Core lab seminar at the University of Hong Kong (HKU)
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Join us on December 8th at the University of Hong Kong, for an exciting afternoon of talks from local researchers using nanopore sequencing. The agenda also includes a technical update from the Oxford Nanopore team, Q&A with the presenters, and a product display.
Space is limited! Please register early to secure your spot.
Agenda
Time | Agenda | Speaker |
|---|---|---|
1:30 PM - 2:00 PM | Registration | |
2:00 PM - 2:20 PM | Welcome address | |
2:20 PM - 2:50 PM | Applications of Nanopore Sequencing in Environmental Microbiome and AMR studies | Tong Zhang The University of Hong Kong |
2:50 PM - 3:20 PM | Long-read Small Variant Calling | Ruibang Laurent Luo The University of Hong Kong |
3:20 PM - 3:50 PM | Oxford Nanopore Tech-update | Chris Wu Oxford Nanopore Technologies |
3:50 PM - 4:10 PM | Tea-break | |
4:10 PM - 4:40 PM | Characterising the changing epidemiology of respiratory viruses in Hong Kong through public health genomics | Vijaykrishna Dhanasekaran The University of Hong Kong |
4:40 PM - 5:10 PM | Rapid polyA tail length prediction using deep learning and applications to SARS-Cov2 and host response | Lachlan Coin The University of Melbourne |
5:10 PM - 5:20 PM | Closing remarks |
Meet the Speakers
This talk will present the applications of Nanopore in 1) the assembly of genomes in metagenomics, 2) assembly of genome of pure culture isolates using Nanopore only, 3) absolute quantification of microbial populations and antibiotics resistance genes, 4) exploring host-genetics element relationship, in the environmental samples and clinical samples.
This talk will present the applications of Nanopore in 1) the assembly of genomes in metagenomics, 2) assembly of genome of pure culture isolates using Nanopore only, 3) absolute quantification of microbial populations and antibiotics resistance genes, 4) exploring host-genetics element relationship, in the environmental samples and clinical samples.
Tong Zhang, - - - Efforts have been made to detect SNPs and Indels sensitively, accurately, and efficiently using long reads. Clairvoyante, released in 2020, was the first deep-learning-based germline smaller variant caller that works with ONT long reads, followed by upgrades Clair in 2021, and Clair3 in 2022. Clair3 is now one of the top choices for long-read germline small variant calling. Clair3-Trio and Clair3-Multi-Platform are two extensions that make the best out of the data of additional family members and sequencing platforms. ClairS, released in 2023, addresses long-read somatic small variant calling using tumor-normal pairs and has achieved SNV calling performance comparable to established short-read workflows. Looking forward, we will release Clair3-RNA for germline variant calling with RNA-Seq data, and ClairS-Tumor-Only for somatic small variant calling with tumors without matching normal.
Efforts have been made to detect SNPs and Indels sensitively, accurately, and efficiently using long reads. Clairvoyante, released in 2020, was the first deep-learning-based germline smaller variant caller that works with ONT long reads, followed by upgrades Clair in 2021, and Clair3 in 2022. Clair3 is now one of the top choices for long-read germline small variant calling. Clair3-Trio and Clair3-Multi-Platform are two extensions that make the best out of the data of additional family members and sequencing platforms. ClairS, released in 2023, addresses long-read somatic small variant calling using tumor-normal pairs and has achieved SNV calling performance comparable to established short-read workflows. Looking forward, we will release Clair3-RNA for germline variant calling with RNA-Seq data, and ClairS-Tumor-Only for somatic small variant calling with tumors without matching normal.
Ruibang Laurent, - - - Vijaykrishna Dhanasekaran, - - - Dr Vijaykrishna Dhanasekaran was appointed as Associate Professor in the School of Public Health (SPH) at HKU in 2020. Before joining SPH, he was faculty at Duke-NUS Medical School Singapore from 2010 and Monash University Australia from 2016, and prior to that a postdoctoral fellow and research assistant professor at HKU Department of Microbiology. He has a PhD in microbial ecology and evolution from HKU (2002-2005).
Polyadenylation of RNA is important for RNA stability, nuclear export, and translation. However, accurate determination of polyA tail length is challenging with short read technologies. Direct RNA sequencing on Oxford Nanopore Sequencing Technologies, provides the opportunity to directly measure polyA tail length on millions of RNA molecules. However, until recently, determining polyA tail length from nanopore RNA sequencing has been computationally expensive. We have developed a deep learning approach for rapid estimation of polyA tails, called BoostNano. We demonstrate its effectiveness using both synthetic RNA (sequins) as well experimental datasets. We have also sequenced RNA from a number of different SARS-Cov2 variants, as well as at different time points during cellular infection. In this talk I will outline the results on differential viral polyadenylation between variants. I will also discuss host immune response transcripts which are differentially polyadenylated during the course of infection.
Polyadenylation of RNA is important for RNA stability, nuclear export, and translation. However, accurate determination of polyA tail length is challenging with short read technologies. Direct RNA sequencing on Oxford Nanopore Sequencing Technologies, provides the opportunity to directly measure polyA tail length on millions of RNA molecules. However, until recently, determining polyA tail length from nanopore RNA sequencing has been computationally expensive. We have developed a deep learning approach for rapid estimation of polyA tails, called BoostNano. We demonstrate its effectiveness using both synthetic RNA (sequins) as well experimental datasets. We have also sequenced RNA from a number of different SARS-Cov2 variants, as well as at different time points during cellular infection. In this talk I will outline the results on differential viral polyadenylation between variants. I will also discuss host immune response transcripts which are differentially polyadenylated during the course of infection.
Lachlan Coin, - - - Chris Wu, - - - Chris Wu graduated from Jinan University, majoring in genetics. He has been worked with Eppendorf, Illumina and many other organisations. With more than 10 years of technical support experience in molecular biology and genomics, Chris has gained rich experience in the principles of second-generation sequencing and third-generation sequencing technologies, library construction, instrument operation and bioinformatics analysis.
