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Book ; Conference proceedings: Novel methods in mathematical genetics

Holmans, Peter

(Human heredity ; 64,1)

2007

Event/congress	European Mathematical Genetics Meeting (34, 2006, Cardiff)
Author's details	34th European Mathematical Genetics Meeting, Cardiff, April 6 - 7, 2006. Ed. Peter Holmans
Series title	Human heredity ; 64,1
Collection
Language	English
Size	88 S. : Ill., graph. Darst.
Publisher	Karger
Publishing place	Basel u.a.
Publishing country	Switzerland
Document type	Book ; Conference proceedings
HBZ-ID	HT015828251
ISBN	978-3-8055-8314-5 ; 3-8055-8314-1
Database	Catalogue ZB MED Medicine, Health

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Article ; Online: Using Genetics to Increase Specificity of Outcome Prediction in Psychiatric Disorders: Prospects for Progression.

Holmans, Peter A

The American journal of psychiatry

2020 Volume 177, Issue 10, Page(s) 884–887

MeSH term(s)	Bipolar Disorder ; Depressive Disorder ; Humans ; Mental Disorders/genetics ; Multifactorial Inheritance ; Psychotic Disorders ; Sensitivity and Specificity
Language	English
Publishing date	2020-09-30
Publishing country	United States
Document type	Editorial ; Comment
ZDB-ID	280045-7
ISSN	1535-7228 ; 0002-953X
ISSN (online)	1535-7228
ISSN	0002-953X
DOI	10.1176/appi.ajp.2020.20081181
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Article ; Online: Modelling Disease progression of Multiple Sclerosis in a South Wales Cohort.

Uzochukwu, Emeka C / Harding, Katharine E / Hrastelj, James / Kreft, Karim L / Holmans, Peter / Robertson, Neil P / Tallantyre, Emma C / Lawton, Michael

Neuroepidemiology

2024

Abstract: Objectives: To model multiple sclerosis (MS) disease progression and compare disease trajectories by sex, age of onset, and year of diagnosis.: Study design and settings: Longitudinal EDSS scores were collected since 1985 for relapse-onset MS ... ...

Abstract	Objectives: To model multiple sclerosis (MS) disease progression and compare disease trajectories by sex, age of onset, and year of diagnosis. Study design and settings: Longitudinal EDSS scores were collected since 1985 for relapse-onset MS patients at MS clinics in South Wales and modelled using a multilevel model (MLM). The MLM adjusted for baseline covariates (sex, age of onset, year of diagnosis, and disease modifying treatments (DMTs)), and included interactions between baseline covariates and time variables. Results: The optimal model was truncated at 30 years after disease onset and excluded EDSS recorded within 3 months of relapse. As expected, older age of onset was associated with faster disease progression at 15 years (effect size (ES): 0.75; CI: 0.63, 0.86; P: <0.001) and female sex progressed more slowly at 15 years (ES: -0.43; CI: -0.68, -0.18; P: <0.001). Patients diagnosed more recently (defined as 2007-2011 and >2011) progressed more slowly than those diagnosed historically (<2006); (ES: -0.46; CI: -0.75, -0.16; P: 0.006) and (ES: -0.95; CI: -1.20, -0.70; P: <0.001), respectively. Conclusion: We present a novel model of MS outcomes, accounting for the nonlinear trajectory of MS and effects of baseline covariates, validating well-known risk factors (sex and age of onset) associated with disease progression. Also, patients diagnosed more recently progressed more slowly than those diagnosed historically.
Language	English
Publishing date	2024-02-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	603189-4
ISSN	1423-0208 ; 0251-5350
ISSN (online)	1423-0208
ISSN	0251-5350
DOI	10.1159/000536427
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Article ; Online: The relationship between case-control differential gene expression from brain tissue and genetic associations in schizophrenia.

Clifton, Nicholas E / Schulmann, Anton / Holmans, Peter A / O'Donovan, Michael C / Vawter, Marquis P

American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics

2023 Volume 192, Issue 5-6, Page(s) 85–92

Abstract: Large numbers of genetic loci have been identified that are known to contain common risk alleles for schizophrenia, but linking associated alleles to specific risk genes remains challenging. Given that most alleles that influence liability to ... ...

