There are just two weeks to go until London Calling 2021 online (19th-21st May), and from now until the big event, we’ll be sharing a weekly preview of what’s to come from the latest additions to our speaker line-up. For more details on the talks announced so far, covering everything from clinical research to environmental metagenomics, take a look at the agenda here. The conference is totally free to attend – simply register here to get set up.
The genomics of a cross-kingdom pathogen
The banana infecting fungus, Fusarium musae, is also capable of infecting humans; however, its mode of transfer from plants to humans is not fully understood. Comparative analyses using genome assemblies and annotated genomes are central to deducing the genomic components responsible for virulence and transmission mechanisms. While small relative to some genomes, fungi DNA contains a high proportion of repetitive segments, making high-quality assemblies challenging to construct with short-read sequences alone. Using nanopore long sequencing reads, Luca Degradi (University of Milan) generated an assembly of the F. musae genome which was shown to be more complete than the equivalent reference NCBI genome assembled with short reads alone. Additionally, Medaka polishing further improved the assembly, producing a BUSCO completeness of 99.8%. The detection of circular sequences from the same nanopore sequencing dataset also allowed for mitochondrial genome assembly, with successful identification of all annotated genes. Nanopore sequencing in this research provides the required detail for comparative genomics at the genome and nuclear level, thereby furthering our understanding of the pathophysiology of this species and providing the tools to advance fungi genomics research.
11 human genome assemblies in 9 days
In collaboration with the genomics group at Google health, Kishwar Shafin (University of California, Santa Cruz, USA) developed a pipeline designed to identify variants from long and ultra-long reads. Capable of identifying single nucleotide variants (SNVs) in segmental duplications and regions inaccessible to short-read sequencing, the variant calling pipeline PEPPER-Margin-DeepVariant and de novo assembler Shasta present an exciting step forward for high-quality genome assembly and small variant calling. Sequencing on a PromethION and assembling the data with Shasta, eleven human genomes were successfully assembled in nine days, with SNV detection results indicating outperformance of short-read-based equivalents at the whole genome level.
Investigating methylation in colorectal cancer
Gene regulation in mammalian cells is controlled in part by DNA methylation. Determining how these base modifications change cellular processes with short-read sequences is challenging due to the involvement of long-range interactions between different genetic elements. Using a PromethION to sequence colorectal cancer cell lines, Roham Razaghi (Johns Hopkins University, USA) obtained >100 Gb long-read sequences (N50 80 Kb+). Enabling both the capture of methylation data from native DNA and phasing into parental haplotypes, the ultra-long nanopore reads revealed long-range enhancer-promoter interactions. Shedding light on the 3D architecture of the genome, this ongoing research project shows promise of revealing how genome structure and methylation patterns facilitate and constrain enhancer-promoter interactions.
Detecting fusion transcripts with long nanopore reads
Fusion genes can drive cancer; characterising the fusion transcripts they produce, however, can be challenging when using short sequencing reads. Long nanopore reads can span full-length transcripts, enabling identification of these fusions. In data analysis, fusion-finding algorithms designed for short reads are not compatible with long reads. To address this, Nadia Davidson (Peter MacCallum Cancer Centre, Australia) developed JAFFAL, a cross-functional tool to identify fusions from long-read nanopore transcript data. Testing JAFFAL on simulation data and data from cell lines and clinical research samples, the tool was shown to effectively capture fusion transcript splicing – even detecting fusions at the single cell level.
Optimising neural networks: top tips on how to train methylation calling models
Nanopore sequencing enables direct methylation detection - without the need for bisulphite conversion or extra laboratory techniques. Optimising the extraction of base modification data from long and ultra-long sequences computationally can improve efficiency resulting in higher accuracy at lower coverage. Processing tools consisting of multi-layered neural networks which learn from data inputs, or deep learning, present an opportunity to enhance computational methods further. DeepSignal is a deep learning computational tool that enables the training and use of models to call DNA methylation from nanopore sequences. Using a PromethION to sequence Coturnix japonica DNA, Paul Terzian (National Institute of Agricultural Research, France) evaluated various neural networks, revealing strategies for training methylation calling models.
That’s all for this week! Until next time, keep an eye on @nanoporeconf on Twitter for more speaker announcements, and the latest London Calling 2021 updates.
