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Article ; Online: Testing at scale during the COVID-19 pandemic.

Mercer, Tim R / Salit, Marc

2021 Volume 22, Issue 7, Page(s) 415–426

Abstract: Assembly and publication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in January 2020 enabled the immediate development of tests to detect the new virus. This began the largest global testing programme in history, in which ... ...

Abstract	Assembly and publication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in January 2020 enabled the immediate development of tests to detect the new virus. This began the largest global testing programme in history, in which hundreds of millions of individuals have been tested to date. The unprecedented scale of testing has driven innovation in the strategies, technologies and concepts that govern testing in public health. This Review describes the changing role of testing during the COVID-19 pandemic, including the use of genomic surveillance to track SARS-CoV-2 transmission around the world, the use of contact tracing to contain disease outbreaks and testing for the presence of the virus circulating in the environment. Despite these efforts, widespread community transmission has become entrenched in many countries and has required the testing of populations to identify and isolate infected individuals, many of whom are asymptomatic. The diagnostic and epidemiological principles that underpin such population-scale testing are also considered, as are the high-throughput and point-of-care technologies that make testing feasible on a massive scale.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/genetics ; COVID-19/transmission ; Humans ; Pandemics ; Public Health ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity
Language	English
Publishing date	2021-05-04
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2035157-4
ISSN	1471-0064 ; 1471-0056
ISSN (online)	1471-0064
ISSN	1471-0056
DOI	10.1038/s41576-021-00360-w
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Article ; Online: The potential of long noncoding RNA therapies.

Mercer, Tim R / Munro, Trent / Mattick, John S

Trends in pharmacological sciences

2022 Volume 43, Issue 4, Page(s) 269–280

Abstract: The human genome expresses vast numbers of long noncoding RNAs (lncRNA) that fulfil diverse roles in gene regulation, cell biology, development, and human disease. These roles are often mediated by sequence motifs and secondary structures bound by ... ...

Abstract	The human genome expresses vast numbers of long noncoding RNAs (lncRNA) that fulfil diverse roles in gene regulation, cell biology, development, and human disease. These roles are often mediated by sequence motifs and secondary structures bound by proteins and can regulate epigenetic, transcriptional, and translational pathways. These functional domains can be further optimised and engineered into RNA devices that are widely used in synthetic biology. We propose that natural lncRNA structures can be explored and exploited for the rational design and assembly of synthetic RNA therapies. This potential has been enabled by advances in the stability, immunogenicity, manufacture, and delivery of other RNA-based therapies, from which we can anticipate the pharmacological properties of lncRNA therapies that have not yet otherwise entered clinical trials.
MeSH term(s)	Gene Expression Regulation ; Genome, Human ; Humans ; RNA, Long Noncoding/genetics
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2022-02-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	282846-7
ISSN	1873-3735 ; 0165-6147
ISSN (online)	1873-3735
ISSN	0165-6147
DOI	10.1016/j.tips.2022.01.008
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Article ; Online: The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine.

Mercer, Tim R / Xu, Joshua / Mason, Christopher E / Tong, Weida

Genome biology

2021 Volume 22, Issue 1, Page(s) 306

MeSH term(s)	Circulating Tumor DNA ; DNA Methylation ; Genomics ; High-Throughput Nucleotide Sequencing/standards ; Humans ; Neoplasms/genetics ; Precision Medicine/standards ; Quality Control ; Sequence Analysis, RNA ; Single-Cell Analysis
Chemical Substances	Circulating Tumor DNA
Language	English
Publishing date	2021-11-08
Publishing country	England
Document type	Editorial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02528-3
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Article ; Online: Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests.

Madala, Bindu Swapna / Reis, Andre L M / Deveson, Ira W / Rawlinson, William / Mercer, Tim R

Scientific reports

2021 Volume 11, Issue 1, Page(s) 2636

Abstract: DNA synthesis in vitro has enabled the rapid production of reference standards. These are used as controls, and allow measurement and improvement of the accuracy and quality of diagnostic tests. Current reference standards typically represent target ... ...

