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Article ; Online: A Revolution Is Brewing in How We Understand the Shared Genetic Causes of Psychiatric Disorders.

Ronald, Angelica / Pain, Oliver

2022 Volume 179, Issue 11, Page(s) 791–793

MeSH term(s)	Humans ; Mental Disorders/genetics ; Bipolar Disorder/genetics ; Attention Deficit Disorder with Hyperactivity/genetics ; Autism Spectrum Disorder/genetics
Language	English
Publishing date	2022-11-01
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.20220777
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Article ; Online: Could interventions on physical activity mitigate genomic liability for obesity? Applying the health disparity framework in genetically informed studies.

Herle, Moritz / Pickles, Andrew / Pain, Oliver / Viner, Russell / Pingault, Jean-Baptiste / De Stavola, Bianca L

European journal of epidemiology

2023 Volume 38, Issue 4, Page(s) 403–412

Abstract: Polygenic scores (PGS) are now commonly available in longitudinal cohort studies, leading to their integration into epidemiological research. In this work, our aim is to explore how polygenic scores can be used as exposures in causal inference-based ... ...

Abstract	Polygenic scores (PGS) are now commonly available in longitudinal cohort studies, leading to their integration into epidemiological research. In this work, our aim is to explore how polygenic scores can be used as exposures in causal inference-based methods, specifically mediation analyses. We propose to estimate the extent to which the association of a polygenic score indexing genetic liability to an outcome could be mitigated by a potential intervention on a mediator. To do this this, we use the interventional disparity measure approach, which allows us to compare the adjusted total effect of an exposure on an outcome, with the association that would remain had we intervened on a potentially modifiable mediator. As an example, we analyse data from two UK cohorts, the Millennium Cohort Study (MCS, N = 2575) and the Avon Longitudinal Study of Parents and Children (ALSPAC, N = 3347). In both, the exposure is genetic liability for obesity (indicated by a PGS for BMI), the outcome is late childhood/early adolescent BMI, and the mediator and potential intervention target is physical activity, measured between exposure and outcome. Our results suggest that a potential intervention on child physical activity can mitigate some of the genetic liability for childhood obesity. We propose that including PGSs in a health disparity measure approach, and causal inference-based methods more broadly, is a valuable addition to the study of gene-environment interplay in complex health outcomes.
MeSH term(s)	Adolescent ; Child ; Humans ; Cohort Studies ; Exercise ; Genomics ; Longitudinal Studies ; Pediatric Obesity ; Mediation Analysis
Language	English
Publishing date	2023-03-11
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	632614-6
ISSN	1573-7284 ; 0393-2990
ISSN (online)	1573-7284
ISSN	0393-2990
DOI	10.1007/s10654-023-00980-y
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Article ; Online: Stratified genome-wide association analysis of type 2 diabetes reveals subgroups with genetic and environmental heterogeneity.

Christiansen, Colette E / Arathimos, Ryan / Pain, Oliver / Molokhia, Mariam / Bell, Jordana T / Lewis, Cathryn M

Human molecular genetics

2023 Volume 32, Issue 16, Page(s) 2638–2645

Abstract: Type 2 diabetes (T2D) is a heterogeneous illness caused by genetic and environmental factors. Previous genome-wide association studies (GWAS) have identified many genetic variants associated with T2D and found evidence of differing genetic profiles by ... ...

Abstract	Type 2 diabetes (T2D) is a heterogeneous illness caused by genetic and environmental factors. Previous genome-wide association studies (GWAS) have identified many genetic variants associated with T2D and found evidence of differing genetic profiles by age-at-onset. This study seeks to explore further the genetic and environmental drivers of T2D by analyzing subgroups on the basis of age-at-onset of diabetes and body mass index (BMI). In the UK Biobank, 36 494 T2D cases were stratified into three subgroups, and GWAS was performed for all T2D cases and for each subgroup relative to 421 021 controls. Altogether, 18 single nucleotide polymorphisms were significantly associated with T2D genome-wide in one or more subgroups and also showed evidence of heterogeneity between the subgroups (Cochrane's Q P < 0.01), with two SNPs remaining significant after multiple testing (in CDKN2B and CYTIP). Combined risk scores, on the basis of genetic profile, BMI and age, resulted in excellent diabetes prediction [area under the ROC curve (AUC) = 0.92]. A modest improvement in prediction (AUC = 0.93) was seen when the contribution of genetic and environmental factors was evaluated separately for each subgroup. Increasing sample sizes of genetic studies enables us to stratify disease cases into subgroups, which have sufficient power to highlight areas of genetic heterogeneity. Despite some evidence that optimizing combined risk scores by subgroup improves prediction, larger sample sizes are likely needed for prediction when using a stratification approach.
MeSH term(s)	Humans ; Diabetes Mellitus, Type 2/genetics ; Genome-Wide Association Study ; Genetic Predisposition to Disease ; Risk Factors ; Polymorphism, Single Nucleotide/genetics
Language	English
Publishing date	2023-07-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddad093
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Article ; Online: Transcriptome-wide association study of HIV-1 acquisition identifies