Abstract	Large numbers of genetic loci have been identified that are known to contain common risk alleles for schizophrenia, but linking associated alleles to specific risk genes remains challenging. Given that most alleles that influence liability to schizophrenia are thought to do so by altered gene expression, intuitively, case-control differential gene expression studies should highlight genes with a higher probability of being associated with schizophrenia and could help identify the most likely causal genes within associated loci. Here, we test this hypothesis by comparing transcriptome analysis of the dorsolateral prefrontal cortex from 563 schizophrenia cases and 802 controls with genome-wide association study (GWAS) data from the third wave study of the Psychiatric Genomics Consortium. Genes differentially expressed in schizophrenia were not enriched for common allelic association statistics compared with other brain-expressed genes, nor were they enriched for genes within associated loci previously reported to be prioritized by genetic fine-mapping. Genes prioritized by Summary-based Mendelian Randomization were underexpressed in cases compared to other genes in the same GWAS loci. However, the overall strength and direction of expression change predicted by SMR were not related to that observed in the differential expression data. Overall, this study does not support the hypothesis that genes identified as differentially expressed from RNA sequencing of bulk brain tissue are enriched for those that show evidence for genetic associations. Such data have limited utility for prioritizing genes in currently associated loci in schizophrenia.
MeSH term(s)	Humans ; Schizophrenia/genetics ; Genome-Wide Association Study ; Genetic Predisposition to Disease ; Brain ; Gene Expression/genetics ; Polymorphism, Single Nucleotide/genetics
Language	English
Publishing date	2023-01-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2108616-3
ISSN	1552-485X ; 1552-4841 ; 0148-7299
ISSN (online)	1552-485X
ISSN	1552-4841 ; 0148-7299
DOI	10.1002/ajmg.b.32931
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Article ; Online: Using Genomic Data to Find Disease-Modifying Loci in Huntington's Disease (HD).

Holmans, Peter / Stone, Tim

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1780, Page(s) 443–461

Abstract: In this chapter, genetic modifiers are defined, and the rationale for investigating them in HD explained. Issues involved in modeling the phenotype are discussed, using age at motor onset as an example. The statistical methods for analyzing genetic data ( ...

Abstract	In this chapter, genetic modifiers are defined, and the rationale for investigating them in HD explained. Issues involved in modeling the phenotype are discussed, using age at motor onset as an example. The statistical methods for analyzing genetic data (linkage and association) are discussed, along with the advantages and disadvantages of each. In particular, the advantage of a genome-wide approach over one based on candidate genes is stressed. Genome-wide association studies (GWAS) are current method of choice to detect genetic modifiers. The power of GWAS is discussed, along with sources of error, and how these might be detected and corrected. Extensions to GWAS, such as gene- and pathway-wide analyses, are discussed, and also how GWAS may be used to estimate genetic risks and trait heritability. Since GWAS are most effective to detect common genetic variants, methods for analyzing rare variation are also discussed. The uses of other types of genomic data (notably, expression) are discussed, and how they might be integrated with genetic data to find causal genes and variants. The chapter ends with a short overview of future prospects for detecting genetic modifiers of HD.
MeSH term(s)	Data Analysis ; Genetic Loci/genetics ; Genetic Variation ; Genome-Wide Association Study/instrumentation ; Genome-Wide Association Study/methods ; Genomics/instrumentation ; Genomics/methods ; Humans ; Huntington Disease/genetics ; Linkage Disequilibrium/genetics ; Phenotype ; Polymorphism, Single Nucleotide/genetics
Language	English
Publishing date	2018-05-31
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7825-0_20
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Article ; Online: What is the Pathogenic CAG Expansion Length in Huntington's Disease?

Donaldson, Jasmine / Powell, Sophie / Rickards, Nadia / Holmans, Peter / Jones, Lesley

Journal of Huntington's disease

2021 Volume 10, Issue 1, Page(s) 175–202

Abstract: Huntington's disease (HD) (OMIM 143100) is caused by an expanded CAG repeat tract in the HTT gene. The inherited CAG length is known to expand further in somatic and germline cells in HD subjects. Age at onset of the disease is inversely correlated with ... ...

