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Article ; Online: Exploring THAP11 Repeat Expansion beyond Chinese-Ancestry Cohorts: An Examination of 1000 Genomes and UK Biobank Data.

Fearnley, Liam G / Rafehi, Haloom / Bennett, Mark F / Bahlo, Melanie

Movement disorders : official journal of the Movement Disorder Society

2023 Volume 38, Issue 12, Page(s) 2320–2322

MeSH term(s)	Humans ; UK Biobank ; Biological Specimen Banks ; Spinocerebellar Ataxias/genetics ; Nerve Tissue Proteins/genetics ; China ; Trinucleotide Repeat Expansion ; Repressor Proteins
Chemical Substances	Nerve Tissue Proteins ; THAP11 protein, human ; Repressor Proteins
Language	English
Publishing date	2023-12-19
Publishing country	United States
Document type	Letter
ZDB-ID	607633-6
ISSN	1531-8257 ; 0885-3185
ISSN (online)	1531-8257
ISSN	0885-3185
DOI	10.1002/mds.29636
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Article: Measuring pathway database coverage of the phosphoproteome.

Huckstep, Hannah / Fearnley, Liam G / Davis, Melissa J

PeerJ

2021 Volume 9, Page(s) e11298

Abstract: Protein phosphorylation is one of the best known post-translational mechanisms playing a key role in the regulation of cellular processes. Over 100,000 distinct phosphorylation sites have been discovered through constant improvement of mass spectrometry ... ...

Abstract	Protein phosphorylation is one of the best known post-translational mechanisms playing a key role in the regulation of cellular processes. Over 100,000 distinct phosphorylation sites have been discovered through constant improvement of mass spectrometry based phosphoproteomics in the last decade. However, data saturation is occurring and the bottleneck of assigning biologically relevant functionality to phosphosites needs to be addressed. There has been finite success in using data-driven approaches to reveal phosphosite functionality due to a range of limitations. The alternate, more suitable approach is making use of prior knowledge from literature-derived databases. Here, we analysed seven widely used databases to shed light on their suitability to provide functional insights into phosphoproteomics data. We first determined the global coverage of each database at both the protein and phosphosite level. We also determined how consistent each database was in its phosphorylation annotations compared to a global standard. Finally, we looked in detail at the coverage of each database over six experimental datasets. Our analysis highlights the relative strengths and weaknesses of each database, providing a guide in how each can be best used to identify biological mechanisms in phosphoproteomic data.
Language	English
Publishing date	2021-05-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.11298
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Article ; Online: Measuring pathway database coverage of the phosphoproteome

Hannah Huckstep / Liam G. Fearnley / Melissa J. Davis

PeerJ, Vol 9, p e

2021 Volume 11298

Abstract	Protein phosphorylation is one of the best known post-translational mechanisms playing a key role in the regulation of cellular processes. Over 100,000 distinct phosphorylation sites have been discovered through constant improvement of mass spectrometry based phosphoproteomics in the last decade. However, data saturation is occurring and the bottleneck of assigning biologically relevant functionality to phosphosites needs to be addressed. There has been finite success in using data-driven approaches to reveal phosphosite functionality due to a range of limitations. The alternate, more suitable approach is making use of prior knowledge from literature-derived databases. Here, we analysed seven widely used databases to shed light on their suitability to provide functional insights into phosphoproteomics data. We first determined the global coverage of each database at both the protein and phosphosite level. We also determined how consistent each database was in its phosphorylation annotations compared to a global standard. Finally, we looked in detail at the coverage of each database over six experimental datasets. Our analysis highlights the relative strengths and weaknesses of each database, providing a guide in how each can be best used to identify biological mechanisms in phosphoproteomic data.
Keywords	Phosphoproteomics ; Databases ; Proteomics ; Bioinformatics ; Medicine ; R ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
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Article ; Online: Metabolomics in epidemiology: from metabolite concentrations to integrative reaction networks.

Fearnley, Liam G / Inouye, Michael

International journal of epidemiology

2016 Volume 45, Issue 5, Page(s) 1319–1328

Abstract: Metabolomics is becoming feasible for population-scale studies of human disease. In this review, we survey epidemiological studies that leverage metabolomics and multi-omics to gain insight into disease mechanisms. We outline key practical, technological ...

