22 highlights to remember from 2022
Sat 31st December 2022
It's been yet another incredible year, with our customers continuing to push the boundaries with endlessly inspiring genomics and our own teams driving huge progress with the technology. Below we have outlined just a few of the best bits, but we know there is so much more going on across the whole Nanopore Community and I have no doubt there will be even more in 2023.
All the best,
1. Research community showcases more comprehensive cancer insights
The cancer research community has made huge strides this year in resolving broader variants and epigenetic modifications across entire genomes, targeting large genomic regions of interest or single genes without PCR, and detecting and characterising known and novel full-length transcripts — up to single-cell resolution. We’ve been excited to see many publications emerge, like this one from Yeung et al and this from Thijssen et al.
2. The journey towards the analysis of anything, by anyone, anywhere: A lab in a tent in the Gobi Desert
In May Massimo Delledonne took a group of scientists into the Gobi Desert to capture small mammals, including bats, to study their microbiome, all from a makeshift genomics lab in a tent. They demonstrated the utility of the MinION and VolTRAX in the harsh, off grid and sandy desert environment!
3. The complete human genome is published
The mission to sequence the whole human genome started more than 30 years ago and we were delighted to see the Telomere-to-Telomere Consortium finish and publish the first truly complete, more than 3 billion base pair sequence. Oxford Nanopore’s high accuracy and ultra-long sequencing capabilities finally removed technological barriers and enabled the final 8% of the genome to be revealed. Congratulations to all the fantastic scientists that contributed to this ground-breaking project!
Watch Karen Miga talk at this year’s NCM about taking this forward and improving diversity in the data here.
4. The year that rapid human genetics became ultra-rapid
Two research studies broke new records this year, the first was led by Euan Ashley’s team at Stanford University School of Medicine who developed a workflow for ultra-rapid nanopore sequencing that resulted in actionable characterisation of genetic disease in under eight hours. In one iteration of their experimental setup the PromethION 48 generated 204 Gb in 2 hours and 42 minutes, just over 60-fold coverage of the human genome with one complete pass sequenced every ~2.5 minutes. This even won them a Guinness World Record!
The second was from Danny Miller’s team at University of Washington and Seattle Children’s Hospital. They developed an ultra-rapid analysis using whole genome sequencing with Oxford Nanopore technology that combined prior information about a genetic disease to target a single gene to characterise inheritance of specific familial variants in under three hours from birth.
Geneticist @euanashley and his @StanfordMed colleagues cut the time it takes to sequence a human genome from several weeks to 5 hours and 2 minutes.— Stanford University (@Stanford) August 1, 2022
The feat earned the team a rare accolade in medicine: a Guinness World Record. ⬇️ https://t.co/E1AU3JzXdJ
How quickly can @nanopore be used to assess genetic risk? In this preprint we show that we could determine whether a newborn inherited two known familial variants within 3 hours of birth by WGS and targeted analysis 1/n: https://t.co/N3OFjrm3lT— Danny E. Miller MD PhD (@danrdanny) September 13, 2022
5. Opening up genomics with the PromethION 2 (P2) Solo.
We have always designed products that redefine what is possible in genomics, and our teams proactively design products in a way that is designed to open up important science to broader communities. So, this year we were excited to roll out the world’s most accessible high-yield sequencing device – the palm sized P2 Solo. We want this to open up genomics by enabling anyone, anywhere, access to human-scale genomic data at the highest levels of accuracy.
We have already seen some great results from early access customers!
The second, and fundamental, piece of our new @nanopore sequencing adventure. The new PromethION 2 Solo is in Florence. We are very excited to exploit it for our new high-resolution genomics and epigenomics projects! Stay tuned. #PrecisionHealth #CancerEpigenomics pic.twitter.com/mvk19qEQun— Alberto Magi (@alberto_magi) October 19, 2022
6. Having nanopore cake and eating it: new chemistry to combine high accuracy and high yield
This year the Oxford Nanopore R&D team successfully modified the nanopore, motor and run conditions so that high accuracy could be achieved at high speeds for high-performance, high-yield nanopore data. This latest update has been included in a new kit (Kit V14), to be used alongside flow cells that include a new nanopore (R10.4.1). We have been enjoying reports from the brilliant early access customers who have shown >Q20 raw read (single molecule) accuracy with “Super Accuracy” base calling on default run conditions of 400 bps, and we are now focused on supporting the broader communities to do the same.