Abstract	DNA synthesis in vitro has enabled the rapid production of reference standards. These are used as controls, and allow measurement and improvement of the accuracy and quality of diagnostic tests. Current reference standards typically represent target genetic material, and act only as positive controls to assess test sensitivity. However, negative controls are also required to evaluate test specificity. Using a pair of chimeric A/B RNA standards, this allowed incorporation of positive and negative controls into diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The chimeric standards constituted target regions for RT-PCR primer/probe sets that are joined in tandem across two separate synthetic molecules. Accordingly, a target region that is present in standard A provides a positive control, whilst being absent in standard B, thereby providing a negative control. This design enables cross-validation of positive and negative controls between the paired standards in the same reaction, with identical conditions. This enables control and test failures to be distinguished, increasing confidence in the accuracy of results. The chimeric A/B standards were assessed using the US Centres for Disease Control real-time RT-PCR protocol, and showed results congruent with other commercial controls in detecting SARS-CoV-2 in patient samples. This chimeric reference standard design approach offers extensive flexibility, allowing representation of diverse genetic features and distantly related sequences, even from different organisms.
MeSH term(s)	Amino Acid Sequence ; COVID-19/diagnosis ; COVID-19/virology ; Chimera ; Humans ; RNA, Viral/standards ; Reference Standards ; Reproducibility of Results ; SARS-CoV-2/chemistry ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Sensitivity and Specificity
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-01-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-81760-0
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Article ; Online: A universal molecular control for DNA, mRNA and protein expression.

Gunter, Helen M / Youlten, Scott E / Reis, Andre L M / McCubbin, Tim / Madala, Bindu Swapna / Wong, Ted / Stevanovski, Igor / Cipponi, Arcadi / Deveson, Ira W / Santini, Nadia S / Kummerfeld, Sarah / Croucher, Peter I / Marcellin, Esteban / Mercer, Tim R

Nature communications

2024 Volume 15, Issue 1, Page(s) 2480

Abstract: The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are ... ...

Abstract	The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.
MeSH term(s)	RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Proteomics ; DNA/genetics ; Genomics ; RNA
Chemical Substances	RNA, Messenger ; DNA (9007-49-2) ; RNA (63231-63-0)
Language	English
Publishing date	2024-03-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46456-9
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Article: Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

Troskie, Robin-Lee / Jafrani, Yohaann / Mercer, Tim R / Ewing, Adam D / Faulkner, Geoffrey J / Cheetham, Seth W

Genome biology. 2021 Dec., v. 22, no. 1

2021

Abstract: Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we ... ...

Abstract	Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes expressed in tissue-specific patterns. Some pseudogene transcripts have intact open reading frames and are translated in cultured cells, representing unannotated protein-coding genes. To assess the biological impact of noncoding pseudogenes, we CRISPR-Cas9 delete the nucleus-enriched pseudogene PDCL3P4 and observe hundreds of perturbed genes. This study highlights pseudogenes as a complex and dynamic component of the human transcriptional landscape.
Keywords	evolution ; humans ; neoplasm cells ; pseudogenes ; transcription (genetics) ; transcriptome
Language	English
Dates of publication	2021-12
Size	p. 146.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02369-0
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Article: Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome

Reis, Andre L. M. / Deveson, Ira W. / Madala, Bindu Swapna / Wong, Ted / Barker, Chris / Xu, Joshua / Lennon, Niall / Tong, Weida / Mercer, Tim R.

Genome biology. 2022 Dec., v. 23, no. 1

2022

Abstract: BACKGROUND: Next-generation sequencing (NGS) can identify mutations in the human genome that cause disease and has been widely adopted in clinical diagnosis. However, the human genome contains many polymorphic, low-complexity, and repetitive regions that ...

Institution	on behalf of the SEQC2 Consortium
Abstract	BACKGROUND: Next-generation sequencing (NGS) can identify mutations in the human genome that cause disease and has been widely adopted in clinical diagnosis. However, the human genome contains many polymorphic, low-complexity, and repetitive regions that are difficult to sequence and analyze. Despite their difficulty, these regions include many clinically important sequences that can inform the treatment of human diseases and improve the diagnostic yield of NGS. RESULTS: To evaluate the accuracy by which these difficult regions are analyzed with NGS, we built an in silico decoy chromosome, along with corresponding synthetic DNA reference controls, that encode difficult and clinically important human genome regions, including repeats, microsatellites, HLA genes, and immune receptors. These controls provide a known ground-truth reference against which to measure the performance of diverse sequencing technologies, reagents, and bioinformatic tools. Using this approach, we provide a comprehensive evaluation of short- and long-read sequencing instruments, library preparation methods, and software tools and identify the errors and systematic bias that confound our resolution of these remaining difficult regions. CONCLUSIONS: This study provides an analytical validation of diagnosis using NGS in difficult regions of the human genome and highlights the challenges that remain to resolve these difficult regions.
Keywords	DNA ; bioinformatics ; chromosomes ; computer simulation ; computer software ; humans ; microsatellite repeats
Language	English
Dates of publication	2022-12
Size	p. 19.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02579-6
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Reference standards for next-generation sequencing.