Abstract	Metabolomics is becoming feasible for population-scale studies of human disease. In this review, we survey epidemiological studies that leverage metabolomics and multi-omics to gain insight into disease mechanisms. We outline key practical, technological and analytical limitations while also highlighting recent successes in integrating these data. The use of multi-omics to infer reaction rates is discussed as a potential future direction for metabolomics research, as a means of identifying biomarkers as well as inferring causality. Furthermore, we highlight established analysis approaches as well as simulation-based methods currently used in single- and multi-cell levels in systems biology.
Language	English
Publishing date	2016-10
Publishing country	England
Document type	Review ; Journal Article
ZDB-ID	187909-1
ISSN	1464-3685 ; 0300-5771
ISSN (online)	1464-3685
ISSN	0300-5771
DOI	10.1093/ije/dyw046
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Article ; Online: An intronic GAA repeat expansion in FGF14 causes the autosomal-dominant adult-onset ataxia SCA27B/ATX-FGF14.

Rafehi, Haloom / Read, Justin / Szmulewicz, David J / Davies, Kayli C / Snell, Penny / Fearnley, Liam G / Scott, Liam / Thomsen, Mirja / Gillies, Greta / Pope, Kate / Bennett, Mark F / Munro, Jacob E / Ngo, Kathie J / Chen, Luke / Wallis, Mathew J / Butler, Ernest G / Kumar, Kishore R / Wu, Kathy Hc / Tomlinson, Susan E /

Tisch, Stephen / Malhotra, Abhishek / Lee-Archer, Matthew / Dolzhenko, Egor / Eberle, Michael A / Roberts, Leslie J / Fogel, Brent L / Brüggemann, Norbert / Lohmann, Katja / Delatycki, Martin B / Bahlo, Melanie / Lockhart, Paul J

American journal of human genetics

2023 Volume 110, Issue 6, Page(s) 1018

Language	English
Publishing date	2023-05-29
Publishing country	United States
Document type	Published Erratum
ZDB-ID	219384-x
ISSN	1537-6605 ; 0002-9297
ISSN (online)	1537-6605
ISSN	0002-9297
DOI	10.1016/j.ajhg.2023.05.005
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Article ; Online: NEK1 and STMN2 short tandem repeat lengths are not associated with Australian amyotrophic lateral sclerosis risk.

Grima, Natalie / Henden, Lyndal / Fearnley, Liam G / Rowe, Dominic B / D'Silva, Susan / Pamphlett, Roger / Adams, Lorel / Kiernan, Matthew C / Mazumder, Srestha / Timmins, Hannah C / Zoing, Margaret / Bahlo, Melanie / Blair, Ian P / Williams, Kelly L

Neurobiology of aging

2022 Volume 116, Page(s) 92–95

Abstract: Sporadic amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a complex genetic architecture. The lengths of two short tandem repeats (STRs), at the NEK1 and STMN2 loci, were recently associated with ALS risk in cohorts of ... ...

Abstract	Sporadic amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a complex genetic architecture. The lengths of two short tandem repeats (STRs), at the NEK1 and STMN2 loci, were recently associated with ALS risk in cohorts of European descent. The STMN2 STR was proposed to be predictive of clinical features including the age of onset and disease duration in bulbar onset cases. We sought to investigate NEK1 and STMN2 STR lengths in a cohort of Australian sporadic ALS cases (n = 608) and neurologically healthy controls (n = 4689) of European ancestry. ExpansionHunter was used to determine NEK1 and STMN2 STR length genotypes from whole-genome sequencing data followed by PCR validation of predicted lengths. No significant association was identified between sporadic ALS risk and the length of either STR. Further, neither NEK1 nor STMN2 STR lengths were indicative of the age of onset or disease duration. We report that the NEK1 and STMN2 STRs were not associated with ALS risk or clinical features in this Australian sporadic ALS cohort.
MeSH term(s)	Amyotrophic Lateral Sclerosis/genetics ; Amyotrophic Lateral Sclerosis/metabolism ; Australia ; Humans ; Microsatellite Repeats ; NIMA-Related Kinase 1/genetics ; NIMA-Related Kinase 1/metabolism ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/metabolism ; Stathmin/genetics ; Stathmin/metabolism
Chemical Substances	STMN2 protein, human ; Stathmin ; NEK1 protein, human (EC 2.7.11.1) ; NIMA-Related Kinase 1 (EC 2.7.11.1)
Language	English
Publishing date	2022-05-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	604505-4
ISSN	1558-1497 ; 0197-4580
ISSN (online)	1558-1497
ISSN	0197-4580
DOI	10.1016/j.neurobiolaging.2022.04.012
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Zs.MG 10: Show issues