Duarte, Rodrigo R R / Pain, Oliver / Furler, Robert L / Nixon, Douglas F / Powell, Timothy R

iScience

2022 Volume 25, Issue 9, Page(s) 104854

Abstract: The host genetic factors conferring protection against HIV type 1 (HIV-1) acquisition remain elusive, and in particular the contributions of common genetic variants. Here, we performed the largest genome-wide association meta-analysis of HIV-1 ... ...

Abstract	The host genetic factors conferring protection against HIV type 1 (HIV-1) acquisition remain elusive, and in particular the contributions of common genetic variants. Here, we performed the largest genome-wide association meta-analysis of HIV-1 acquisition, which included 7,303 HIV-1-positive individuals and 587,343 population controls. We identified 25 independent genetic loci with suggestive association, of which one was genome-wide significant within the major histocompatibility complex (MHC) locus. After exclusion of the MHC signal, linkage disequilibrium score regression analyses revealed a SNP heritability of 21% and genetic correlations with behavioral factors. A transcriptome-wide association study identified 15 susceptibility genes, including
Language	English
Publishing date	2022-08-04
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.104854
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Article ; Online: A tool for translating polygenic scores onto the absolute scale using summary statistics.

Pain, Oliver / Gillett, Alexandra C / Austin, Jehannine C / Folkersen, Lasse / Lewis, Cathryn M

European journal of human genetics : EJHG

2022 Volume 30, Issue 3, Page(s) 339–348

Abstract: There is growing interest in the clinical application of polygenic scores as their predictive utility increases for a range of health-related phenotypes. However, providing polygenic score predictions on the absolute scale is an important step for their ... ...

Abstract	There is growing interest in the clinical application of polygenic scores as their predictive utility increases for a range of health-related phenotypes. However, providing polygenic score predictions on the absolute scale is an important step for their safe interpretation. We have developed a method to convert polygenic scores to the absolute scale for binary and normally distributed phenotypes. This method uses summary statistics, requiring only the area-under-the-ROC curve (AUC) or variance explained (R
MeSH term(s)	Genetic Predisposition to Disease ; Genome-Wide Association Study/methods ; Humans ; Multifactorial Inheritance ; Phenotype ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2022-01-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1141470-4
ISSN	1476-5438 ; 1018-4813
ISSN (online)	1476-5438
ISSN	1018-4813
DOI	10.1038/s41431-021-01028-z
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Article ; Online: Genetic overlap between psychotic experiences in the community across age and with psychiatric disorders.

Barkhuizen, Wikus / Pain, Oliver / Dudbridge, Frank / Ronald, Angelica

Translational psychiatry

2020 Volume 10, Issue 1, Page(s) 86

Abstract: This study explores the degree to which genetic influences on psychotic experiences are stable across adolescence and adulthood, and their overlap with psychiatric disorders. Genome-wide association results were obtained for adolescent psychotic ... ...

