HGSA 2026
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Oxford Nanopore are sponsoring, exhibiting and presenting the HGSA 2026 conference. This conference features a comprehensive scientific programme showcasing the latest advances in clinical and research genetics, bringing together researchers, clinicians, laboratory scientists and academics working in human genetics and genomics.
Visit us at our booth #13 and join us for the lunch workshop showcasing innovative application of Oxford Nanopore techniques.
Oxford Nanopore Industry Session
- Monday, 3 August 2026 | 2:45pm - 3:45pm
Time | Agenda | Speaker |
|---|---|---|
14:45 - 15:05 | Using Oxford Nanopore Technologies long-read sequencing to resolve unexplained hereditary colorectal cancer and polyposis syndrome patients | Eric Joo, University of Melbourne |
15:05 - 15:25 | Genetic testing solves mystery of teens’ sudden deaths | Zoe Ward, University of Auckland |
15:25 - 15:45 | Genome-wide phasing using routine clinical samples | Neblina Sikta, Victorian Clinical Genetics Services (VCGS) |
Speakers
Background: Current hereditary colorectal cancer multigene panel testing uses conventional short-read next-generation sequencing, which can miss complex genetic variations such as structural variants (SVs) and single nucleotide variants (SNVs) in repetitive regions. We aimed to assess diagnostically challenging hereditary colorectal cancer and polyposis patients with unexplained aetiology using Oxford Nanopore Technologies (ONT) long-read sequencing. Methods: We performed ONT Adaptive Sampling of 385 known hereditary cancer genes in 16 colorectal cancer and polyposis patients without known germline pathogenic variants (PVs). This included unexplained adenomatous polyposis (UAP, n = 11), unexplained hamartomatous polyposis (n = 2 family members), familial colorectal cancer Type X (FCCТX, n = 2 family members), suspected Lynch syndrome (n = 4), and serrated polyposis syndrome (SPS, n = 4). All UAP cases had previously tested negative for APC mosaicism. Basecalling was performed using the Dorado super accuracy model and variants were called using the wf-human-variation workflow incorporating Sniffles2 and Clair3. Results: ONT sequencing identified a novel predicted loss-of-function APC intronic variant (NM_000038.6: c.1958+428G>T) in one proband and the relative with UAP. The SpliceAI in silico tool predicted this variant to create an abnormal acceptor splicing site (score = 0.25). The variant was absent from the gnomAD database and overlapped a 300 bp short interspersed nuclear element. No SVs or predicted PVs were identified in the remaining UAP cases. One SPS patient was identified with a novel 6.5 kb deletion in RNF43. One suspected Lynch syndrome family was identified with a 3.2 kb SVA insertion in MSH2. No SVs or complex predicted PVs in known CRC and polyposis genes were identified in the unexplained hamartomatous polyposis or FCCTX cases. Conclusions: ONT long-read sequencing technology provides an accurate, cost- and time-effective approach to detect complex genetic variants in diagnostically challenging hereditary colorectal cancer and polyposis syndrome patients.
Background: Current hereditary colorectal cancer multigene panel testing uses conventional short-read next-generation sequencing, which can miss complex genetic variations such as structural variants (SVs) and single nucleotide variants (SNVs) in repetitive regions. We aimed to assess diagnostically challenging hereditary colorectal cancer and polyposis patients with unexplained aetiology using Oxford Nanopore Technologies (ONT) long-read sequencing. Methods: We performed ONT Adaptive Sampling of 385 known hereditary cancer genes in 16 colorectal cancer and polyposis patients without known germline pathogenic variants (PVs). This included unexplained adenomatous polyposis (UAP, n = 11), unexplained hamartomatous polyposis (n = 2 family members), familial colorectal cancer Type X (FCCТX, n = 2 family members), suspected Lynch syndrome (n = 4), and serrated polyposis syndrome (SPS, n = 4). All UAP cases had previously tested negative for APC mosaicism. Basecalling was performed using the Dorado super accuracy model and variants were called using the wf-human-variation workflow incorporating Sniffles2 and Clair3. Results: ONT sequencing identified a novel predicted loss-of-function APC intronic variant (NM_000038.6: c.1958+428G>T) in one proband and the relative with UAP. The SpliceAI in silico tool predicted this variant to create an abnormal acceptor splicing site (score = 0.25). The variant was absent from the gnomAD database and overlapped a 300 bp short interspersed nuclear element. No SVs or predicted PVs were identified in the remaining UAP cases. One SPS patient was identified with a novel 6.5 kb deletion in RNF43. One suspected Lynch syndrome family was identified with a 3.2 kb SVA insertion in MSH2. No SVs or complex predicted PVs in known CRC and polyposis genes were identified in the unexplained hamartomatous polyposis or FCCTX cases. Conclusions: ONT long-read sequencing technology provides an accurate, cost- and time-effective approach to detect complex genetic variants in diagnostically challenging hereditary colorectal cancer and polyposis syndrome patients.
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Eric Joo, University of MelbourneZoe Ward, University of Auckland )
Neblina Sikta, Clinical Bioinformatician, Victorian Clinical Genetics Services (VCGS)Steven is a Field Applications Scientist at Oxford Nanopore Technologies and the microbiology subject matter expert for Australia and New Zealand. He supports laboratories in implementing nanopore sequencing technologies for rapid, high‑resolution genomic analysis. Steven has a background in microbial genomics, with five years of postdoctoral research experience prior to joining Nanopore.
