Ira W. Deveson
A5082250184- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Genetic Neurodegenerative Diseases
- Genomics and Rare Diseases
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- SARS-CoV-2 and COVID-19 Research
- Algorithms and Data Compression
- Molecular Biology Techniques and Applications
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genomic variations and chromosomal abnormalities
- Bacteriophages and microbial interactions
- SARS-CoV-2 detection and testing
- Cancer-related molecular mechanisms research
- CRISPR and Genetic Engineering
- Genetic factors in colorectal cancer
- Advanced biosensing and bioanalysis techniques
- Gene expression and cancer classification
- CAR-T cell therapy research
- Nanopore and Nanochannel Transport Studies
- Hereditary Neurological Disorders
- Animal Behavior and Reproduction
- Mitochondrial Function and Pathology
- Genetics and Neurodevelopmental Disorders
- RNA Research and Splicing
Garvan Institute of Medical Research
2016-2025
Murdoch Children's Research Institute
2022-2025
UNSW Sydney
2017-2025
St Vincent's Clinic
2018-2025
St Vincent's Health
2025
University of Wisconsin–Madison
2024
Hanover College
2024
John Wiley & Sons (United States)
2024
The Kinghorn Cancer Centre
2021-2024
Genomics (United Kingdom)
2023
Abstract Viral whole-genome sequencing (WGS) provides critical insight into the transmission and evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability cost, compared to established short-read platforms for viral WGS (e.g., Illumina). However, adoption ONT SARS-CoV-2 surveillance has been limited due common concerns around accuracy. To address this,...
<ns3:p>Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations biological concern were reported, one the United Kingdom and South Africa. Using a combination data from routine surveillance, genomic sequencing international travel we track dispersal lineages B.1.1.7 B.1.351 (variant 501Y-V2). We account for potential biases surveillance efforts by including passenger volumes location where lineage was first London Africa...
<ns3:p>Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations biological concern were reported, one the United Kingdom and South Africa. Using a combination data from routine surveillance, genomic sequencing international travel we track dispersal lineages B.1.1.7 B.1.351 (variant 501Y-V2). We account for potential biases surveillance efforts by including passenger volumes location where lineage was first London Africa...
Fusion genes are a major cause of cancer. Their rapid and accurate diagnosis can inform clinical action, but current molecular diagnostic assays restricted in resolution throughput. Here, we show that targeted RNA sequencing (RNAseq) overcome these limitations. First, establish fusion gene detection with RNAseq is both sensitive quantitative by optimising laboratory bioinformatic variables using spike-in standards cell lines. Next, analyse patient cohort improve the overall rate from 63%...
More than 50 neurological and neuromuscular diseases are caused by short tandem repeat (STR) expansions, with 37 different genes implicated to date. We describe the use of programmable targeted long-read sequencing Oxford Nanopore’s ReadUntil function for parallel genotyping all known neuropathogenic STRs in a single assay. Our approach enables accurate, haplotype-resolved assembly DNA methylation profiling STR sites, from list predetermined candidates. This correctly diagnoses individuals...
Abstract Nanopore sequencing depends on the FAST5 file format, which does not allow efficient parallel analysis. Here we introduce SLOW5, an alternative format engineered for parallelization and acceleration of nanopore data Using example DNA methylation profiling a human genome, analysis runtime is reduced from more than two weeks to approximately 10.5 h typical high-performance computer. SLOW5 25% smaller delivers consistent improvements different computer architectures.
Alternative splicing in chromatin-modifying genes is associated with temperature-dependent sex divergent reptile lineages.
The complexity of microbial communities, combined with technical biases in next-generation sequencing, pose a challenge to metagenomic analysis. Here, we develop set internal DNA standards, termed "sequins" (sequencing spike-ins), that together constitute synthetic community artificial genomes. Sequins are added environmental samples prior library preparation, and undergo concurrent sequencing the accompanying sample. We validate performance sequins by comparison mock demonstrate their use...
Abstract Accumulating evidence supports the high prevalence of co-infections among Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) patients, and their potential to worsen clinical outcome COVID-19. However, there are few data on Southern Hemisphere populations, most studies date have investigated a narrow spectrum viruses using targeted qRT-PCR. Here we assessed respiratory viral SARS-CoV-2 patients in Australia, through virome characterization. Nasopharyngeal swabs 92...
Abstract Oculopharyngodistal myopathy (OPDM) is an inherited manifesting with ptosis, dysphagia and distal weakness. Pathologically it characterised by rimmed vacuoles intranuclear inclusions on muscle biopsy. In recent years CGG • CCG repeat expansion in four different genes were identified OPDM individuals Asian populations. None of these have been found affected non-Asian ancestry. this study we describe the identification expansions ABCD3 , ranging from 118 to 694 repeats, 35 across...
In silico simulation of high-throughput sequencing data is a technique used widely in the genomics field. However, there currently lack effective tools for creating simulated from nanopore devices, which measure DNA or RNA molecules form time-series current signal data. Here, we introduce Squigulator, fast and simple tool realistic Squigulator takes reference genome, transcriptome, read sequences, generates corresponding raw This compatible with basecalling software Oxford Nanopore...
ABSTRACT Objective The hereditary spastic‐ataxia spectrum disorders are a group of disabling neurological diseases. traditional genetic testing pathway is complex, multistep and leaves many cases unsolved. We aim to streamline improve this process using long‐read sequencing. Methods developed targeted sequencing strategy with the capacity characterise variation all types sizes within 469 disease‐associated genes, in single assay. applied cohort 34 individuals unsolved spastic‐ataxia. An...
DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, particular cancer-related hypomethylation, affects higher-order levels of architecture is still unclear. Here, using Repli-Seq, single-cell Hi-C, we show that genome-wide methylation loss both concordant precision deregulation 3D organization. Notably, find disruption compartmentalization, striking gains...
A recent study proposed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijacks the LINE-1 (L1) retrotransposition machinery to integrate into DNA of infected cells. If confirmed, this finding could have significant clinical implications. Here, we apply deep (>50×) long-read Oxford Nanopore Technologies (ONT) sequencing HEK293T cells with SARS-CoV-2 and do not find virus integrated genome. By examining ONT data from separate cultivars, completely resolve 78 L1 insertions...
Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools , an intuitive toolkit handling SLOW5 format. Slow5tools enables lossless conversion range tools interacting files. uses multi-threading, multi-processing, other engineering strategies to achieve fast manipulation, including live FAST5-to-SLOW5 during sequencing....
Abstract Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal Torres Strait Islander ancestries are historically under-represented in genomics research almost completely missing from reference datasets 1–3 . Addressing this representation gap is critical, both to advance our understanding of global human diversity as a prerequisite for ensuring equitable outcomes medicine. Here we apply population-scale whole-genome long-read sequencing 4 profile structural...