Abstract	This study explores the degree to which genetic influences on psychotic experiences are stable across adolescence and adulthood, and their overlap with psychiatric disorders. Genome-wide association results were obtained for adolescent psychotic experiences and negative symptom traits (N = 6297-10,098), schizotypy (N = 3967-4057) and positive psychotic experiences in adulthood (N = 116,787-117,794), schizophrenia (N = 150,064), bipolar disorder (N = 41,653), and depression (N = 173,005). Linkage disequilibrium score regression was used to estimate genetic correlations. Implicated genes from functional and gene-based analyses were compared. Mendelian randomization was performed on trait pairs with significant genetic correlations. Results indicated that subclinical auditory and visual hallucinations and delusions of persecution during adulthood were significantly genetically correlated with schizophrenia (r
MeSH term(s)	Adolescent ; Adult ; Depressive Disorder, Major/genetics ; Genome-Wide Association Study ; Hallucinations/genetics ; Humans ; Psychotic Disorders/genetics ; Schizophrenia/genetics
Language	English
Publishing date	2020-03-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2609311-X
ISSN	2158-3188 ; 2158-3188
ISSN (online)	2158-3188
ISSN	2158-3188
DOI	10.1038/s41398-020-0765-2
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Article ; Online: A systematic review of genome-wide research on psychotic experiences and negative symptom traits: new revelations and implications for psychiatry.

Ronald, Angelica / Pain, Oliver

Human molecular genetics

2018 Volume 27, Issue R2, Page(s) R136–R152

Abstract: We present a systematic review of genome-wide research on psychotic experience and negative symptom (PENS) traits in the community. We integrate these new findings, most of which have emerged over the last four years, with more established behaviour ... ...

Abstract	We present a systematic review of genome-wide research on psychotic experience and negative symptom (PENS) traits in the community. We integrate these new findings, most of which have emerged over the last four years, with more established behaviour genetic and epidemiological research. The review includes the first genome-wide association studies of PENS, including a recent meta-analysis, and the first SNP heritability estimates. Sample sizes of <10 000 participants mean that no genome-wide significant variants have yet been replicated. Importantly, however, in the most recent and well-powered studies, polygenic risk score prediction and linkage disequilibrium (LD) score regression analyses show that all types of PENS share genetic influences with diagnosed schizophrenia and that negative symptom traits also share genetic influences with major depression. These genetic findings corroborate other evidence in supporting a link between PENS in the community and psychiatric conditions. Beyond the systematic review, we highlight recent work on gene-environment correlation, which appears to be a relevant process for psychotic experiences. Genes that influence risk factors such as tobacco use and stressful life events are likely to be harbouring 'hits' that also influence PENS. We argue for the acceptance of PENS within the mainstream, as heritable traits in the same vein as other sub-clinical psychopathology and personality styles such as neuroticism. While acknowledging some mixed findings, new evidence shows genetic overlap between PENS and psychiatric conditions. In sum, normal variations in adolescent and adult thinking styles, such as feeling paranoid, are heritable and show genetic associations with schizophrenia and major depression.
MeSH term(s)	Adult ; Affect/physiology ; Bipolar Disorder/genetics ; Depressive Disorder, Major/genetics ; Female ; Gene-Environment Interaction ; Genetic Predisposition to Disease/genetics ; Genetic Testing/methods ; Genome-Wide Association Study ; Genotype ; Humans ; Linkage Disequilibrium/genetics ; Male ; Multifactorial Inheritance/genetics ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Psychiatry/methods ; Psychometrics/methods ; Psychometrics/trends ; Psychotic Disorders/genetics ; Risk Factors ; Schizophrenia/genetics
Language	English
Publishing date	2018-05-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddy157
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Article ; Online: Delineating the Genetic Component of Gene Expression in Major Depression.

Dall'Aglio, Lorenza / Lewis, Cathryn M / Pain, Oliver

Biological psychiatry

2020 Volume 89, Issue 6, Page(s) 627–636

Abstract: Background: Major depression (MD) is determined by a multitude of factors including genetic risk variants that regulate gene expression. We examined the genetic component of gene expression in MD by performing a transcriptome-wide association study ( ... ...

