Oxford Nanopore User Group Meeting, Hong Kong
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Join us on Monday, 14th of September in Hong Kong, for an exciting series of talks from local researchers using nanopore sequencing. The agenda also includes a technical update from the Oxford Nanopore team, as well as a Q&A with the presenters and a product display.
Space is limited! Please register early to secure your spot. For further details, please contact events@nanoporetech.com.
Confirmed speakers so far
Elvis Dong, Chinese University of Hong Kong
Kevin To, Queen Mary Hospital
Nike K C Lau, Princess Margaret Hospital
Liang Gong, Zhejiang University Medical Center
Thidathip Wongsurawat, Siriraj Hospital, Mahidol University
Speakers
X-linked genetic diseases affect sexes differently due to X-chromosome inactivation-driven differential methylation in females. Targeted long-read sequencing (LRS) via adaptive sampling (AS) characterizes genomic composition and methylation, but performs poorly with non-high-molecular-weight (non-HMW) DNA. We optimized an AS-based LRS protocol for non-HMW DNA and validated its diagnostic utility in 20 families with known X-linked defects previously identified by routine methods. Incorporating optimized DNA fragmentation, size selection, and library construction, our protocol achieved a >15-fold target enrichment compared to 8.1-fold using standard methods. The optimized LRS successfully detected all previously reported variants and uncovered novel genomic findings in 7/20 families (35%). By resolving structural variant breakpoints and determining gene methylation status, this protocol led to variant reclassification in 3/20 cases (15%). Ultimately, this optimized AS-based approach enables comprehensive genomic and methylation profiling of non-HMW DNA, offering a robust tool for evaluating X-linked defects with potential application to other disease states.
X-linked genetic diseases affect sexes differently due to X-chromosome inactivation-driven differential methylation in females. Targeted long-read sequencing (LRS) via adaptive sampling (AS) characterizes genomic composition and methylation, but performs poorly with non-high-molecular-weight (non-HMW) DNA. We optimized an AS-based LRS protocol for non-HMW DNA and validated its diagnostic utility in 20 families with known X-linked defects previously identified by routine methods. Incorporating optimized DNA fragmentation, size selection, and library construction, our protocol achieved a >15-fold target enrichment compared to 8.1-fold using standard methods. The optimized LRS successfully detected all previously reported variants and uncovered novel genomic findings in 7/20 families (35%). By resolving structural variant breakpoints and determining gene methylation status, this protocol led to variant reclassification in 3/20 cases (15%). Ultimately, this optimized AS-based approach enables comprehensive genomic and methylation profiling of non-HMW DNA, offering a robust tool for evaluating X-linked defects with potential application to other disease states.
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Zirui Dong (Elvis), Chinese University of Hong KongAlport syndrome (AS) is a prevalent inherited kidney disorder mainly caused by mutations in COL4A3, COL4A4, and COL4A5 genes. To elucidate the genetic variants of AS, we implemented a sequential sequencing strategy within a Chinese cohort of 555 patients, comprising whole-exome sequencing (WES) for all participants, followed by whole-genome sequencing (WGS), RNA sequencing (RNA-seq), and nanopore long-read sequencing (NLR-seq) for selected individuals. We identify 431 distinct variants in 509 (91.7%) patients, with 42.2% being novel. Beyond WES, additional sequencing approaches resolve 23 patients with noncoding, copy number, or structural variants. Notably, noncoding variants account for 16.2% of detected variants and exhibit ethnic-specific mutagenesis patterns. More interestingly, NLR-seq uncovers two novel types of structural variants, namely large insertions in intronic regions and complex duplication-inversion variants. This study provides deeper insights into the genetic architecture of AS and proposes a research paradigm for improving the genetic diagnosis of inherited diseases.
Alport syndrome (AS) is a prevalent inherited kidney disorder mainly caused by mutations in COL4A3, COL4A4, and COL4A5 genes. To elucidate the genetic variants of AS, we implemented a sequential sequencing strategy within a Chinese cohort of 555 patients, comprising whole-exome sequencing (WES) for all participants, followed by whole-genome sequencing (WGS), RNA sequencing (RNA-seq), and nanopore long-read sequencing (NLR-seq) for selected individuals. We identify 431 distinct variants in 509 (91.7%) patients, with 42.2% being novel. Beyond WES, additional sequencing approaches resolve 23 patients with noncoding, copy number, or structural variants. Notably, noncoding variants account for 16.2% of detected variants and exhibit ethnic-specific mutagenesis patterns. More interestingly, NLR-seq uncovers two novel types of structural variants, namely large insertions in intronic regions and complex duplication-inversion variants. This study provides deeper insights into the genetic architecture of AS and proposes a research paradigm for improving the genetic diagnosis of inherited diseases.
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Liang Gong, Liangzhu Laboratory, Zhejiang University