Overcoming the complexities of plant T-DNA insertion arrays
The insertion of transfer DNA (T-DNA) into plant genomes is widely used in plant research and agriculture to investigate gene function and introduce desirable traits. However, T-DNA inserts randomly into genomes and can cause significant genomic alterations. Establishing the number and locations of these T-DNA inserts is critical. However, this can prove challenging using short reads due to the often large, repetitive nature of plant genomes and the complexity of T-DNA insertion arrays. Sequencing Arabidopsis thaliana genomes with long nanopore reads, Boas Pucker (University of Cambridge, UK) characterised large, complex T-DNA insertion arrays, rearrangements, and chromosome arm translocations - and identify 11 previously unknown T-DNA insertions which were not identified via traditional methods.
Revealing variation in ribosomal RNA gene repeats
Ribosomal DNA (rDNA) research to date has relied on the assumption that repeat rDNA copies - present in their hundreds in the human genome - are identical to each other. With studies generally using short reads to generate a consensus for a single repeat, little is known of rDNA variation and its effects on ribosome activity. To investigate rDNA variation, Emiliana Weiss (ANU, Australia) generated nanopore reads spanning >100 kb, containing a total of 3,300 candidate rDNA repeat units, with an average of 3-4 units per read. Using this data, in combination with direct sequencing of the corresponding RNA product, this research showed that rDNA variation resulted in rRNA changes in a considerable proportion of samples. Furthermore, nanopore sequencing revealed that differential CpG methylation profiles altered the end-product RNA. This research highlights several previously unrecognised ways through which rDNA may influence ribosome rRNA composition and cell function.
Investigating disrupted methylation patterns in SHH medulloblastoma
Sonic Hedgehog (SHH) medulloblastoma is a malignant childhood brain tumour. While survival rates are comparatively high relative to other brain tumour types, a subset of patients’ tumours do not respond to treatment, or relapse with a more aggressive tumour shortly thereafter. Rene Snajder (German Cancer Research Center, Germany) used nanopore sequencing to compare tumour clinical research samples taken from a pediatric patient with SHH medulloblastoma, before and after treatment on relapse. The samples were characterised by both complex chromosomal rearrangements – indicating chromothripsis - and altered methylation. The long-read, PCR-free nanopore data enabled both haplotyped reconstruction of the complex rearrangements present and analysis of methylation status, providing a complete view of the complexity of these tumour samples.
Characterising structural variants in rare disease
Rare diseases collectively affect millions worldwide; although the majority are suspected to be genetic in origin, the molecular basis of many rare diseases is unknown. Katherine Dixon (Canada's Michael Smith Genome Sciences Centre, Canada) performed whole genome nanopore sequencing to detect pathogenic structural variants (SVs). In addition to successful gene discovery in multiple clinical research samples from patients with no prior diagnosis of rare or inheritable disease, nanopore sequencing allowed for the characterisation of variants that could not be wholly resolved using other methods. This rare disease research marks a turning point, driven by long nanopore sequencing reads, in germline SV detection at unprecedented resolution and sensitivity.
Genomic surveillance: redefining outbreak response
Through the COVID-19 pandemic, the importance of sequencing data in identifying variants, understanding transmission patterns, and informing effective public health decision-making has become increasingly clear. Rapid SARS-CoV-2 sequencing and data sharing is crucial to this effort. Alexander Dilthey (Heinrich Heine University Düsseldorf, Germany) evaluated the impact of incorporating nanopore sequencing, together with contact tracing data, into a fully integrated system for SARS-CoV-2 outbreak response This ‘genomic surveillance’ shed light on viral population structure and previously undetected routes of transmission, demonstrating its potential as a powerful tool to complement contact tracing efforts to help control the spread of a virus.
That’s all for this week! Until next time, keep an eye on @nanoporeconf on Twitter for more speaker announcements, and the latest London Calling 2021 updates.
Monitoring a critically endangered species with eDNA
There are only 205 kākāpō parrots alive today. Detailed, quantitative monitoring of the intra- and inter-specific diversity of critically endangered species such as the kākāpō is crucial in the fight to improve biodiversity. Lara Urban (University of Otago, New Zealand) used a MinION to monitor kākāpō via environmental DNA, or eDNA, extracted from soil samples from their wild habitats. Using real-time target enrichment via adaptive sampling, the long nanopore reads enabled phasing of variants in the kākāpō genome, allowing identification to the individual level. Using this sensitive and non-invasive monitoring technique, The Kākāpō Recovery Team will be implementing nanopore sequencing in their crucial efforts to conserve this elusive species.
Identifying unique immune response signatures in infectious disease
Bacterial and viral infections are a global concern, particularly in low-resource settings, with the ongoing SARS-CoV-2 pandemic and risk of other emerging infections representing a further threat. Rapid and sensitive identification of the pathogen present is crucial; however, many infectious diseases - such as typhoid fever and SARS-CoV-2 - present with overlapping symptoms, and current tests can be slow or lack sensitivity. To investigate the potential of transcriptome analysis in distinguishing these diseases, Irina Chelysheva (University of Oxford, UK), used a PromethION to perform nanopore cDNA sequencing of blood samples from individuals with COVID-19 and typhoid fever. This revealed immune response signatures specific to each infection, successfully distinguishing between the two, demonstrating the potential of nanopore sequencing for the future development of rapid diagnostics.
