scholarly journals Polygenic risk scores lack prognostic value for adults with severe mental illness

2021 ◽  
Author(s):  
Isotta Landi ◽  
Deepak Kaji ◽  
Liam Cotter ◽  
Tielman Van Vleck ◽  
Gillian Belbin ◽  
...  
Keyword(s):  
Mental Illness ◽  
Severe Mental Illness ◽  
Prognostic Value ◽  
Outcome Prediction ◽  
Risk Scores ◽  
Polygenic Risk Score ◽  
Psychiatric Interview ◽  
Genetic Traits ◽  
Polygenic Risk ◽  
Common Diseases

Schizophrenia (SCZ) is the archetypal severe mental illness and one of the most deeply characterized human genetic traits. Like most common diseases SCZ is highly polygenic, and as such its genetic liability can be summarized at the individual level by a polygenic risk score (PRS). Polygenic risk scores are a cornerstone of the precision medicine vision, as it is widely anticipated they will come to serve as biomarkers of disease and poor outcomes in real-world clinical practice. However, to date, few studies have assessed their actual prognostic value relative to current standards-of-care. SCZ is an ideal test case towards this end because the predictive power of the SCZ PRS exceeds that of most other common diseases. Here, we analyzed clinical and genetic data from two multi-ethnic cohorts totaling 8,541 adults with SCZ and related psychotic disorders, assessing whether the SCZ PRS improves poor outcome prediction relative to clinical features captured in a standard psychiatric interview. For all outcomes investigated, the SCZ PRS did not improve the performance of predictive models, an observation that was generally robust to divergent case definitions and ancestral backgrounds of study participants. These findings demonstrate the limited potential of even the most powerful contemporary polygenic risk scores as a tool for individualized outcome prediction.

scholarly journals Validity and Prognostic Value of a Polygenic Risk Score for Parkinson’s Disease

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1859
Author(s):  
Sebastian Koch ◽  
Björn-Hergen Laabs ◽  
Meike Kasten ◽  
Eva-Juliane Vollstedt ◽  
Jos Becktepe ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Prognostic Value ◽  
Later Life ◽  
Risk Scores ◽  
Polygenic Risk Score ◽  
Data Sets ◽  
Data Set ◽  
Polygenic Risk ◽  
Individual Level

Idiopathic Parkinson’s disease (PD) is a complex multifactorial disorder caused by the interplay of both genetic and non-genetic risk factors. Polygenic risk scores (PRSs) are one way to aggregate the effects of a large number of genetic variants upon the risk for a disease like PD in a single quantity. However, reassessment of the performance of a given PRS in independent data sets is a precondition for establishing the PRS as a valid tool to this end. We studied a previously proposed PRS for PD in a separate genetic data set, comprising 1914 PD cases and 4464 controls, and were able to replicate its ability to differentiate between cases and controls. We also assessed theoretically the prognostic value of the PD-PRS, i.e., its ability to predict the development of PD in later life for healthy individuals. As it turned out, the PD-PRS alone can be expected to perform poorly in this regard. Therefore, we conclude that the PD-PRS could serve as an important research tool, but that meaningful PRS-based prognosis of PD at an individual level is not feasible.

Symptom dimensions of major depression in a large community-based cohort

2021 ◽  
pp. 1-8
Author(s):  
Michael Wainberg ◽  
Peter Zhukovsky ◽  
Sean L. Hill ◽  
Daniel Felsky ◽  
Aristotle Voineskos ◽  
...  
Keyword(s):  
Primary Care ◽  
Major Depression ◽  
Risk Scores ◽  
Polygenic Risk Score ◽  
Psychiatric Diagnoses ◽  
Uk Biobank ◽  
Community Based ◽  
Symptom Dimensions ◽  
Polygenic Risk ◽  
Large Community

