21 moments we’ll remember from 2021
Dear all,
At the end of 2021 we would like to wish all of our friends and collaborators a happy 2022.
This year we took the next step on our journey and became a publicly listed company, but that hasn’t changed our commitment to continuing to develop a sensing platform that we believe can bring benefit to society through greater access to biological information. Our mission remains the same — to enable the analysis of anything by anyone, anywhere.
2021 has been amazing, thanks to the innovative applications from the Nanopore Community. We’ve pulled together some highlights below, but this really is just the tip of the iceberg in what has been another phenomenal year for genomics research.
Whilst COVID-19 genomic epidemiology has remained, and will continue to remain, a key tool in the fight against a changing pandemic, you have been innovating in so many other areas. The epigenome has come into focus this year, with researchers across a breadth of areas taking advantage of the direct nature of nanopore sequencing, to detect base modifications alongside nucleotide sequence. We’ve also seen the development of many clinical research pipelines which could offer real-time disease insights in the future, and the scale up of sequencing to gain a more comprehensive picture of the human genome.
I have no doubt that you will continue to break scientific boundaries in 2022 and look forward to supporting you with a continually improving technology.
All the best for 2022.
Gordon
A complete human genome, at last!
~8% of the human genome has been inaccessible to traditional sequencing technologies. Addressing this, the Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055 billion base pair (bp) sequence of a human genome, representing the largest improvement to the human reference genome since its initial release.
The new T2T-CHM13 reference includes gapless assemblies for all 22 autosomes plus Chromosome X, corrects numerous errors, and introduces nearly 200 million bp of novel sequence. Nanopore ultra-long reads were vital in being able to scaffold and bring the assembly together. The team also used nanopore sequencing to profile the epigenetic landscape of the entire genome as part of this project.
#anythinganyoneanywhere
This year, Reindert Nijland took our anything, anyone anywhere mantra to a new level and sequenced shark DNA on his Mk1C whilst riding his bike home from the lab! Check out the #anythinganyoneanywhere hashtag on twitter to find out how else MinION has been pushed through its paces this year. You can also find some fantastic examples on our portable sequencing page.
Sequencing on a bike, revisited. I just sequenced shark DNA using a R10.3 flowcell in the @nanopore #Mk1C, while biking between the lab and home. It keeps blowing my mind this is possible! #realrealtime #anythinganyoneanywhere pic.twitter.com/3UPUnvV171
— Reindert Nijland (@ReindertN) February 25, 2021
COVID-19 surveillance – a truly global effort
The international scientific and public health Community has continued to provide a phenomenal response to the changing COVID-19 pandemic — identifying new variants, establishing surveillance networks where not previously possible, and responding to the challenge ahead of them by rapidly scaling up to sequence 1000’s of samples per day.
Loss of biodiversity is an urgent problem – the nanopore community moves to support this issue
In May this year, ORG. one was launched to support the sequencing of critically endangered species. Thanks to a fantastic response from the Nanopore Community, we've seen 23 species sequenced so far, and the data shared openly. We look forward to seeing this progress in 2022.
The promise of same-day metagenomics
A team from Guys & St Thomas’ and The Quadram Institute have developed a same-day workflow using nanopore technology which successfully identifies secondary infections for patients on intensive care units (ICU) in hours, rather than days.
A new SARS-CoV-2 WGS method for ultimate speed, flexibility and scale
Building on the work of the ARTIC network, Nikki Freed and Olin Silander developed the Midnight protocol for SARS-CoV-2 whole genome sequencing, which has enabled faster turnaround of samples, scalability, and a reduced price per sample.
A new kit and flow cells enabling >99% raw read accuracy
Having trialled ‘Q20+’ chemistry in an Early Access Programme, in December we announced the launch of Kit 12 and R10.4 flow cells for >Q20 (>99%) raw read and around Q30 (99.9%) Duplex sequencing accuracy.