Understanding HPV integration ‘superspreading’ events with ultra-long nanopore reads
Human papillomaviruses (HPV) cause nearly all cervical cancers. The virus is able to hijack cellular DNA repair enzymes in order to replicate, causing chromosome instability - but this process is difficult to study. Nicole Rossi and Michael Dean (National Cancer Institute, USA) are using full-length transcript sequencing of cervical cancer cell lines to investigate the large integrated HPV concatemers arising from a 'superspreading' event, revealing how this phenomenon affects gene expression. Making use of real-time targeted sequencing through adaptive sampling, they then enriched for full-length HPV reads to identify mixed genome concatemers reaching >42 kb, revealing how these superspreading events may be initiated, and indicating some parallels with changes observed in non-viral cancers. With ultra-long reads, the team demonstrate the potential to fully characterise HPV concatemers in cell lines and tumour samples.
Revealing the role of ‘jumping genes’ in Parkinson’s and Alzheimer’s disease
Transposable elements (TEs) are sequences of DNA that can move, or transpose, themselves to new positions within the genome, earning themselves the name 'jumping genes.' Alu and L1 element recombination contributes to evolution and genetic disorders, but has been little studied in healthy genomes. Giovanni Pascarella (RIKEN MS, Japan) used long nanopore reads to reveal extensive somatic recombination of these elements in human genomic samples. Characterisation of Alu elements enabled the team to shed light on the role of Alu elements in cancer gene recombination hotspots, whilst analysis of retroelement recombination in Parkinson's and Alzheimer's disease revealed a link with genomic instability in neurodegeneration.
Taking crop research to the pangenome level
Pangenome research aims to disentangle environmental and genomic factors to better understand their impacts on species diversity and genomic variants. However, applying this approach to plant genomes via short reads has presented challenges. Francois Sabot (French National Research Institute for Sustainable Development, France) is using nanopore long reads to tackle this, employing a hybrid approach to generate high-quality rice genome sequences and create pangenome graphs, to enable the investigation of the impact of domestication on this important crop.
Demonstrating potential for rapid tumour profiling during open brain surgery with nanopore sequencing
Brain tumour patients’ prognosis and suitability for surgery are currently determined with imaging and biopsies. These approaches can be inaccurate, invasive, and time-intensive: it is generally not possible to tell the type of tumour a patient has until weeks afterwards, which may be too late to intervene appropriately, particularly in the case of aggressive tumours. In the opening plenary of London Calling 2021 online, Luna Djirackor (Oslo University Hospital, Norway) will share how nanopore methylation analysis showed the future potential to classify brain tumours in as little as 91 minutes – quick enough for results to be returned to the operating table during brain surgery. Strikingly, in 60% of the samples sequenced in the study, the information obtained would have altered the pre-planned surgical strategy, demonstrating how this approach has the potential to significantly improve surgical outcomes in future.
Capturing the previously uncapturable: the role of SVs in neurodegenerative disease
After Alzheimer's disease, Parkinson’s disease (PD) is the second most common neurodegenerative disorder. PD is a heritable disease, with 30% of cases driven by single mutations or SNPs. Structural variation (SV) is also implicated in disease onset and progression; however, establishing the functional impact of these larger, repetitive variants using short-read sequencing is challenging, largely due to their size. To determine the role of SVs in driving PD, Anastasia Illarionova (DZNE Tübingen, Germany) generated long-read sequencing data from healthy, carrier and disease-affected neuron samples. Swift SV detection in coding and non-coding regions of the genome enabled by nanopore sequencing using a PromethION, in combination with the DNA and RNA long-read datasets, allowed cause and effect of genetic differences to be determined – shedding new light on neurodegenerative disease research.
Going beyond gene-level expression with full-length isoform sequencing
Alternative splicing of messenger RNA is the process by which multiple transcripts are produced from a single gene. Research has shown that this process is critical in human development and affects 95% of all human genes. Mutations which impact the regulation of alternative splicing are directly associated with a range of diseases. However, the use of short-read sequencing data has limited efforts to identify and link these mutations with their effects. Wilfried Haerty (Earlham Institute, UK) used long nanopore reads to thoroughly investigate differential expression in a neuroblastoma cell line. This revealed >2,500 novel transcripts and >5,600 differentially expressed transcripts. Crucially, the over a quarter of the genes encoding these differentially expressed transcripts were not differentially expressed at the gene level, highlighting the need for the transcript-level analysis made possible with long nanopore reads.