Abstract	Huntington's disease (HD) (OMIM 143100) is caused by an expanded CAG repeat tract in the HTT gene. The inherited CAG length is known to expand further in somatic and germline cells in HD subjects. Age at onset of the disease is inversely correlated with the inherited CAG length, but is further modulated by a series of genetic modifiers which are most likely to act on the CAG repeat in HTT that permit it to further expand. Longer repeats are more prone to expansions, and this expansion is age dependent and tissue-specific. Given that the inherited tract expands through life and most subjects develop disease in mid-life, this implies that in cells that degenerate, the CAG length is likely to be longer than the inherited length. These findings suggest two thresholds- the inherited CAG length which permits further expansion, and the intracellular pathogenic threshold, above which cells become dysfunctional and die. This two-step mechanism has been previously proposed and modelled mathematically to give an intracellular pathogenic threshold at a tract length of 115 CAG (95% confidence intervals 70- 165 CAG). Empirically, the intracellular pathogenic threshold is difficult to determine. Clues from studies of people and models of HD, and from other diseases caused by expanded repeat tracts, place this threshold between 60- 100 CAG, most likely towards the upper part of that range. We assess this evidence and discuss how the intracellular pathogenic threshold in manifest disease might be better determined. Knowing the cellular pathogenic threshold would be informative for both understanding the mechanism in HD and deploying treatments.
MeSH term(s)	DNA Repair/genetics ; Humans ; Huntington Disease/genetics ; Spinocerebellar Ataxias/genetics ; Trinucleotide Repeat Expansion/genetics
Language	English
Publishing date	2021-02-10
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	2673033-9
ISSN	1879-6400 ; 1879-6397
ISSN (online)	1879-6400
ISSN	1879-6397
DOI	10.3233/JHD-200445
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Article: Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits.

Holmans, Peter

Advances in genetics

2010 Volume 72, Page(s) 141–179

Abstract: A number of statistical methods have been developed to test for associations between pathways (collections of genes related biologically) and complex genetic traits. Pathway analysis methods were originally developed for analyzing gene expression data, ... ...

Abstract	A number of statistical methods have been developed to test for associations between pathways (collections of genes related biologically) and complex genetic traits. Pathway analysis methods were originally developed for analyzing gene expression data, but recently methods have been developed to perform pathway analysis on genome-wide association study (GWAS) data. The purpose of this review is to give an overview of these methods, enabling the reader to gain an understanding of what pathway analysis involves, and to select the method most suited to their purposes. This review describes the various types of statistical methods for pathway analysis, detailing the strengths and weaknesses of each. Factors influencing the power of pathway analyses, such as gene coverage and choice of pathways to analyze, are discussed, as well as various unresolved statistical issues. Finally, a list of computer programs for performing pathway analysis on genome-wide association data is provided.
MeSH term(s)	Animals ; Disease/genetics ; Genome-Wide Association Study ; Humans ; Models, Genetic
Language	English
Publishing date	2010-11-22
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	148-x
ISSN	0065-2660
ISSN	0065-2660
DOI	10.1016/B978-0-12-380862-2.00007-2
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Article: Irritability in young people with copy number variants associated with neurodevelopmental disorders (ND-CNVs).

Hall, Jessica H / Chawner, Samuel J R A / Wolstencroft, Jeanne / Skuse, David / Holmans, Peter / Owen, Michael J / van den Bree, Marianne B M

medRxiv : the preprint server for health sciences

2023

Abstract: Background: A range of rare mutations involving micro-deletion or -duplication of genetic material (copy number variants (CNVs)) have been associated with high neurodevelopmental and psychiatric risk (ND-CNVs). Irritability is frequently observed in ... ...

Abstract	Background: A range of rare mutations involving micro-deletion or -duplication of genetic material (copy number variants (CNVs)) have been associated with high neurodevelopmental and psychiatric risk (ND-CNVs). Irritability is frequently observed in childhood neurodevelopmental conditions, yet its aetiology is largely unknown. Genetic variation may play a role, but there is a sparsity of studies investigating presentation of irritability in young people with ND-CNVs. Aims: This study aimed to investigate whether there is a difference in irritability in young people with rare ND-CNVs compared to those without ND-CNVs, and to what extent irritability is associated with psychiatric diagnoses and cognitive ability (IQ). Methods: Irritability and broader psychopathology was assessed in 485 young people with ND-CNVs and 164 sibling controls, using the child and adolescent psychiatric assessment (CAPA). Autism was assessed using the Social Communication Questionnaire (SCQ), and Intelligence Quotient (IQ) by the Wechsler Abbreviated Scale of Intelligence (WASI). Results: 54% of young people with ND-CNVs met the threshold for irritability; significantly more than controls (OR = 3.77, CI = 3.07-7.90, p= 5.31 × 10 Conclusions: Irritability is an important aspect of the clinical picture in young people with ND-CNVs. This work shows that genetic variation is associated with irritability in young people with ND-CNVs, independent of psychiatric comorbidities or IQ impairment. Clinicians should be aware of this increased risk to inform management and interventions.
Language	English
Publishing date	2023-12-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.05.23299440
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Article ; Online: Family-based analysis of the contribution of rare and common genetic variants to school performance in schizophrenia.