Abstract	Background: Major depression (MD) is determined by a multitude of factors including genetic risk variants that regulate gene expression. We examined the genetic component of gene expression in MD by performing a transcriptome-wide association study (TWAS), inferring gene expression-trait relationships from genetic, transcriptomic, and phenotypic information. Methods: Genes differentially expressed in depression were identified with the TWAS FUSION method, based on summary statistics from the largest genome-wide association analysis of MD (n = 135,458 cases, n = 344,901 controls) and gene expression levels from 21 tissue datasets (brain; blood; thyroid, adrenal, and pituitary glands). Follow-up analyses were performed to extensively characterize the identified associations: colocalization, conditional, and fine-mapping analyses together with TWAS-based pathway investigations. Results: Transcriptome-wide significant differences between cases and controls were found at 94 genes, approximately half of which were novel. Of the 94 significant genes, 6 represented strong, colocalized, and potentially causal associations with depression. Such high-confidence associations include NEGR1, CTC-467M3.3, TMEM106B, LRFN5, ESR2, and PROX2. Lastly, TWAS-based enrichment analysis highlighted dysregulation of gene sets for, among others, neuronal and synaptic processes. Conclusions: This study sheds further light on the genetic component of gene expression in depression by characterizing the identified associations, unraveling novel risk genes, and determining which associations are congruent with a causal model. These findings can be used as a resource for prioritizing and designing subsequent functional studies of MD.
MeSH term(s)	Depression ; Depressive Disorder, Major/genetics ; Gene Expression Profiling ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Membrane Proteins ; Nerve Tissue Proteins ; Transcriptome
Chemical Substances	Membrane Proteins ; Nerve Tissue Proteins ; TMEM106B protein, human
Language	English
Publishing date	2020-09-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209434-4
ISSN	1873-2402 ; 0006-3223
ISSN (online)	1873-2402
ISSN	0006-3223
DOI	10.1016/j.biopsych.2020.09.010
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Article: Clinicians' Perceptions towards Precision Medicine Tools for Cardiovascular Disease Risk Stratification in South Africa.

Kamp, Michelle / Pain, Oliver / May, Andrew / Lewis, Cathryn M / Ramsay, Michèle

Journal of personalized medicine

2022 Volume 12, Issue 9

Abstract: Cardiovascular diseases (CVDs) are a leading cause of mortality and morbidity in South Africa. Risk stratification is the preferred approach to disease prevention, but identifying patients at high risk for CVD remains challenging. Assessing genetic risk ... ...

Abstract	Cardiovascular diseases (CVDs) are a leading cause of mortality and morbidity in South Africa. Risk stratification is the preferred approach to disease prevention, but identifying patients at high risk for CVD remains challenging. Assessing genetic risk could improve stratification and inform a clinically relevant precision medicine (PM) approach. Clinicians are critical to PM adoption, thus, this study explores practicing clinicians’ perceptions of PM-based CVD risk stratification in South Africa’s public health setting. Practicing clinicians (n = 109) at four teaching hospitals in Johannesburg, South Africa, completed an electronic self-administered survey. The effect of demographic and professional characteristics on PM-based CVD risk stratification perceptions was assessed. Fewer than 25% of respondents used clinical genetic testing, and 14% had formal genetics training. 78% had a low mean knowledge score, with higher scores associated with genetic training (p < 0.0005) and research involvement (p < 0.05). Despite limited knowledge and resources, 84% perceived PM approaches positively. 57% felt confident in applying the PM-based approach, with those already undertaking CVD risk stratification more confident (p < 0.001). High cost and limited access to genetics services are key barriers. Integrating genetic information into established clinical tools will likely increase confidence in using PM approaches. Addressing the genetics training gap and investment into the country’s genomics capacity is needed to advance PM in South Africa.
Language	English
Publishing date	2022-08-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662248-8
ISSN	2075-4426
ISSN	2075-4426
DOI	10.3390/jpm12091360
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Article ; Online: On the climate emergency and the health of our patients: comment on the article by Dellaripa et al.

Hospach, Toni / Belot, Alexandre / Beresford, Michael W / Dressler, Frank / Kallinich, Tilmann / Oommen, Prassad / Pain, Clare E / Tenbrock, Klaus / Weller, Frank / Roth, Johannes / Minden, Kirsten / Hinze, Claas / Sander, Oliver / Hedrich, Christian M

Arthritis & rheumatology (Hoboken, N.J.)

2023 Volume 75, Issue 8, Page(s) 1493–1494

MeSH term(s)	Humans ; Climate ; Patients
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	2756371-6
ISSN	2326-5205 ; 2326-5191
ISSN (online)	2326-5205
ISSN	2326-5191
DOI	10.1002/art.42483
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