London Calling final day: more groundbreaking research from across the globe, as well as a STEM session and informatics updates
The final day of this year’s London Calling started with a hugely popular informatics update that saw four Oxford Nanopore experts sharing their latest work. This covered the future of basecalling with Dorado, realising the most from GPUs and the best way to leverage Nextflow for the analysis of anything, anywhere, by anyone.
As is customary now, 60 school children were welcomed to Old Billingsgate for a STEM day of talks and workshops to provide an insight into what it’s like to work in a scientific technology company. During the day, the students had the opportunity to get hands-on with the tech, hear from scientists using it around the world, and talk to them about their work.
This year we had another great series of Spotlight speakers pitching for the chance to present on the main stage and we congratulate Kalinka Sand Knudsen, Aalborg University, Denmark for winning this. Her talk on ‘Fantastic methanotrophs and where to find them’ was a big hit.
You can watch a great summary of this year’s brilliant conference here and check out our Twitter account to hear from people around London Calling and see what it was like on the ground.
Welcome back!
Back on the main stage in the auditorium, Rosemary Sinclair Dokos welcomed the live and virtual audiences to the final day. Rosemary announced new flow cell pricing for high-output, high-performance sequencing and shared key platform improvements to further improve reliability during her product update. These updates are designed to make high-output sequencing more affordable and accessible — and the Oxford Nanopore platform simpler and more robust to support a variety of different users.
scNanoATAC-seq: a long-read single-cell assay to simultaneously detect chromatin accessibility and genetic variants - Fuchou Tang, Biomedical Pioneering Innovation Center, Peking University, China
Fuchou began his talk by describing a long-read single-cell ATAC (assay for transposase-accessible chromatin) sequencing method to detect open chromatin regions within individual cells — providing information on the regulation of gene expression. Using the nanopore sequencing platform to develop the method, they were able to obtain ‘long contigs to identify many exciting features’ including individual cell type, isoforms, and transcription patterns. Similar methods focus on 100–300 bp chromatin regions, which can be achieved using alternative short-read sequencing technology; however, short-read sequencing technology does not enable structural variants or haplotype phasing to be investigated. Using long nanopore reads, genomic variation — single nucleotide variants, large scale copy number variants, and structural variants — and chromatin accessibility can be clearly and simultaneously identified within individual cells.
Previous benchmarking studies revealed scNanoATAC-seq performed well in identifying different cell populations and key regulatory features of chromatin accessibility. Fuchou went on to describe the ‘beautiful results’ they obtained showing the different cell stages of embryonic development — a process with very few cells. The open and closed chromatin states provided direct evidence of co-accessibility between neighbouring allele-specific peaks — where the chromatin accessibility of two sites in the same single cell and, in fact on the same allele, was detected simultaneously in a long read.
Population-scale nanopore sequencing to further understand the genetics of Alzheimer’s disease and related dementias - Kimberley Billingsley, NIH Center for Alzheimer’s and Related Dementias, USA
Kimberley is a member of the NIH intramural Center of Alzheimer’s and Related Dementias (CARD). A comprehensive understanding of the genetic components of these diseases is critical for their research, but previous use of short-read sequencing technology and SNP arrays has poorly captured important variants such as repeat expansions and structural variants (SVs).
The group are utilising long nanopore reads to sequence ~4,000 human brain clinical research samples, to further understanding of Alzheimer’s disease and related dementias. Samples were sequenced on a PromethION 48, generating >30x depth of coverage with read length N50s of ~30 kb.
Kimberley highlighted that the Oxford Nanopore data ‘has reduced SNP error rate compared to [a short-read sequencing technology], especially in low-mappability regions’. For SV calling, the F1 score was comparable to that of an alternative long-read technology, ‘but at a lower cost and greater throughput’. The data also enabled resolution of differentially methylated regions. Sequencing 222 control frontal cortex clinical research samples, they detected >80,000 SVs and identified cell type-specific methylation.
Galapagos Genetic Barcode: a model for island economic resilience during the COVID-19 pandemic - Jaime A. Chaves, San Francisco State University, USA & Universidad San Francisco de Quito, Ecuador
Jaime began by introducing his work on The Galapagos Genetic Barcode project; a project which encompasses science and community. Jaime explained that The Galapagos Islands are dependent on the ecosystem, especially for tourism. The islands suffered from economic stress during the epidemic, due to a lack of tourism. In response to this, Jaime wanted to create new employment opportunities for the community and transfer new skills.
Jaime explained that Oxford Nanopore sequencing technology was used to reach the goals of this project, which was performed in collaboration with local scientists. This project represents the largest citizen science project on the islands, and all 74 employees on the project were local to the islands, and all of the data was kept within the island. Jaime explained that this is democratising science and went on to summarise the findings of four research projects.
In his final remarks, Jaime explained that the Galapagos Barcode Project is “a model that should and could be implemented in regions where communities understand the importance of preserving ecosystems, and where technologies like nanopore could really help in decision making, and deciphering and understanding biodiversity to protect those environments, to help the livelihoods of the native communities there.”
Panel plenary: The future of clinical genomics
The panel all shared the common belief that genomics is empowering clinicians and their patients by characterising disease, yet short-read sequencing leaves many without a genetic diagnosis due to inherent limitations with the technology. The disease-relevant variants they could be missing include structural variants (SVs), variants in complex genomic regions, methylation abnormalities, repeat expansions, plus limited phasing. In light of this, the presenters shared their studies demonstrating the future and transformative potential of nanopore sequencing in the clinic. Next week we’ll be sharing more from Emma Baple, Royal Devon University Healthcare NHS Foundation Trust and University of Exeter, Ahmad Abou Tayoun Al Jalila Children's Specialty Hospital, Janessa Laskin Canada's Michael Smith Genome Sciences Centre at BC Cancer and Manop Pithukpakorn Siriraj Genomics, Mahidol University.
Nanopore sequencing for real-time genomic surveillance of Plasmodium falciparum - William Hamilton, Wellcome Sanger Institute, UK
The greatest burden of malaria is on African children — in 2021, young children made up 76% of recorded cases. William presented work on malaria biology and sequencing in Ghana, featuring drug resistance trends and vaccine antigen diversity, and showed the progress of laboratory techniques training in Navrongo. Highlighting that the project had a strong focus on all steps being performed in Ghana, William described how the DNA extraction and sequencing, through to the bioinformatic analysis was achieved through the training of local students. The workflow included targeted sequencing with multiplex PCR and base-calling with Guppy, while the bioinformatics work featured their custom workflow “Nano-rave,” which involved mapping with Minimap 2 and variance calling with Medaka.
William described how sequencing was performed using the MinION, some with R10.4.1 flow cells, and 24 samples were multiplexed per flow cell. Their results included resistance marker data, which provides valuable information on which malaria treatments are likely to be effective. Furthermore, nanopore sequencing enabled insights into the Csp antigen of the malaria vaccine, which had been a significant challenge to do by short-read sequencing due to a highly repetitive genomic region. William concluded by highlighting the benefits that nanopore sequencing had brought to the project — portable instruments, real-time data, and accessible pricing.
Closing
Gordon Sanghera closed this year’s conference and said he’s looking forward to seeing you all in Singapore and Houston for the Nanopore Community Meetings!
Finally, if you missed yesterday’s technology update from CTO Clive Brown, you can watch this on demand here.