Rammos, Alexandros / Kirov, George / Hubbard, Leon / Walters, James T R / Holmans, Peter / Owen, Michael J / O'Donovan, Michael C / Rees, Elliott

Molecular psychiatry

2023 Volume 28, Issue 5, Page(s) 2081–2087

Abstract: Impaired cognition in schizophrenia is associated with worse functional outcomes. While genetic factors are known to contribute to variation in cognition in schizophrenia, few rare coding variants with strong effects have been identified, and the ... ...

Abstract	Impaired cognition in schizophrenia is associated with worse functional outcomes. While genetic factors are known to contribute to variation in cognition in schizophrenia, few rare coding variants with strong effects have been identified, and the relative effects from de novo, inherited and non-transmitted alleles are unknown. We used array and exome sequencing data from 656 proband-parent trios to examine the contribution of common and rare variants to school performance, and by implication cognitive function, in schizophrenia. Parental transmission of common alleles contributing to higher educational attainment (p value = 0.00015; OR = 2.63) and intelligence (p value = 0.00009; OR = 2.80), but not to schizophrenia, were associated with higher proband school performance. No significant effects were seen for non-transmitted parental common alleles. Probands with lower school performance were enriched for damaging de novo coding variants in genes associated with developmental disorders (DD) (p value = 0.00026; OR = 11.6). Damaging, ultra-rare coding variants in DD genes that were transmitted or non-transmitted from parents, had no effects on school performance. Among probands with lower school performance, those with damaging de novo coding variants in DD genes had a higher rate of comorbid mild intellectual disability (p value = 0.0002; OR = 15.6). Overall, we provide evidence for rare and common genetic contributions to school performance in schizophrenia. The strong effects for damaging de novo coding variants in DD genes provide further evidence that cognitive impairment in schizophrenia has a shared aetiology with developmental disorders. Furthermore, we report no evidence in this sample that non-transmitted parental common alleles for cognitive traits contributed to school performance in schizophrenia via indirect effects on the environment.
MeSH term(s)	Humans ; Schizophrenia/genetics ; Mutation ; Genetic Predisposition to Disease/genetics ; Intellectual Disability/genetics ; Family
Language	English
Publishing date	2023-03-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1330655-8
ISSN	1476-5578 ; 1359-4184
ISSN (online)	1476-5578
ISSN	1359-4184
DOI	10.1038/s41380-023-02013-2
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Article ; Online: A polygenic resilience score moderates the genetic risk for schizophrenia: Replication in 18,090 cases and 28,114 controls from the Psychiatric Genomics Consortium.

Hess, Jonathan L / Mattheisen, Manuel / Greenwood, Tiffany A / Tsuang, Ming T / Edenberg, Howard J / Holmans, Peter / Faraone, Stephen V / Glatt, Stephen J

American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics

2023 Volume 195, Issue 2, Page(s) e32957

Abstract: Identifying heritable factors that moderate the genetic risk for schizophrenia (SCZ) could help clarify why some individuals remain unaffected despite having relatively high genetic liability. Previously, we developed a framework to mine genome-wide ... ...

Abstract	Identifying heritable factors that moderate the genetic risk for schizophrenia (SCZ) could help clarify why some individuals remain unaffected despite having relatively high genetic liability. Previously, we developed a framework to mine genome-wide association (GWAS) data for common genetic variants that protect high-risk unaffected individuals from SCZ, leading to derivation of the first-ever "polygenic resilience score" for SCZ (resilient controls n = 3786; polygenic risk score-matched SCZ cases n = 18,619). Here, we performed a replication study to verify the moderating effect of our polygenic resilience score on SCZ risk (OR = 1.09, p = 4.03 × 10
MeSH term(s)	Humans ; Schizophrenia/genetics ; Genome-Wide Association Study ; Resilience, Psychological ; Genetic Predisposition to Disease ; Multifactorial Inheritance/genetics ; Genomics ; Polymorphism, Single Nucleotide/genetics
Language	English
Publishing date	2023-08-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2108616-3
ISSN	1552-485X ; 1552-4841 ; 0148-7299
ISSN (online)	1552-485X
ISSN	1552-4841 ; 0148-7299
DOI	10.1002/ajmg.b.32957
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