Abstract Background Our understanding of major depression is complicated by substantial heterogeneity in disease presentation, which can be disentangled by data-driven analyses of depressive symptom dimensions. We aimed to determine the clinical portrait of such symptom dimensions among individuals in the community. Methods This cross-sectional study consisted of 25 261 self-reported White UK Biobank participants with major depression. Nine questions from the UK Biobank Mental Health Questionnaire encompassing depressive symptoms were decomposed into underlying factors or ‘symptom dimensions’ via factor analysis, which were then tested for association with psychiatric diagnoses and polygenic risk scores for major depressive disorder (MDD), bipolar disorder and schizophrenia. Replication was performed among 655 self-reported non-White participants, across sexes, and among 7190 individuals with an ICD-10 code for MDD from linked inpatient or primary care records. Results Four broad symptom dimensions were identified, encompassing negative cognition, functional impairment, insomnia and atypical symptoms. These dimensions replicated across ancestries, sexes and individuals with inpatient or primary care MDD diagnoses, and were also consistent among 43 090 self-reported White participants with undiagnosed self-reported depression. Every dimension was associated with increased risk of nearly every psychiatric diagnosis and polygenic risk score. However, while certain psychiatric diagnoses were disproportionately associated with specific symptom dimensions, the three polygenic risk scores did not show the same specificity of associations. Conclusions An analysis of questionnaire data from a large community-based cohort reveals four replicable symptom dimensions of depression with distinct clinical, but not genetic, correlates.

scholarly journals Polygenic Risk Score of Longevity Predicts Longer Survival Across an Age Continuum

2020 ◽  
Author(s):  
Niccolo’ Tesi ◽  
Sven J van der Lee ◽  
Marc Hulsman ◽  
Iris E Jansen ◽  
Najada Stringa ◽  
...  
Keyword(s):  
Older Adults ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Association Studies ◽  
Risk Scores ◽  
Human Longevity ◽  
Polygenic Risk Score ◽  
Genome Wide Association Studies ◽  
Polygenic Risk ◽  
Age Related

Abstract Studying the genome of centenarians may give insights into the molecular mechanisms underlying extreme human longevity and the escape of age-related diseases. Here, we set out to construct polygenic risk scores (PRSs) for longevity and to investigate the functions of longevity-associated variants. Using a cohort of centenarians with maintained cognitive health (N = 343), a population-matched cohort of older adults from 5 cohorts (N = 2905), and summary statistics data from genome-wide association studies on parental longevity, we constructed a PRS including 330 variants that significantly discriminated between centenarians and older adults. This PRS was also associated with longer survival in an independent sample of younger individuals (p = .02), leading up to a 4-year difference in survival based on common genetic factors only. We show that this PRS was, in part, able to compensate for the deleterious effect of the APOE-ε4 allele. Using an integrative framework, we annotated the 330 variants included in this PRS by the genes they associate with. We find that they are enriched with genes associated with cellular differentiation, developmental processes, and cellular response to stress. Together, our results indicate that an extended human life span is, in part, the result of a constellation of variants each exerting small advantageous effects on aging-related biological mechanisms that maintain overall health and decrease the risk of age-related diseases.

Abstract P256: Genetic Determinants Of Blood Pressure Associate With Apparent Treatment Resistant Hypertension

Hypertension ◽  
2021 ◽  
Vol 78 (Suppl_1) ◽  
Author(s):  
Joseph H Breeyear ◽  
Megan M Shuey ◽  
Todd L Edwards ◽  
Jacklyn Hellwege
Keyword(s):  
Blood Pressure ◽  
Risk Scores ◽  
Uncontrolled Hypertension ◽  
Polygenic Risk Score ◽  
Genetic Determinants ◽  
Treatment Resistant ◽  
Polygenic Risk ◽  
Blood Pressures ◽  
The Uk ◽  
Hispanic White

