission. The closest pair differed by three single-nucleotide variants (SNVs) and came from the same patient five months apart, consistent with within-host persistence rather than transmission. Complete assemblies also exposed AMR architecture. Acquired AMR genes were mainly plasmid-borne, yet chromosome-resolved assemblies identified important chromosomal structures. In two near-identical sequence type (ST)15 co-isolates from one specimen, nanopore sequencing resolved different copy numbers of an IS26/Tn3-associated AMR module carrying qnrB1–blaSHV-12–aac(6′)-Ib-cr5–blaOXA-1–catB3, associated with Vitek 2 category shifts for selected oxyimino-beta-lactams.

Hospital-based nanopore sequencing can do more than confirm outbreaks. In this study, it ruled out sustained transmission, provided genomic reassurance for infection prevention and control, and revealed the mobile and chromosomal architecture shaping AMR in a routine clinical isolate collection.

Cancer is a collection of diseases with complex molecular mechanisms and, correspondingly, is associated with a wide range of biomarkers and treatment strategies. Precision oncology is increasingly becoming a standard of care in various contexts worldwide, driven by the growing availability of targeted treatments. However, this often results in the need for multiple laboratory tests and is rapidly increasing the resources and turnaround time needed for routine standard care. This puts strain on clinical laboratories and is particularly challenging for resource-limited healthcare settings such as those in Aotearoa New Zealand, Australia, and the broader Asia-Pacific region. The ability of nanopore sequencing to generate multiple outputs with a rapid turnaround time makes it an attractive option for efficient, comprehensive cancer diagnoses. Part 1: Clinical diagnostics for CNS tumours. The gold-standard diagnostic criteria for brain cancers, as defined by the World Health Organisation, rely heavily on methylation profiling, as well as copy number variation (CNV) and single-nucleotide variants (SNVs). Recent advances using nanopore sequencing have resulted in several brain tumour classification tools. These not only perform methylation profiling but also provide SNV analysis and estimates of genomic amplification and deletion. These are being actively trialled in clinical centres around the world, including at RPA Neuropathology. Part 2: A novel tool for solid tumour classification While these classification tools have been developed using established methylation classifiers and other molecular diagnostic tests, nanopore sequencing offers a fresh opportunity for a flexible and integrated approach to classifier development. Panorama is a newly developed bioinformatic tool designed to enable comprehensive tumour profiling directly from nanopore sequencing data. It facilitates molecular profiling of SNVs, methylation, and immune infiltrate, tailored to a user-defined panel of biomarkers. Nanopore sequencing enables faster, integrated, resource-efficient cancer diagnostics and supports advances in personalised tumour classification and precision medicine.

Rare disorders are overrepresented in neonatal care and are a significant cause of infant mortality. These disorders can be both genetic or epigenetic in origin, meaning that rapid sequencing of native DNA with the addition of base modifications can improve diagnostic rates and support genetic findings of variants with unknown significance. We have established an acute care clinical sequencing pipeline based on long-read whole genome sequencing (LRS) of parents and infants. This pipeline integrates the PromethION P2 system (Oxford Nanopore Technologies) with a Bayesian AI-based clinical decision support tool (Fabric GEMTM software). We present results for the first 22 families, where clinically relevant variants were identified in 72% of cases. We have utilised DNA methylation basecalling to support genetic findings in our acute care pipeline in three main ways. First, by identifying differentially methylated regions, we have detected methylation at loci indicative of known imprinting disorders. Secondly, we have tested for over 100 disorders using episignatures, which have supported genetic diagnoses in two cases. Thirdly, cell-type deconvolution methods have identified three cases with outlier immune cell fractions. Additionally, in a patient diagnosed with NOCARH syndrome, we utilised cell-type deconvolution methods to provide insights into post-transplant immune cell turnover rates in the lung. By adding DNA methylation basecalling, we can expand the number of disorders tested and support cases with ambiguous genetic variant findings. This can potentially reduce the number of iterative, invasive tests often needed to obtain a diagnosis and, one day, help to end the diagnostic odyssey for patients and their families.

Cardiovascular disease continues to disproportionately affect Pacific peoples in Aotearoa New Zealand, yet Pacific communities remain significantly underrepresented in genetic and cardiovascular research. This project investigates cardiac biomarker concentrations in a heart healthy Pacific community and explores the role of structural genomic variants that may contribute to differences in biomarker concentrations among Pacific peoples.