Shaun Carswell

HIVepsilon-seq—scalable characterization of intact persistent proviral HIV reservoirs in women

Jillian M. Hammond, Martin A. Smith, Shaun Carswell, Adaora A. Adimora et autres

IMPORTANCE: The lack of a reliable method to accurately detect when replication-competent HIV has been cleared is a major challenge in developing a cure. This study introduces a new approach called the HIVepsilon-seq (HIVε-seq) assay, which uses long-read sequencing technology and bioinformatics …

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HIVepsilon-seq—scalable characterization of intact persistent proviral HIV reservoirs in women

Kirston Barton, James M. Ferguson, Ira W. Deveson, Shane D. Falcinelli et autres

ABSTRACT The persistence of replication-competent HIV-1 in people living with HIV (PLWH) is a barrier to a cure for HIV. Early-phase studies of clinical interventions to deplete the intact persistent HIV-1 reservoir are ongoing. However, the ability to distinguish intact proviruses is …

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Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

Nasir Riaz, Preston Leung, Kirston Barton, Martin A. Smith et autres

BACKGROUND: Hepatitis C (HCV) and many other RNA viruses exist as rapidly mutating quasi-species populations in a single infected host. High throughput characterization of full genome, within-host variants is still not possible despite advances in next generation sequencing. This limitation constrains viral …

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Additional file 2 of Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

Nasir Riaz, Preston Leung, Kirston Barton, Martin A. Smith et autres

Additional file 2: Supplementary file 2. Sequences of HCV inserts in plasmid experiments.

Additional file 3 of Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

Nasir Riaz, Preston Leung, Kirston Barton, Martin A. Smith et autres

Additional file 3: Supplementary file 3–6. An example of Nano-Q tool output (4 files in *.txt format): a) Reference sequence (HITP300157_Reference), b) Nano-Q tool progress report (HITP300157_Nano-Q_output), c) All variants generated (HITP300157_all_variants), d) Consensus of clusters of variants that met the user …

Additional file 5 of Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

Nasir Riaz, Preston Leung, Kirston Barton, Martin A. Smith et autres

Additional file 5: Supplementary file 8. Within-host variants generated using Nano-Q tool for subjects in Fig. 4.

Additional file 4 of Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

Nasir Riaz, Preston Leung, Kirston Barton, Martin A. Smith et autres

Additional file 4: Supplementary file 7. GenBank accession numbers of consensus sequences shown in Fig. 4.

Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2

Mark Corbett, Thessa Kroes, Liana Veneziano, Mark F. Bennett et autres

Familial Adult Myoclonic Epilepsy (FAME) is characterised by cortical myoclonic tremor usually from the second decade of life and overt myoclonic or generalised tonic-clonic seizures. Four independent loci have been implicated in FAME on chromosomes (chr) 2, 3, 5 and 8. Using …

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High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

Mandeep Singh, Ghamdan Al‐Eryani, Shaun Carswell, James M. Ferguson et autres

High-throughput single-cell RNA sequencing is a powerful technique but only generates short reads from one end of a cDNA template, limiting the reconstruction of highly diverse sequences such as antigen receptors. To overcome this limitation, we combined targeted capture and long-read sequencing …

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Unexpected host dependency of Antarctic Nanohaloarchaeota

Joshua N. Hamm, Susanne Erdmann, Emiley A. Eloe‐Fadrosh, Allegra Angeloni et autres

In hypersaline environments, Nanohaloarchaeota (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota [DPANN] superphylum) are thought to be free-living microorganisms. We report cultivation of 2 strains of Antarctic Nanohaloarchaeota and show that they require the haloarchaeon Halorubrum lacusprofundi for growth. By performing growth using enrichments …

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Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions

Simon A. Hardwick, Dominik C. Kaczorowski, James Blackburn, Kirston Barton et autres

The human brain is one of the last frontiers of biomedical research. Genome-wide association studies (GWAS) have succeeded in identifying thousands of haplotype blocks associated with a range of neuropsychiatric traits, including disorders such as schizophrenia, Alzheimer’s and Parkinson’s disease. However, the …

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TARGETED, HIGH-RESOLUTION RNA SEQUENCING OF NON-CODING GENOMIC REGIONS ASSOCIATED WITH NEUROPSYCHIATRIC FUNCTIONS

Simon A. Hardwick, Samuel D. Bassett, Dominik C. Kaczorowski, James Blackburn et autres

The human brain is one of the last frontiers of biomedical research. Genome-wide association studies (GWAS) have succeeded in identifying thousands of haplotype blocks associated with a range of neuropsychiatric traits, including disorders such as schizophrenia, Alzheimer’s and Parkinson’s disease. However, the …

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