Hypertension is estimated to affect more than 49.6% of US adults 20 years and older. Of those individuals with hypertension, more than ten million are classified as apparent treatment resistant hypertensive (aTRH). The attributable risk of uncontrolled hypertension was estimated to be 49% for cardiovascular disease and 62% for stroke. We developed a polygenic risk score (PRS) for systolic (SBP) and diastolic (DBP) blood pressure to examine the association between the genetic determinants of blood pressure and aTRH with the goal of identifying high risk individuals. The meta-analyzed transethnic results of Giri et al., Biobank Japan, and Liang et al. were used to generate a PRS with PRS-CS followed by p -value thresholding, and validation in the UK Biobank (n max =341,930). Associations were modeled with logistic regression adjusted for age, age-squared, BMI, sex, and ten principal components of ancestry in BioVU’s transethnic population (n max =37,978), as well as non-Hispanic Black (n max =5,026) and non-Hispanic White (n max =28,545) subsets. The SBP PRS was significantly associated with an increased aTRH risk in the non-Hispanic White subset (1.08 (1.04 - 1.12), p = 0.00037) and transethnic (1.08 (1.04 - 1.13), p = 0.00020) populations, but not the non-Hispanic Black subset. The DBP PRS was not associated with aTRH in any population. Our findings present evidence that individuals with a higher genetic predisposition towards hypertension are at higher risk of aTRH. By integrating polygenic risk scores and clinical covariates in prediction of aTRH, individuals’ therapeutic regimens may be tailored to help maintain stable blood pressures, therefore reducing their risk of comorbidities.

scholarly journals An atlas of polygenic risk score associations to highlight putative causal relationships across the human phenome

2018 ◽  
Author(s):  
Tom G. Richardson ◽  
Sean Harrison ◽  
Gibran Hemani ◽  
George Davey Smith
Keyword(s):  
Web Application ◽  
Large Scale ◽  
Complex Disease ◽  
Association Studies ◽  
Risk Scores ◽  
Polygenic Risk Score ◽  
Genome Wide Association Studies ◽  
Genetic Liability ◽  
Polygenic Risk ◽  
The Uk

AbstractThe age of large-scale genome-wide association studies (GWAS) has provided us with an unprecedented opportunity to evaluate the genetic liability of complex disease using polygenic risk scores (PRS). In this study, we have analysed 162 PRS (P<5×l0 05) derived from GWAS and 551 heritable traits from the UK Biobank study (N=334,398). Findings can be investigated using a web application (http://mrcieu.mrsoftware.org/PRS_atlas/), which we envisage will help uncover both known and novel mechanisms which contribute towards disease susceptibility.To demonstrate this, we have investigated the results from a phenome-wide evaluation of schizophrenia genetic liability. Amongst findings were inverse associations with measures of cognitive function which extensive follow-up analyses using Mendelian randomization (MR) provided evidence of a causal relationship. We have also investigated the effect of multiple risk factors on disease using mediation and multivariable MR frameworks. Our atlas provides a resource for future endeavours seeking to unravel the causal determinants of complex disease.

scholarly journals Multiplex melanoma families are enriched for polygenic risk

2020 ◽  
Vol 29 (17) ◽  
pp. 2976-2985
Author(s):  
Matthew H Law ◽  
Lauren G Aoude ◽  
David L Duffy ◽  
Georgina V Long ◽  
Peter A Johansson ◽  
...  
Keyword(s):  
Cutaneous Melanoma ◽  
Cumulative Effect ◽  
Risk Scores ◽  
Polygenic Risk Score ◽  
Single Family ◽  
Polygenic Risk ◽  
Complex Disorders ◽  
Risk Variants ◽  
High Penetrance ◽  
Genetic Risks

Abstract Cancers, including cutaneous melanoma, can cluster in families. In addition to environmental etiological factors such as ultraviolet radiation, cutaneous melanoma has a strong genetic component. Genetic risks for cutaneous melanoma range from rare, high-penetrance mutations to common, low-penetrance variants. Known high-penetrance mutations account for only about half of all densely affected cutaneous melanoma families, and the causes of familial clustering in the remainder are unknown. We hypothesize that some clustering is due to the cumulative effect of a large number of variants of individually small effect. Common, low-penetrance genetic risk variants can be combined into polygenic risk scores. We used a polygenic risk score for cutaneous melanoma to compare families without known high-penetrance mutations with unrelated melanoma cases and melanoma-free controls. Family members had significantly higher mean polygenic load for cutaneous melanoma than unrelated cases or melanoma-free healthy controls (Bonferroni-corrected t-test P = 1.5 × 10−5 and 6.3 × 10−45, respectively). Whole genome sequencing of germline DNA from 51 members of 21 families with low polygenic risk for melanoma identified a CDKN2A p.G101W mutation in a single family but no other candidate high-penetrance melanoma susceptibility genes. This work provides further evidence that melanoma, like many other common complex disorders, can arise from the joint action of multiple predisposing factors, including rare high-penetrance mutations, as well as via a combination of large numbers of alleles of small effect.