Researchers are also starting to become more familiar with Duplex data, where sequencing the template and complement strands can result in single molecule >Q30 accuracy ("Duplex rate" is the proportion of Duplex data in an experiment, versus Simplex data of just one strand),
The new flow cells and kits will move from early access to general release in Q1 2023 so look out for more amazing data
7. The gold-standard in methylation
As methylation is increasingly being thought to have an important role in cancer and many other areas of genomics, we were really pleased to support this research by releasing Remora, a high-performance tool for methylation analysis, into our operating software, MinKNOW. This now means that all Oxford Nanopore users have easy access to precise whole genome methylation detection from PCR-free nanopore sequencing using Remora. You can read more about Remora here.
Not just satisfied with the better-known types of base modifications, we announced at the Nanopore Community Meeting that we are also developing ways for users to be able to look at more exotic modifications. Work is in progress on an all-context 6mA model and we have initiated early research into 8oxoG and ribo-bases in DNA. You can hear more from Lakmal Jayasinghe at NCM here.
8. An aftereffect of lockdown: a much more accessible London Calling conference.
We strive for accessibility in genomics, and lockdown accelerated another part of our innovation – creating a fully immersive conference platform for London Calling. This year we were thrilled to open the doors to Old Billingsgate at the same time as our virtual doors to a global audience. Our first hybrid London Calling moved the live audience from 600 in 2019 to >5,000
While there are no favourites in the diverse agenda, popular talks included ‘exploring the genomic and epigenomic landscape of acute myeloid leukemia with nanopore sequencing’ with Alberto Magi, ‘using nanopore sequencing to ensure the quality of mRNA vaccines’ with Tim Mercer and a whole host of plant and animal genomic research.
9. Rapid response to Mpox outbreak with viral metagenomics
The broad implementation of Oxford Nanopore devices for SARS-CoV-2 sequencing during the COVID-19 pandemic has increased - and importantly broadened - infectious diseases sequencing capacity globally. With many pathogens being more routinely sequenced, from tuberculosis to avian flu, this year we saw the community respond rapidly to an emerging Mpox outbreak. The first Mpox genomes were sequenced using nanopore technology and the assemblies were shared openly so that scientists could rapidly begin to understand this emerging outbreak.
A protocol was then developed by the team at Guy’s and St Thomas’ to allow scientists to rapidly detect and identify unknown DNA and RNA viruses directly from human clinical samples. This enabled the early characterisation of novel and emerging viral pathogens and comprehensive viral surveillance in a public health context. Find out more here.
We continue to be proud that our technology is having such a positive impact in the fight against many pathogen outbreaks around the world.
Watch our talk on pathogen genomic surveillance with rapid nanopore sequencing here.
10. Closer to understanding TB and its drug resistance patterns
Tackling the biggest challenges to global health, like drug resistant TB (DR-TB), requires innovative, accessible solutions that deliver their benefits where and when they are needed. So, we were excited to announce on World TB Day that together with the Quadram Institute, Oxford Nanopore successfully completed phase I of a DR-TB targeted study as part of Seq&Treat, grant funded by Unitaid and led by FIND, the global alliance for diagnostics. This involved the development of a rapid end-to-end sequencing workflow to identify mutations associated with drug-resistance across the TB genome, directly from clinical samples as part of a research study.
Read the full announcement here.
More broadly, multiple teams are working to deploy rapid, near-sample TB sequencing like this.
11. Rapid tissue typing: a key to enabling better organ donation?
In deceased donor transplantation, HLA typing is used to match the donor and recipient as closely as possible to reduce the risk of rejection. The closer the match, the lower the risk of rejection and the better the chances of a successful transplant. HLA typing is typically done using a blood sample from the donor and the recipient, and fast turnaround times are key.
At this year’s European Federation for Immunogenetics, the team at Omixon discussed their product development approach for rapid characterisation of HLA using nanopore sequencing. Other companies, like GenDx, also see the value in partnering with us to serve the HLA community and together we hope to deliver even more in this area in 2023.