Hardwick, Simon A / Deveson, Ira W / Mercer, Tim R

Nature reviews. Genetics

2017 Volume 18, Issue 8, Page(s) 473–484

Abstract: Next-generation sequencing (NGS) provides a broad investigation of the genome, and it is being readily applied for the diagnosis of disease-associated genetic features. However, the interpretation of NGS data remains challenging owing to the size and ... ...

Abstract	Next-generation sequencing (NGS) provides a broad investigation of the genome, and it is being readily applied for the diagnosis of disease-associated genetic features. However, the interpretation of NGS data remains challenging owing to the size and complexity of the genome and the technical errors that are introduced during sample preparation, sequencing and analysis. These errors can be understood and mitigated through the use of reference standards - well-characterized genetic materials or synthetic spike-in controls that help to calibrate NGS measurements and to evaluate diagnostic performance. The informed use of reference standards, and associated statistical principles, ensures rigorous analysis of NGS data and is essential for its future clinical use.
MeSH term(s)	Animals ; High-Throughput Nucleotide Sequencing/standards ; Humans ; Reference Standards ; Sequence Analysis, DNA/standards
Language	English
Publishing date	2017-08
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2035157-4
ISSN	1471-0064 ; 1471-0056
ISSN (online)	1471-0064
ISSN	1471-0056
DOI	10.1038/nrg.2017.44
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Article ; Online: Structure and function of long noncoding RNAs in epigenetic regulation.

Mercer, Tim R / Mattick, John S

Nature structural & molecular biology

2013 Volume 20, Issue 3, Page(s) 300–307

Abstract: Genomes of complex organisms encode an abundance and diversity of long noncoding RNAs (lncRNAs) that are expressed throughout the cell and fulfill a wide variety of regulatory roles at almost every stage of gene expression. These roles, which encompass ... ...

Abstract	Genomes of complex organisms encode an abundance and diversity of long noncoding RNAs (lncRNAs) that are expressed throughout the cell and fulfill a wide variety of regulatory roles at almost every stage of gene expression. These roles, which encompass sensory, guiding, scaffolding and allosteric capacities, derive from folded modular domains in lncRNAs. In this diverse functional repertoire, we focus on the well-characterized ability for lncRNAs to function as epigenetic modulators. Many lncRNAs bind to chromatin-modifying proteins and recruit their catalytic activity to specific sites in the genome, thereby modulating chromatin states and impacting gene expression. Considering this regulatory potential in combination with the abundance of lncRNAs suggests that lncRNAs may be part of a broad epigenetic regulatory network.
MeSH term(s)	Binding Sites ; Cytoplasm/genetics ; DNA/metabolism ; Epigenesis, Genetic ; Genome, Human ; Humans ; Proteins/metabolism ; RNA/metabolism ; RNA, Double-Stranded/chemistry ; RNA, Long Noncoding/chemistry ; RNA, Long Noncoding/physiology
Chemical Substances	Proteins ; RNA, Double-Stranded ; RNA, Long Noncoding ; RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2013-03-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/nsmb.2480
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Article ; Online: Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome.

Troskie, Robin-Lee / Jafrani, Yohaann / Mercer, Tim R / Ewing, Adam D / Faulkner, Geoffrey J / Cheetham, Seth W

Genome biology

2021 Volume 22, Issue 1, Page(s) 146

Abstract	Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes expressed in tissue-specific patterns. Some pseudogene transcripts have intact open reading frames and are translated in cultured cells, representing unannotated protein-coding genes. To assess the biological impact of noncoding pseudogenes, we CRISPR-Cas9 delete the nucleus-enriched pseudogene PDCL3P4 and observe hundreds of perturbed genes. This study highlights pseudogenes as a complex and dynamic component of the human transcriptional landscape.
MeSH term(s)	Cell Line ; DNA, Complementary/genetics ; Gene Deletion ; Haploidy ; Humans ; Promoter Regions, Genetic/genetics ; Pseudogenes ; Sequence Analysis, DNA ; Transcriptome/genetics
Chemical Substances	DNA, Complementary
Language	English
Publishing date	2021-05-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02369-0
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