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Article ; Online: PATHLOGIC-S: a scalable Boolean framework for modelling cellular signalling.

Fearnley, Liam G / Nielsen, Lars K

PloS one

2012 Volume 7, Issue 8, Page(s) e41977

Abstract: Curated databases of signal transduction have grown to describe several thousand reactions, and efficient use of these data requires the development of modelling tools to elucidate and explore system properties. We present PATHLOGIC-S, a Boolean ... ...

Abstract	Curated databases of signal transduction have grown to describe several thousand reactions, and efficient use of these data requires the development of modelling tools to elucidate and explore system properties. We present PATHLOGIC-S, a Boolean specification for a signalling model, with its associated GPL-licensed implementation using integer programming techniques. The PATHLOGIC-S specification has been designed to function on current desktop workstations, and is capable of providing analyses on some of the largest currently available datasets through use of Boolean modelling techniques to generate predictions of stable and semi-stable network states from data in community file formats. PATHLOGIC-S also addresses major problems associated with the presence and modelling of inhibition in Boolean systems, and reduces logical incoherence due to common inhibitory mechanisms in signalling systems. We apply this approach to signal transduction networks including Reactome and two pathways from the Panther Pathways database, and present the results of computations on each along with a discussion of execution time. A software implementation of the framework and model is freely available under a GPL license.
MeSH term(s)	Cells/metabolism ; Metabolic Networks and Pathways ; Models, Biological ; Reproducibility of Results ; Signal Transduction ; Software ; Systems Biology/methods
Language	English
Publishing date	2012-08-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0041977
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Article ; Online: Short tandem repeat expansions in sporadic amyotrophic lateral sclerosis and frontotemporal dementia.

Science advances

2023 Volume 9, Issue 18, Page(s) eade2044

Abstract: Pathogenic short tandem repeat (STR) expansions cause over 20 neurodegenerative diseases. To determine the contribution of STRs in sporadic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), we used ExpansionHunter, REviewer, and ... ...

Abstract	Pathogenic short tandem repeat (STR) expansions cause over 20 neurodegenerative diseases. To determine the contribution of STRs in sporadic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), we used ExpansionHunter, REviewer, and polymerase chain reaction validation to assess 21 neurodegenerative disease-associated STRs in whole-genome sequencing data from 608 patients with sporadic ALS, 68 patients with sporadic FTD, and 4703 matched controls. We also propose a data-derived outlier detection method for defining allele thresholds in rare STRs. Excluding
MeSH term(s)	Humans ; Frontotemporal Dementia/genetics ; Amyotrophic Lateral Sclerosis/genetics ; C9orf72 Protein/genetics ; DNA Repeat Expansion/genetics ; Spinocerebellar Ataxias/genetics ; Fragile X Mental Retardation Protein/genetics
Chemical Substances	C9orf72 Protein ; FMR1 protein, human ; Fragile X Mental Retardation Protein (139135-51-6)
Language	English
Publishing date	2023-05-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.ade2044
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Article ; Online: Multi-level remodelling of chromatin underlying activation of human T cells.

Bediaga, Naiara G / Coughlan, Hannah D / Johanson, Timothy M / Garnham, Alexandra L / Naselli, Gaetano / Schröder, Jan / Fearnley, Liam G / Bandala-Sanchez, Esther / Allan, Rhys S / Smyth, Gordon K / Harrison, Leonard C

Scientific reports

2021 Volume 11, Issue 1, Page(s) 528

Abstract: Remodelling of chromatin architecture is known to regulate gene expression and has been well characterized in cell lineage development but less so in response to cell perturbation. Activation of T cells, which triggers extensive changes in ... ...