You can read more at the Omixon blog here.
12. Genomics England: towards faster, information-rich cancer genomes for Cancer 2.0
The teams at Genomics England are pioneering new methods to deliver rich insights into cancer genomes, in meaningful timelines that have the potential to improve patient care. We have been proud to collaborate on this work, and this year saw successful proof-of-concept work as nanopore sequencing continues to deliver rich insights across the entirety of the human genome.
In April we were delighted to be embark on the next phase and support Genomics England to sequence many more cancer genomes and to extend the application of our technology to more programmes to drive pioneering science and better clinical and health outcomes for patients in the UK and around the world.
13. Gordon Sanghera on ‘Jazz Shapers with Mishcon de Reya’
Gordon was interviewed for the podcast and Jazz FM programme “Jazz Shapers”, which shares music from the risk takers, leaders and influencers of jazz, soul and blues, alongside interviews with their equivalent in the business world: entrepreneurs who have defined and shaped business categories and ways of operating. Regular attendees of our conferences will know the importance of musical disruption on the Oxford Nanopore ethos; find out more about this by listening to the podcast.
14. The growing importance of diverse data
Diverse data is important in genomics because it helps to ensure that research findings and applications are representative of the wider population. Traditional genomic datasets did not represent global communities, a challenging ethical situation and scientifically important as different populations may have different patterns of genetic variations, which can affect prevalence of certain diseases or, how those populations respond to certain treatments or therapies. By studying diverse data, researchers can better understand the genomic differences between different populations and how these differences may impact health outcomes.
Several programmes launched this year with a goal of broadening genomics datasets. The Human Pangenome Project, Genomics England’s Diverse Data Programme and the Garvan Institute have all been using nanopore sequencing for their work. By using diverse data, researchers can more accurately represent the needs and characteristics of different populations, which can help to reduce these inequities and improve health outcomes for all individuals. We are proud to work with these programmes, and strive through the design of our technology, pricing and service models to open up genomics to as many communities as possible.
Hear more from the Garvan Institute here.
15. Scientist Voices from the 2022 Nanopore Community Meeting
At this year’s NCM we spoke to some of our wonderful customers to hear about their work and what it was like at this year’s conference, check them out:
"The @Space_Station (ISS) is an extreme environment'... you can say that again! Christian Castro, @NASA_Johnson, shared how @NASA are using #nanopore sequencing to better understand the microbes inhabiting the ISS and why MinION is the perfect tool for the job. @ISS_Research pic.twitter.com/3Kmy3A4w4X— Oxford Nanopore (@nanopore) December 14, 2022
We spoke to @timaitman about the advantages of long #nanopore reads for the detection of structural variants and the potential to identify clinically relevant variants, missed by other technologies. #nanoporeconf pic.twitter.com/VIIghFDDfv— Oxford Nanopore (@nanopore) December 7, 2022
We caught up with @SeanW_PHLNGS at this year's #Nanopore Community Meeting to talk about the impact of nanopore sequencing on pathogen surveillance and genomic epidemiology. #nanoporeconf pic.twitter.com/0Dt77jz0sh— Oxford Nanopore (@nanopore) December 7, 2022
16. School age sequencing
Continuing the theme of our goal to enable anyone to analyse anything, anywhere… When 17-year-old Indeever Madireddy pet angelfish died, he decided to sequence its genome – the first time this species has been sequenced. Indeever said “although my fish was dead, I wanted to preserve it forever. So, I decided to sequence the genome of the angelfish with the hopes that I could contribute that information to the scientific community, while also paying a small tribute to my pet!”
Read the full New Scientist article here and wait for more news in 2023 on nanopore sequencing as an educational tool.
Wow. I didn't realize this fun project of mine would gain so much traction! I did in fact use my dead pet fish for this research. Even though my fish isn't alive, I'm glad a piece of it is still living on forever! @nanopore https://t.co/2Q6TIGae4S— Indeever Madireddy (@indeever_m) October 19, 2022
17. Responsible exploration of our planet's biodiversity
Around the world, we are proud that entrepreneurs and researchers choose to take nanopore sequencing close to environments, to better understand biodiversity. This year, we learned more about one company’s journey, Basecamp Research, which is pioneering biodesign and responsible exploration of our planet's biodiversity. Hear below how they are working with a diverse team from diplomats to explorers to provide a comprehensive and unique view of Earth's metagenome.
