What You’re Missing Matters: How Oxford Nanopore sequencing can power deeper discovery with greater efficiency

The DDD-Africa study was established to facilitate the translation of next generation sequencing technologies for diagnosing developmental disorders in Africa. In this talk, hear more about how long read sequencing enables superior resolution of complex genomic regions, often missed by short-read approaches, and provides a unified platform for investigating multiple classes of variation and may increase detection rate in exome-negative rare disease cohorts.

Short-read whole genome sequencing (WGS) improves germline variant detection but does not capture genome-wide DNA methylation. Oxford Nanopore Technologies (ONT) long-read WGS enables simultaneous sequencing of germline DNA and direct detection of epigenetic modifications, providing additional resolution in unresolved hereditary breast cancer cases. In this study, we evaluated the added clinical and molecular value of ONT long-read WGS compared with targeted multi-gene NGS and short-read WGS. In the study, ONT long-read WGS provided a unified platform for integrated genomic and epigenomic profiling in familial breast cancer. By enabling direct methylation detection alongside variant analysis, this approach has the potential to resolve genetically uncharacterised cases and contribute to the future of equitable access to precision oncology.

Oxford Nanopore Technologies (ONT) has transformed genomic research by enabling long-read sequencing, real-time data generation, and direct detection of epigenetic modifications from native DNA. These capabilities are particularly valuable for studying genetically diverse African populations, where complex genomic regions and structural variation remain underrepresented in conventional sequencing datasets. This presentation will showcase how ONT sequencing has been integrated into our research programme to investigate the genetic and epigenetic determinants of infectious diseases, with a focus on HIV and tuberculosis. Applications include whole-genome sequencing, high-resolution HLA typing, and genome-wide DNA methylation profiling to better understand host immune responses, disease susceptibility, and treatment outcomes. By combining long-read sequencing with functional genomics, we are uncovering variation within highly polymorphic immune-related genes that are challenging to resolve using short-read technologies. The presentation will also discuss the practical implementation of ONT workflows, including sample preparation, sequencing optimisation, bioinformatic analyses, and lessons learned while establishing long-read sequencing capacity within a South African research setting. Finally, we will highlight how ONT is enabling more inclusive genomic research by generating high-quality datasets from African populations, contributing to improved precision medicine approaches and expanding opportunities for genomic discovery across the continent.

Diagnostic genetic testing remains severely limited in South Africa, leaving countless families with suspected rare and undiagnosed conditions without answers. This presentation will explore sub-Saharan Africa's first Undiagnosed Disease Programme (UDP), where Oxford Nanopore Technologies (ONT) long-read whole genome sequencing (lrWGS) was implemented by Stellenbosch University as a key part of a comprehensive diagnostic solution for patients who had exhausted conventional testing pathways, and how this programme demonstrates that comprehensive, single-platform genomic testing is both feasible and transformative in a resource-constrained public health setting.

Oxford Nanopore Technology (ONT) long-read sequencing has the potential to transform rare disease genomics by enabling resolution of genomic sequences inaccessible to short-read platforms. This talk introduces the ONT research use DNA sequencing workflow — from raw signal data through basecalling and modified base calling, to secondary analysis (structural variant detection, repeat expansion analysis, copy-number analysis, methylation calling) and tertiary analysis. The bioinformatics architecture underlying these steps is outlined for a clinical genomics audience. Primary ciliary dyskinesia (PCD) is presented as an exemplar application. PCD is a rare, genetically heterogeneous motile ciliopathy affecting approximately 1:10,000 individuals, caused by pathogenic variants in over 60 genes. Standard short-read NGS panels achieve a molecular diagnosis in only 50–70% of cases; problem genes with pseudogene homology (notably HYDIN/HYDIN2), complex structural variants, and deep-intronic splice variants account for much of the residual diagnostic gap. Correct pathogenicity interpretation of PCD variants requires knowledge of tissue-specific transcript usage, as variants are interpreted in the context of relevant transcripts. We present data from a collaboration between sanobis GmbH and the University of Münster, in which ONT long-read RNA (cDNA) sequencing was applied to three matched tissues: Air-liquid interface (ALI)-cultured multiciliated respiratory epithelial cells, dermal fibroblasts, and peripheral blood leukocytes. Results demonstrate pronounced tissue-restricted expression of motile-cilia genes, a novel DNAH5 isoform detected only in non-blood tissues, and — in a HYDIN variant patient — aberrant transcript exclusively detectable in the respiratory sample. These findings establish tissue-appropriate ALI culture as a prerequisite for isoform-level PCD diagnosis and support long-read multi-omics as a future second-tier diagnostic strategy for unsolved cases.

Since 2016, the South African Medical Research Council and the Department of Science and Innovation have collaborated to advance genomic and precision medicine research, innovation and implementation in South Africa. Building on this foundation, South Africa is developing the South African 110K Human Genome Programme, a national initiative that aims to sequence 110,000 human genomes and establish a representative genomic resource linked to relevant health and phenotypic data. The programme seeks to leverage South Africa’s existing scientific expertise, longitudinal cohorts, sequencing capacity and research infrastructure, while strengthening the broader genomic medicine ecosystem through targeted investment in national data infrastructure, governance frameworks, workforce development and shared analytical resources. The first implementation phase, the SA 110K HGP 10K Pilot, has begun, the aim to sequence 10,000 genomes from selected longitudinal cohorts. The pilot will provide an opportunity to evaluate approaches to cohort inclusion, ethics and governance, phenotype and metadata harmonisation, sequencing standardisation, data management and secure access to genomic and health data. This presentation will describe the strategic and operational approach of the programme, and its potential to address gaps in the representation of African populations in genomic research. It will further consider how the programme can contribute to the development of a robust national health-data environment and generate the evidence, infrastructure and capabilities required to support the responsible implementation of genomic and precision medicine in South Africa. Through the development of a nationally coordinated and sustainable genomic resource, the South African 110K Human Genome Programme aims to support more relevant research, improve understanding of disease within South Africa’s diverse populations and create a foundation for more equitable, evidence informed healthcare.