Some key take-aways. The modal raw read accuracy for @nanopore R10.4 is approx., 99% 2/12 pic.twitter.com/2jujMeGU99
— Mads Albertsen (@MadsAlbertsen85) November 11, 2021
Showing that time is of the essence – and can be delivered
This year we’ve seen the emergence of a number of new rapid workflows in clinical research, particularly in the field of cancer. At London Calling, we heard from Luna Dijrackor on her work to characterise the methylation profiles of brain tumour research samples, in just 91 minutes — demonstrating the potential for characterisation during surgery in the future.
At NCM, we were joined by a panel of experts sharing their workflows for rapid characterisation of CNS cancers — you can catch up on Thidathip Wongsurawat, Areeba Patel and Franz-Josef Müller & Helene Kretzmer's talks now. Between them they cover topics including the potential to enable brain tumour classification within the timeframe of an operation, rapid identification of new markers of cancer, and affordable targeted approaches for broader access.
Scaling up nanopore sequencing for human disease insights
Many exciting high-throughput projects launched this year — two examples were from Genomics England, and the other from the NIH Center for Alzheimer's and Related Dementias (CARD).
The team at Genomics England will sequence thousands of human genomes using PromethION, in a project to evaluate its potential to provide rapid, rich insights in cancer genomics. At CARD, researchers have started to generate long-read sequencing data from roughly 4000 patients with Alzheimer’s disease, frontotemporal dementia, Lewy body dementia, and healthy subjects. They are aiming to gain greater insight into challenging regions of the genome which could play a role in driving Alzheimer’s disease and related dementias’ pathology, at a scale not seen before.
That’s a lot of bases...
We think around a whopping 6000 trillion bases have been sequenced using nanopore technology this year! In a single strand, that would be a piece of DNA over 2000 km long, which would take around 4500 years to translocate through a single pore at 420 bases per second.
Assembling the largest known vertebrate genome & genome of the largest tree
Paolo Franchini and team assembled all 43Gb of the lungfish genome in January — that’s the equivalent of 14 human genomes! It’s the largest known vertebrate genome and ultra-long nanopore reads were essential to overcome some of the most challenging regions.
Steven Salzberg and team recently assembled the genome of world’s largest tree — the coast redwood. Analysis of the 26.5 Gb genome (~9x size of human) found 100s of genes unique to the coast redwood, as well as many that help respond to stress, resist disease & repair injury.
Read Paolo’s blog to find out more about the lungfish assembly.
Marking our first day as a public company with a school STEM event at the London Stock Exchange
In 2021, Oxford Nanopore began its journey as a public company. Our goal is to enable the analysis of anything by anyone, anywhere, and over the years we have designed our devices, pricing and support to reflect that accessibility.
To reflect this, we marked our first day by inviting the next generation of scientists — a group of students, aged 16-18 — to the London Stock Exchange to get hands on with nanopore technology and hear from scientists in the field, and members of the Oxford Nanopore team. The students were introduced to the world of biochemistry and learnt how it can be applied both in science as well as business.
Growing nanopore sequencing expertise in Africa
A fantastic training initiative aimed at building capacity in nanopore sequencing & bioinformatics across Africa launched this year. The four-month training programme saw 14 scientist become experts in the field before heading back to their home institutions to help other African researchers take advantage of sequencing to unlock the genetic potential of crops and livestock in Africa.
Introducing PromethION 2 (P2), to bring high-throughput sequencing to anyone
At London Calling this year, the team announced the development of a new device — P2, for very high throughput sequencing in a shoebox-size device. It was confirmed later in the year, at the Nanopore Community Meeting, that P2 will be available as a standalone device with integrated compute, or ‘P2 Solo’, a sequencing device that can be connected to existing compute, including GridION.
With the ability to run one or two PromethION flow cells at a time, and integrated compute, the $10,455k starter pack provides easily accessible, compact and powerful sequencing. P2 Solo will be shipped from Q2 2022 and you can pre order yours here.
By NCM, another 1000 publications to add to the library
Since the start of 2021 we’ve seen another ~1000 papers published by the Nanopore Community, taking the total to nearly 2400 (at the end of November). We never cease to be amazed by the innovative applications of nanopore technology and we love reading your publications highlighting these — keep them coming!