As we move towards our mission to enable the analysis of anything, by anyone, anywhere we love to see where our customers have got to this year! Here are just a few:
Happy #Antarcticaday I’m excited to be heading south as part of @penguin_watch team on board @QuarkExpedition to do some rapid, in-field disease surveillance with my new #labinasuitcase ? ? sponsored by John & Myriam Wylie Foundation & support from @nanopore @FedUniAustralia pic.twitter.com/GDiGC2zBZ0— Meagan Dewar (@DrMeaganDewar) November 30, 2022
During a 15-day oceanographic expedition on board the Mário Ruivo, @microceno & colleagues conducted #realrealtime #DNA sequencing to understand the unexplored microbial diversity from the surrounding deep seafloor of the Madeira-Tore Rise. 1/4 #anythinganyoneanywhere pic.twitter.com/ABtwhG2Sfc— Oxford Nanopore (@nanopore) November 22, 2022
Real-time DNA sequencing of seafloor sediments from Madeira-Tore Rise on board the #NImarioruivo . Thanks for the fantastic experience. @ipma_pt @IRNAS_CSIC @UEvora @nanopore @_EMEPC_ #ROVluso pic.twitter.com/UmCdZxDwgf— Cave Geomicrobiology (@microceno) October 5, 2022
19. Global researchers speak to the BBC World Service about ‘The DNA sequencing revolution’
David Reid from the BBC World Service came to our Oxford head office to speak to Gordon Sanghera and Rosemary Sinclair Dokos about ‘the DNA sequencing revolution’. He followed this up with a series of conversations with Lara Urban, Anna Schuh and Nino Susanto to discuss nanopore sequencing in everything from cancer research to conservation of endangered species.
You can listen in full here.
20. What a year for publications!
While it is impossible to pick from the many hundreds of publications that used nanopore sequencing, here are three that seemed to capture the research community’s imagination this year:
Methylation profiling of cell-free DNA in cancer with nanopore sequencing; provides the potential to use cfDNA methylome characterisation in longitudinal monitoring.
Lau et al. 2022. BioRxiv.
- Using nanopore sequencing, Lau et al demonstrated how they could analyse methylation in cell-free DNA, using PCR-approaches to sequence nanogram amounts or less of cfDNA per sample. With this, they showed how methylation changes correlated with stages of cancer progression, such as metastatsis, showing the potential of this non-invasive approach for longitudinal monitoring of cancer, including relapse and metastasis.
Nanopore-only complete microbial genome assemblies from pure cultures and metagenomes, with Q20+ chemistry. Liu et al. - metagenomics. 2022. Microbiome.
- Introduces the tool ‘NanoPhase’ for reconstruction of reference-quality microbial genomes from complex metagenomic samples using nanopore sequencing, including both Kit 9 chemistry and Q20+ chemistry
- Exploring the application of their approach on the sludge microbiome, the highly accurate genome assemblies obtained from the sample allowed them to fully explore the genetic and metabolic diversity of the microbiome
- They noted that long nanopore reads alone were sufficient for the accurate and comprehensive analysis of reference-quality genome assemblies, negating the need for polishing with short-reads.
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Tegally, Houriiyah, et al. Science. 2022.
21. Bursting into single-cell omics
We were pleased to announce a new collaboration with 10x Genomics to make single-cell and spatial full-length isoform transcript sequencing accessible to any laboratory. A new end-to-end, single-cell nanopore-based sequencing solution brings an easy and affordable option for full-length isoform single-cell and spatial sequencing to enable the exploration of new biology.
· 10x Genomics App Note
· Oxford Nanopore single-cell protocol
22. And finally, how many DNA bases have been sequenced on nanopore technology this year? Tell us on Twitter!
Overall, the Community has sequenced enough DNA in 2022 to stretch for the length of:
- > 26,800,000 MinIONs
- > 256,000 London buses
- > 128,000 blue whales.
Amazingly this would still only weigh the same as a few grains of salt.