Individuals with common diseases but with a low polygenic risk score could be prioritized for rare variant screening

2020 ◽  
Author(s):  
Tianyuan Lu ◽  
Sirui Zhou ◽  
Haoyu Wu ◽  
Vincenzo Forgetta ◽  
Celia M. T. Greenwood ◽  
...  
Keyword(s):  
Rare Variant ◽  
Risk Score ◽  
Polygenic Risk Score ◽  
Polygenic Risk ◽  
Common Diseases

scholarly journals Polygenic risk scores and the prediction of common diseases

2019 ◽  
Vol 49 (1) ◽  
pp. 1-3
Author(s):  
Mika Ala-Korpela ◽  
Michael V Holmes
Keyword(s):  
Risk Scores ◽  
Polygenic Risk ◽  
Common Diseases

Polygenic risk for psychiatric disorder and singleness in patients with severe mental illness and controls

2019 ◽  
Vol 119 ◽  
pp. 60-66 ◽  
Author(s):  
Carsten Hjorthøj ◽  
Md Jamal Uddin ◽  
David Michael Hougaard ◽  
Holger J. Sørensen ◽  
Merete Nordentoft
Keyword(s):  
Mental Illness ◽  
Psychiatric Disorder ◽  
Severe Mental Illness ◽  
Polygenic Risk

scholarly journals Jumping to conclusions, general intelligence, and psychosis liability: findings from the multi-centre EU-GEI case-control study

2020 ◽  
pp. 1-11 ◽  
Author(s):  
Giada Tripoli ◽  
Diego Quattrone ◽  
Laura Ferraro ◽  
Charlotte Gayer-Anderson ◽  
Victoria Rodriguez ◽  
...  
Keyword(s):  
Cognitive Biases ◽  
Population Based ◽  
Case Control ◽  
Risk Scores ◽  
First Episode ◽  
Polygenic Risk Score ◽  
General Intelligence ◽  
Polygenic Risk ◽  
Jumping To Conclusions ◽  
Episode Psychosis

Abstract Background The ‘jumping to conclusions’ (JTC) bias is associated with both psychosis and general cognition but their relationship is unclear. In this study, we set out to clarify the relationship between the JTC bias, IQ, psychosis and polygenic liability to schizophrenia and IQ. Methods A total of 817 first episode psychosis patients and 1294 population-based controls completed assessments of general intelligence (IQ), and JTC, and provided blood or saliva samples from which we extracted DNA and computed polygenic risk scores for IQ and schizophrenia. Results The estimated proportion of the total effect of case/control differences on JTC mediated by IQ was 79%. Schizophrenia polygenic risk score was non-significantly associated with a higher number of beads drawn (B = 0.47, 95% CI −0.21 to 1.16, p = 0.17); whereas IQ PRS (B = 0.51, 95% CI 0.25–0.76, p < 0.001) significantly predicted the number of beads drawn, and was thus associated with reduced JTC bias. The JTC was more strongly associated with the higher level of psychotic-like experiences (PLEs) in controls, including after controlling for IQ (B = −1.7, 95% CI −2.8 to −0.5, p = 0.006), but did not relate to delusions in patients. Conclusions Our findings suggest that the JTC reasoning bias in psychosis might not be a specific cognitive deficit but rather a manifestation or consequence, of general cognitive impairment. Whereas, in the general population, the JTC bias is related to PLEs, independent of IQ. The work has the potential to inform interventions targeting cognitive biases in early psychosis.

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