Core lab webinar: stay at the forefront of genomic technology
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The future of life science research lies in comprehensive genomic, epigenomic, and transcriptomic analyses. However,19 % of the human genome is inaccessible and 40% of all structural variants are missed by short-read sequencing [1,2] , <3% all CpG sites are covered by standard genotyping approaches [3] , all of those can now be addressed through the application of long, direct nanopore sequencing reads[4].
With nanopore sequencing, it is now possible to resolve previously hidden genomic regions and variants, generate telomere-to-telomere genome assemblies, explore base modifications, and perform isoform-level transcriptomics — all on a single platform.
The Oxford Nanopore Core Lab Programme and nanopore sequencing provides deeper insights, expands application portfolios, and helps accelerate all stages of sequencing process for core labs. This allows the research groups to accomplish cutting-edge research projects that was previously inaccessible.
On 13th December, we will be joined with Dr. Gyoungju Nah from Seoul National University, to share her research on leveraging nanopore sequencing for chromosome-Level genome assembly; and Dr. Ira Deveson from Garvan Institute who will share his research on the the landscape of genomic structural variation in Indigenous Australians.
Reference:
- Ahsan, M.U., Liu, Q., Fang, L., and Wang, K. NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks. Genome Biol. 22, 261 (2021). DOI: https://doi.org/10.1186/s13059-021-02472-2
- Flynn, R. et al. Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays. Human molecular genetics, 31(18), 3181–3190 (2022). DOI: https://doi.org/10.1093/hmg/ddac112
- Beyter, D., et al. Long-read sequencing of 3,622 Icelan
- Method of the Year 2022: long-read sequencing. Nat. Methods 20, 1 (2023). DOI: https://doi.org/10.1038/s41592-022-01759-x
Register
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Agenda
Time (JST/KST) | Agenda | Speaker |
|---|---|---|
13:00 - 13:05 | Welcome address | Ross Napoli Oxford Nanopore Technologies |
13:05 - 13:40 | The landscape of genomic structural variation in Indigenous Australians | Ira Deveson Garvan Institute of Medical Research |
13:40 - 14:15 | Towards a Chromosome-Level Genome Using Nanopore Technology | Gyoungju Nah NICEM, Seoul National University |
14:15 - 14:50 | Updating... | TBC |
14:50 - 15:00 | Closing remark | Ross Napoli Oxford Nanopore Technologies |
Meet the Speakers
Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets1,2,3. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here, we apply population-scale whole genome long-read sequencing4 to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large indels (20-49bp; n=136,797), structural variants (SVs; 50bp-50kb; n=159,912) and regions of variable copy-number (>50kb; n=156). The majority are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of SVs appear to be exclusive to Indigenous Australians (12% lower bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short-tandem repeats (STRs) throughout the genome to characterise allelic diversity at fifty known disease loci5, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among STR sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.
Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets1,2,3. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here, we apply population-scale whole genome long-read sequencing4 to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large indels (20-49bp; n=136,797), structural variants (SVs; 50bp-50kb; n=159,912) and regions of variable copy-number (>50kb; n=156). The majority are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of SVs appear to be exclusive to Indigenous Australians (12% lower bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short-tandem repeats (STRs) throughout the genome to characterise allelic diversity at fifty known disease loci5, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among STR sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.
Dr Ira, - - - For the Gold Standard Genome, high-quality genome assembly and chromosome-level scaffolding are important. Nanopore technology is suitable for both de novo genome assembly and scaffolding, allowing the generation of chromosome-level genomes in a one-stop process. Over the past three years, NICEM has generated high-quality whole genome sequencing of more than 170 species (plants, insects, animals, fungi) using ONT PromethION24. Recently, we have been providing service of Pore-C technology using Nanopore. Pore-C is the technology that overcomes the shortcomings of Hi-C in many ways: (1) scaffolding success rate (2) reduction of data generation time (3) cost. We successfully generated scaffolds from 12 plant and insect species, resulting in an equal number of chromosomes and scaffolds. In this talk, we present our case studies on Nanopore technology and suggest Nanopore technology can serve as a platform for the Gold Standard for de novo genome assembly and scaffolding.
For the Gold Standard Genome, high-quality genome assembly and chromosome-level scaffolding are important. Nanopore technology is suitable for both de novo genome assembly and scaffolding, allowing the generation of chromosome-level genomes in a one-stop process. Over the past three years, NICEM has generated high-quality whole genome sequencing of more than 170 species (plants, insects, animals, fungi) using ONT PromethION24. Recently, we have been providing service of Pore-C technology using Nanopore. Pore-C is the technology that overcomes the shortcomings of Hi-C in many ways: (1) scaffolding success rate (2) reduction of data generation time (3) cost. We successfully generated scaffolds from 12 plant and insect species, resulting in an equal number of chromosomes and scaffolds. In this talk, we present our case studies on Nanopore technology and suggest Nanopore technology can serve as a platform for the Gold Standard for de novo genome assembly and scaffolding.
Gyoungju Nah, - - -