Building global sequencing capacity for pandemic preparedness
In June, the Rockefeller Foundation announced over $20 million in funding to help strengthen global capabilities to detect and respond to pandemic threats by strengthening organisations’ ability to sequence and share genomic information alongside other data, rapidly.
Oxford Nanopore is one of 20 organisations collaborating with the Rockefeller Foundation to shape their new Pandemic Prevention Institute and expand global genomic sequencing capacity. We look forward to helping build sequencing capacity globally to bring solutions to the parts of the world where they are needed most.
Shining a light on the lesser-studied epigenome
Using nanopore technology it’s possible to gain information about base modifications alongside nucleotide sequence. In 2021 we’ve seen nanopore technology used across a breadth of applications to gain new insights.
At December’s Nanopore Community Meeting, there were a whole host of talks on the topic — for example, hear from Loan To Nguyen on an epigenetic aging clock for cattle, from Ian Henderson on the epigenetic landscape of the Arabidopsis centromeres, and from Ulf Birkedal on resolving of DMPK hypermethylation in myotonic dystrophy type 1 patients. And you’ll find plenty more examples in the resource centre.
Real world applications of Adaptive Sampling: from rare disease to monitoring biodiversity
Adaptive sampling — the on sequencer targeting approach that rejects sequencing reads that are not of interest, leaving the nanopore available for the region of interest — has come a long way over the last two years, thanks largely to wide adoption by the Nanopore Community to tackle problems across the field of genomics.
Danny Miller’s publication in July titled ‘Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variants’, is just one fantastic example of this. Danny and his team used adaptive sampling on the nanopore platform to identify disease-causing variants in clinical research samples not identified by standard testing. He argues that in the future, nanopore could be used as a single sequencing test to replace nearly all other clinical genetic tests offered today.
Lara urban has leveraged adaptive sampling of environmental DNA for monitoring the critically endangered kākāpō — a flightless, nocturnal parrot, of which there are only 204 left in the wild. In this talk, Lara explains how adaptive sampling of eDNA with nanopore sequencing provides a scalable, cost-efficient way of monitoring biodiversity.
More fantastic spotlight talks from early career scientists
The spotlight sessions at London Calling and the Nanopore Community Meeting have become a mainstay of the nanopore conference. We love hearing from early career scientists about how nanopore sequencing is changing their field of research. The pitches we receive are always creative and fun, with innovative science at the heart. Keep them coming for 2022, and don’t forget we can offer bursaries for other conferences should you have the opportunity to speak somewhere else!
Resolving repeats
Repetitive regions have long been the frustration of geneticists. This year, nanopore sequencing has been used to unravel these genomic structures — from resolving centromeric and telomere regions (Arabidopsis) and enabling telomere-to-telomere assemblies (Human, Banana), to uncovering the relationship between repeat expansion and hypermethylation in Mytonic dystrophy type 1 (watch here).
Ira Deveson’s talk from NCM 2021, epitomises the improvements in the ability to resolve repetitive regions of the genome. He presented how he and his team are investigating the potential of adaptive sampling for future “parallel testing of all disease-associated short tandem repeat genes in a single nanopore assay.” He highlighted how they simultaneously sequenced 37 genes and could examine their methylation profiles — current methods require the clinician to choose one test for one gene at a time.
Resolving repetitive regions with nanopore sequencing
Uncovering the potential of liquid biopsy
Liquid biopsy of plasma or blood samples presents a non-invasive opportunity to detect and monitor the progression of tumours. Several researchers have been using nanopore sequencing this year to try and make this a future reality.
At the beginning of the year, Martignano.F et al. published a paper presenting a workflow for the detection of copy number variations from the plasma of lung cancer patients. At NCM 2021, Jessica Blackburn presented her approach to identify patients with leukemia-associated cell-free DNA in the spinal fluid. This was the first time that cell-free DNA has been used to monitor CNS disease in Acute lymphoblastic leukaemia (ALL) patients.
Bonus content...
If you're looking for some light reading over the holiday break then we’d highly recommend this blog from Lara Marks, detailing the journey of nanopore sequencing — from an initial sketch on the side of the road, to all of the amazing examples you’ve heard about in this post. Enjoy!