Abstract	Remodelling of chromatin architecture is known to regulate gene expression and has been well characterized in cell lineage development but less so in response to cell perturbation. Activation of T cells, which triggers extensive changes in transcriptional programs, serves as an instructive model to elucidate how changes in chromatin architecture orchestrate gene expression in response to cell perturbation. To characterize coordinate changes at different levels of chromatin architecture, we analyzed chromatin accessibility, chromosome conformation and gene expression in activated human T cells. T cell activation was characterized by widespread changes in chromatin accessibility and interactions that were shared between activated CD4
MeSH term(s)	CD4-Positive T-Lymphocytes ; CD8-Positive T-Lymphocytes ; Cells, Cultured ; Chromatin/chemistry ; Chromatin/genetics ; Chromatin Assembly and Disassembly/genetics ; Chromatin Assembly and Disassembly/physiology ; Gene Expression Regulation, Developmental/genetics ; Humans ; Lymphocyte Activation/genetics ; Male ; Nucleosomes/genetics ; T-Lymphocytes/immunology ; Transcription Factors ; Transcription, Genetic/genetics
Chemical Substances	Chromatin ; Nucleosomes ; Transcription Factors
Language	English
Publishing date	2021-01-12
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/s41598-020-80165-9
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Article ; Online: A founder event causing a dominant childhood epilepsy survives 800 years through weak selective pressure.

Grinton, Bronwyn E / Robertson, Erandee / Fearnley, Liam G / Scheffer, Ingrid E / Marson, Anthony G / O'Brien, Terence J / Pickrell, W Owen / Rees, Mark I / Sisodiya, Sanjay M / Balding, David J / Bennett, Mark F / Bahlo, Melanie / Berkovic, Samuel F / Oliver, Karen L

American journal of human genetics

2022 Volume 109, Issue 11, Page(s) 2080–2087

Abstract: ... syndrome characterized by distinctive phenotypic heterogeneity within families. The SCN1B c.363C>G (p ... giving rise to the SCN1B c.363C>G variant in 14 independent families with epilepsy. A common haplotype ...

Abstract	Genetic epilepsy with febrile seizures plus (GEFS+) is an autosomal dominant familial epilepsy syndrome characterized by distinctive phenotypic heterogeneity within families. The SCN1B c.363C>G (p.Cys121Trp) variant has been identified in independent, multi-generational families with GEFS+. Although the variant is present in population databases (at very low frequency), there is strong clinical, genetic, and functional evidence to support pathogenicity. Recurrent variants may be due to a founder event in which the variant has been inherited from a common ancestor. Here, we report evidence of a single founder event giving rise to the SCN1B c.363C>G variant in 14 independent families with epilepsy. A common haplotype was observed in all families, and the age of the most recent common ancestor was estimated to be approximately 800 years ago. Analysis of UK Biobank whole-exome-sequencing data identified 74 individuals with the same variant. All individuals carried haplotypes matching the epilepsy-affected families, suggesting all instances of the variant derive from a single mutational event. This unusual finding of a variant causing an autosomal dominant, early-onset disease in an outbred population that has persisted over many generations can be attributed to the relatively mild phenotype in most carriers and incomplete penetrance. Founder events are well established in autosomal recessive and late-onset disorders but are rarely observed in early-onset, autosomal dominant diseases. These findings suggest variants present in the population at low frequencies should be considered potentially pathogenic in mild phenotypes with incomplete penetrance and may be more important contributors to the genetic landscape than previously thought.
MeSH term(s)	Child ; Humans ; Pedigree ; Electroencephalography ; Seizures, Febrile/genetics ; Phenotype ; Epilepsy/genetics
Language	English
Publishing date	2022-10-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219384-x
ISSN	1537-6605 ; 0002-9297
ISSN (online)	1537-6605
ISSN	0002-9297
DOI	10.1016/j.ajhg.2022.10.004
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