Nanopore Day, DC
Nanopore Day, DC
Nanopore Day, Heidelberg
Nanopore Day, Heidelberg
Nanopore Day, Seoul
Nanopore Day, Seoul
Nanopore Day, Utrecht
Nanopore Day, Utrecht
Mon 28th October 2019
Hear about the latest tech updates for Oxford Nanopore as well as hearing from local users about their latest work using nanopore technology.
There is no delegate fee for this event.
Your place at this event will be confirmed via email from events@nanoporetech.com. Completion of this form does not constitute confirmation. Spaces are limited and will be allocated on a first-come, first-served basis.
Confirmed speakers include:
- Adam Phillippy, National Human Genome Research Institute (NHGRI)
- Dan Garalde, Oxford Nanopore Technologies
- Tim Gilpatrick, Johns Hopkins University
- Narjol Gonzalez-Escalona, FDA
- Gary Vora, Naval Research Labs
Abstracts:
Telomere-to-telomere assembly of complete human chromosomes - Adam Phillippy, NHGRI
After nearly two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to end, and hundreds of unresolved gaps persist. The remaining gaps include ribosomal rDNA arrays, large near-identical segmental duplications, and satellite DNA arrays. These regions harbor largely unexplored variation of unknown consequence, and their absence from the current reference genome can lead to experimental artifacts and hide true variants when re-sequencing additional human genomes. We recently generated a de novo human genome assembly that surpasses the continuity of GRCh38, along with the first gapless, telomere-to-telomere assembly of a human X chromosome. This work was enabled by high-coverage, ultra-long-read nanopore sequencing, combined with complementary technologies for quality improvement and validation. We are currently extending this work to additional chromosomes and I will provide an update on the T2T consortium’s progress towards finishing the first complete human genome.
Beyond A, T, C & G: Nanopore cDNA and Direct RNA sequencing - Dan Garalde, Oxford Nanopore Technologies
Sequencing is an important tool for expanding our understanding of the biological processes mediated by RNA. Oxford Nanopore devices have been used extensively to sequence DNA and cDNA. More recently, direct, electrically-based sequencing of RNA became possible using the same devices. Both Nanopore cDNA and direct RNA-seq methods have potential advantages in the study of RNA by providing full-length, strand-specific RNA sequences. Direct RNA further circumvents reverse transcription and amplification steps that are known to introduce biases. The direct RNA-seq method also permits the detection of chemical modifications in RNA. Here we present direct RNA and cDNA sequencing results and provide the latest updates on both technologies.
Targeted Nanopore Sequencing with Cas9 for studies of methylation, structural variants and mutations - Tim Gilpatrick, Johns Hopkins University
• There is an existing need for clinical tools that can be used to rapidly assess genomic variants and epigenetic changes at medically relevant genes. We have been using the CRISPR/Cas9 system for target-enrichment nanopore sequencing. We show the ability of this method to generate greater than 400X average coverage at 10 genomic loci (mean size 18kb) with a single MinION flow cell. We demonstrate that this high coverage data enables us to (1) profile DNA methylation patterns at cancer driver genes, (2) detect structural variations and query repetitive elements, and (3) survey for the presence of single nucleotide mutations. We demonstrate applications of this technique by examining the well-characterized GM12878 cell line as well as breast cell lines and primary patient tissue.
Foodborne Bacterial Whole Genome Sequencing Using Nanopore - Narjol Gonzalez-Escalona, FDA
Closing bacterial genomes provides high-quality reference genomes that support pathogen source tracking during a foodborne outbreak investigation. Although closing bacterial genomes is usually achieved by PacBio sequencer, a simpler and cheaper sequencer is available: MinION (nanopore). We tested the technology and will be discussing its performance in closing bacterial genomes.
Thu 7th November 2019
Hear about the latest tech updates for Oxford Nanopore as well as hearing from local users about their latest work using nanopore technology.
There is no delegate fee for this event.