Revealing the effects of melting permafrost with a MinION
The visible effect of climate events only tells a fraction of the story; a point that is all too true in high-latitude regions characterised by permafrost, where temperatures are rising at twice the global average. With potential effects of thawing of permafrost-associated soils ranging from the direct – altering soil microbial communities – to the indirect – affecting communities’ participation in land-based culture – characterising and measuring these changes is critical. Using a MinION, Devin Drown (University of Alaska Fairbanks, USA) did exactly that, generating metagenomic data from monthly soil samples and highlighting an inextricable link to pathogen evolution and the broader community’s health.
What can we learn from pangolins' penchant for ants?
The ability to eat ants and termites is a trait that has evolved separately multiple times in mammals, in a classic example of convergent evolution. To further understanding of the mechanisms underpinning this adaptation, Sophie Teullet (University of Montpellier, France) sequenced faecal samples from three ant and termite-eating animals – ground pangolin, aardvark, and southern aardwolf – on MinION. The long nanopore reads enabled assembly of genomes from the metagenomic data, allowing a comparison of the gut microbiomes of these animals, and shedding light on how they have evolved to digest termites and ants.
Here are five speakers who are using nanopore sequencing in their work to advance the frontiers of scientific research.
How is nanopore sequencing unveiling the impact of HPV integration in cervical cancer?
Understanding the consequences of human papillomavirus (HPV) integration on the human genome is crucial to the development of novel therapies to treat cervical cancer – the number one cause of cancer-related mortality for sub-Saharan African women. In her plenary talk, Vanessa Porter will share how nanopore sequencing has enabled her team at the University of British Columbia, Canada, to resolve these previously intractable viral and host genomic consequences – including DNA methylation, haplotypes, and complex structural variants.
Tackling antimicrobial resistance with a MinION
Antimicrobial treatment is an essential method of disease control. However, the effectiveness of antimicrobials has decreased in recent years due to the emergence of antimicrobial-resistant strains representing a significant clinical challenge. Understanding the drivers of antimicrobial resistance (AMR) is therefore critical to overcoming this burden to public health. Genetic processes such as copy number variation have been implicated in the evolution of resistant microbes, but are difficult to investigate. Using a MinION, Elizabeth Skippington (Genentech, USA) sequenced bacteria resistant to a novel antibiotic and successfully identified the resistance mechanisms at play, including copy number variation.
What do whale snot, drones, and nanopore sequencing have in common?
To better understand events linked to ecosystem changes, Eric Bortz and a team of research students at University of Alaska Anchorage, USA, used a combination of MinIONs and drones - affectionately known as ‘snotbots’ - to collect and sample respiratory vapour from humpback whales, identifying various bacteria and eukaryotes in the process. Rapid nanopore sequencing of a wide variety of environmental samples - including stranded marine mammals, seabird survey samples, and sediment (in addition to whale snot) - allowed for metagenomic analysis of low-quantity sparse samples obtained in the wild, providing data valuable in the identification of hallmarks of environmental change.
Microbes & MinIONs, continued: predicting the impact of environmental changes
Stromatolite fossils provide a record of one of the first forms of life on planet Earth. Establishing how these ancient microbial communities responded to extreme environmental changes in the past will likely help us predict the impact of extreme weather events in the future. In the Environmental Metagenomics breakout session, Nicole Wagner (Georgetown University, USA) will demonstrate how metagenomic and metatranscriptomic analyses of Antarctic samples sequenced on a MinION reveal the community structures, metabolic activity, and survival mechanisms of these fascinating ecosystems.
A top tip for growing plants from a MinION user?
Guar gum, extracted from the legume (you guessed it) guar, has a range of industrial applications, from its use in the food industry as a stabiliser to being a central agent in petrochemical development. The nitrogen-fixing bacteria in this legume’s roots also make it critical in the process of field rotation between harvests. Sensitivity to long light cycles, however, have thwarted efforts to cultivate the crop in the Northern hemisphere, where long days are typical of the growing period. Identifying the genes important in generating hybrid plants using short-read sequencing have so far been unsuccessful. Using a MinION, Elizaveta Grigoreva (Saint Petersburg State Forestry University, Russian Federation) employed a hybrid approach to sequence and assemble the guar genome. By enabling genome-guided guar transcriptome assembly, nanopore sequencing has unlocked the first step towards finding hybrid strains capable of thriving in the northern hemisphere.