Your place at this event will be confirmed via email from events@nanoporetech.com. Completion of this form does not constitute confirmation. Spaces are limited and will be allocated on a first-come, first-served basis.
Confirmed Speakers include:
- Anna Dolnik, Charité Universitätsmedizin Berlin
- Andreas Mock, Universitätsklinikum Heidelberg & Deutsches Krebsforschungszentrum
- Florian Kraft, RWTH Aachen
- Harmeet Singh Chawla, Justus Liebig University
- Aaron Brooks, EMBL
- Christoph Dieterich, University Hospital Heidelberg
Measuring transcriptomic diversity induced by genome SCRaMbLEing with direct RNA sequencing - Aaron Brooks, EMBL
Eukaryotic genomes are organized non-randomly. We are studying how abrupt changes to genome organization shapes the transcriptional landscape using Sc2.0, a yeast strain composed entirely of designer, synthetic DNA. Synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) is a key design feature of the synthetic yeast genome project. SCRaMbLE generates stochastic and complex rearrangements at engineered recombinase sites throughout the genome on-demand using Cre-mediated recombination. We have characterized extensive transcriptional diversity in >60 independent SCRaMbLE strains containing a circular synthetic chromosome, synIXR. These transcriptional alterations appear to be isolated to the SCRaMbLEd chromosome and dependent on rearrangements specific to each SCRaMbLE strain. Using direct RNA sequencing, we have observed novel transcriptional events in SCRaMbLEd genomes, including alteration to transcript start and termination sites. Our results suggest an inextricable link between physical organization of the genome and transcript isoform expression.
Mon 11th November 2019
Hear about the latest tech updates for Oxford Nanopore as well as hearing from local users about their latest work using nanopore technology.
Some talks will be given in Korean and some in English. Translation will not be provided.
Confirmed speakers include:
- Jangsup Moon, Seoul National University Hospital
- Hui-Su Kim, KOGIC, UNIST
- Sang-Choon Lee, PHYZEN
- Yong Min Kim, Korea Research Institute of Bioscience & Biotechnology (KRIBB)
- Jungwoo Lee, Cancer Genome Research Center
- James Brayer, Oxford Nanopore Technologies Ltd.
- Jihye Kim, Oxford Nanopore Technologies Ltd.
There is no delegate fee for this event.
Your place at this event will be confirmed via email from events@nanoporetech.com. Completion of this form does not constitute confirmation. Spaces are limited and will be allocated on a first-come, first-served basis.
Nanopore sequencing for Clinical Metagenomics: SNUH experiences - Jangsup Moon, Seoul National University Hospital
Rapid pathogen identification is very important in the treatment of infectious disease. Despite the current efforts to diagnose pathogens, in many cases, they remain undiagnosed. Nanopore sequencing contains many advantages for metagenomics analysis, which are simple library preparation procedure, real-time analysis, and long-read sequencing. We have performed nanopore sequencing in hundreds of clinical samples obtained from various types of infectious disease patients treated at Seoul National University Hospital. In this talk, I will demonstrate the usefulness and benefits of nanopore metagenomics sequencing for the identification of pathogens in the clinical setting. Particularly for bacterial detection, the culture-independent nanopore metagenomics sequencing was faster and more sensitive than conventional culture studies and was capable of polymicrobial detection at once. Nanopore metagenomic sequencing can be of great help to the clinical treatment of patients with infectious diseases through subsequent studies.
Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information - Hui-Su Kim, KOGIC, UNIST
Long DNA reads produced by single molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short read DNA fragments. For de novo assembly, PacBio and Oxford Nanopore Technologies (ONT) are favorite options. However, PacBio’s SMRT sequencing is expensive for a full human genome assembly and costs over 40,000 USD for 30x coverage as of 2019. ONT PromethION sequencing, on the other hand, is one-twelfth the price of PacBio for the same coverage. This study aimed to compare the cost-effectiveness of ONT PromethION and PacBio’s SMRT sequencing in relation to the quality. We performed whole genome de novo assemblies and comparison to construct an improved version of KOREF, the Korean reference genome, using sequencing data produced by PromethION and PacBio. With PromethION, an assembly using sequenced reads with 64x coverage (193 Gb, 3 flowcell sequencing) resulted in 3,725 contigs with N50s of 16.7 Mbp and a total genome length of 2.8 Gbp. It was comparable to a KOREF assembly constructed using PacBio at 62x coverage (188 Gbp, 2,695 contigs and N50s of 17.9 Mbp). When we applied Hi-C-derived long-range mapping data, an even higher quality assembly for the 64x coverage was achieved, resulting in 3,179 scaffolds with an N50 of 56.4 Mbp. The pore-based PromethION approach provides a good quality chromosome-scale human genome assembly at a low cost with long maximum contig and scaffold lengths, and is more cost-effective than PacBio at comparable quality measurements.
Application of Nanopore Sequencing Technology to Genome Assembly of Various Organisms - Sang-Choon Lee, PHYZEN
Nanopore sequencing technology of Oxford Nanopore Technologies (ONT) is the latest third generation sequencing technology for cost-effective high-throughput sequencing of long DNA molecules. At present, this technology is providing new opportunity for efficient and high-quality genome analysis and well demonstrated by more than 300 genomes of various organisms assembled using Nanopore sequencing data. So far, our company sequenced genomes of more than 170 samples and produced total >900 Gb Nanopore sequencing data in Korea. Using the data, we de novo assembled and generated high-quality draft genome sequences of bacteria, fungi, mushrooms, insects and plants. In this talk, we will introduce sequencing and genome assembly results obtained by Nanopore sequencing and bioinformatics analysis of our company.
Sequencing and genome assembly of two plant genomes using ONT technology - Yong-Min Kim, KOBIC, KRIBB
Construction of high-quality genome in plants is an essential and fundamental analysis for further application of genome information from basic science to breeding. However, the high content of repetitive sequences and polyploidy are barriers to constructing a high-quality reference genome. In the case of polyploid species containing large amount of duplicated regions, short reads can produce chimeric sequences and fragmented contigs. Long or ultra-long reads from third-generation sequencing platforms can be a solution for constructing high-quality reference genomes for polyploid species. ONT technology is one of the candidates to quickly and cost-effectively generate longer read length that can facilitate the assembly of complex plant genomes. The read length depends on the physical length of the DNA, which directly affects the sequencing quality. However, extraction of high purity and high molecular DNA have been difficult in plants because of high content of polysaccharides and polyphenols. Therefore, the establishment of DNA extraction method is the most critical step to leverage the value of nanopore sequencing platforms. Here, we report improved sequencing results and genome assemblies of two plant genomes, Solanum lycopersicum Hawaii7996 and Hibiscus syriacus Gangneung.
Long read based transcriptome profiling of Korean colon cancer patients using Nanopore Sequencing - Jungwoo Lee, Cancer Genome Research Center
With the advent of next-generation sequencing (NGS) technology, researchers have been able to capture sequences from the genome for their interest of study. Nonetheless, universal sequencing technology such as Illumina, still contains the insufficient contextual information due to their usage of short fragmented reads, which limits understanding of the complex structures of the genome and transcriptome. Oxford Nanopore Technology (ONT) on the other hand, has allowed the researchers to capture the full-length transcripts, thereby ensuring the full and novel information of transcriptome. Although a large number of short-read based analyses have accumulated the cancer transcriptome profile, the attempts of long-read based profiling for a better understanding of cancer are still in need. To meet this need, we have sequenced 20 pairs of Korean colon cancer patients using cDNA-PCR Nanopore sequencing. We identified the long-read based complex transcriptome profiles and selected colon cancer specific isoforms, as well as fusion gene candidates. We also selected differentially expressed transcript candidates including non-coding RNAs to reveal their molecular and functional analogy which could explain the clinical implication in colon cancer. Overall, we have characterized the transcriptome profiles of Korean colon cancer patients using Nanopore sequencing to identify a potential biomarker that can be used in the clinical field. Using such technology with further validation, we expect to find novel and more precise clinical biomarkers in colon cancer which could lead to a new molecular mechanism to better understand colon carcinogenesis.
Wed 27th November 2019
Hear about the latest tech updates for Oxford Nanopore as well as talks from local scientists about their latest work using nanopore technology.
Confirmed speakers include:
- Ies Nijman, Manager Useq, UMC Utrecht
- Federica Brogioli, Orvion
- Sander van Boheemen, Erasmus MC
- Reindert Nijland, Assistant Professor Molecular Marine Ecology, Wageningen University
- Christina Stangl, UMC Utrecht
- Leila Luheshi, Associate Director, Clinical and Translational Research, Oxford Nanopore Technologies Ltd.
- Olivier Lucas, Associate Director, Regional Sales (Europe South), Oxford Nanopore Technologies Ltd.
There is no delegate fee for this event.
Your place at this event will be confirmed via email from events@nanoporetech.com. Completion of this form does not constitute confirmation. Spaces are limited and will be allocated on a first-come, first-served basis.
The agenda is yet to be confirmed.
Rapid Routine Viral Genotyping using Nanopore Sequencing - Sander van Boheemen, Erasmus MC
Aim: Viral genotyping is an important tool to guide and monitor treatment decisions, support and evaluate (hospital) infection control measures, and contribute to public health surveillance of a broad range of diseases including viral hepatitis, enteroviruses and HIV. For example, the severity of hepatitis can vary between hepatitis B genotypes, and different patterns of resistance-associated mutations are involved in antiviral resistance for various genotypes for hepatitis C virus. Currently, routine genotyping is mostly performed using targeted amplification and subsequent Sanger sequencing, with target choice and performance characteristics tuned to specific use cases. The fast development of deep sequencing platforms offers potential for merging clinical and public health applications into a single combined application, thus potentially cost-saving when used in clinical laboratories with sufficient throughput for pooling of analyses.
Method: We have developed a rapid multiplexing and library preparation protocol using real-time nanopore sequencing to determine the genotypes of multiple viral targets. Thus far, these viral targets include HBV, HCV and measles virus. One nanopore run allows for simultaneous sequencing of multiple viral targets.
Results: Viruses from various species, genotypes and viral loads were rapidly sequenced on the Nanopore platform, demultiplexed and subtyped. All samples were confirmed by Sanger sequencing as gold standard. The reported high error rate associated with the nanopore sequencing chemistry was resolved by adequate read coverage.
Conclusions: We were able to accurately subtype a variety of viral species. Furthermore, multiple samples from different virus species were successfully combined, sequenced, and demultiplexed after one sequencing run. This allowed us to rapidly genotype viruses. Future efforts will determine the feasibility of nanopore sequencing in antiviral resistance testing.
Partner-independent fusion gene detection by multiplexed CRISPR/Cas9 enrichment and long-read Nanopore sequencing - Christina Stangl, UMC Utrecht
Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment possibilities. The promiscuity of fusion genes with respect to partner choice and exact breakpoint-positions restricts their detection in the diagnostic setting. To accurately identify these gene fusions in an unbiased manner, we developed FUDGE: a FUsion gene Detection assay from Gene Enrichment. FUDGE couples target-selected and strand-specific CRISPR/Cas9 activity for enrichment and detection of fusion gene drivers - without prior knowledge of fusion partner or breakpoint-location - to long-read Nanopore sequencing. FUDGE encompasses a dedicated bioinformatics approach (NanoFG) to detect fusion genes from Nanopore sequencing data. Our strategy is flexible with respect to target choice and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in a single sequencing run. We demonstrate that FUDGE effectively identifies fusion genes in cancer cell lines, tumor samples and on whole genome amplified DNA irrespective of partner gene or breakpoint-position in 100% of cases. In summary, we have developed a rapid and versatile fusion gene detection assay, providing an unparalleled opportunity for pan-cancer detection of fusion genes in routine diagnostics.
