Role of Common Genetic Variants for Drug-Resistance to Specific Anti-Seizure Medications

Objective: Resistance to anti-seizure medications (ASMs) presents a significant hurdle in the treatment of people with epilepsy. Genetic markers for resistance to individual ASMs could support clinicians to make better-informed choices for their patients. In this study, we aimed to elucidate whether the response to individual ASMs was associated with common genetic variation.Methods: A cohort of 3,649 individuals of European descent with epilepsy was deeply phenotyped and underwent single nucleotide polymorphism (SNP)-genotyping. We conducted genome-wide association analyses (GWASs) on responders to specific ASMs or groups of functionally related ASMs, using non-responders as controls. We performed a polygenic risk score (PRS) analyses based on risk variants for epilepsy and neuropsychiatric disorders and ASM resistance itself to delineate the polygenic burden of ASM-specific drug resistance.Results: We identified several potential regions of interest but did not detect genome-wide significant loci for ASM-specific response. We did not find polygenic risk for epilepsy, neuropsychiatric disorders, and drug-resistance associated with drug response to specific ASMs or mechanistically related groups of ASMs.Significance: This study could not ascertain the predictive value of common genetic variants for ASM responder status. The identified suggestive loci will need replication in future studies of a larger scale.

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Performance of polygenic risk scores for cancer prediction in an academic biobank.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.1528 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 1528-1528

Author(s):

Heena Desai ◽

Anh Le ◽

Ryan Hausler ◽

Shefali Verma ◽

Anurag Verma ◽

...

Keyword(s):

Risk Score ◽

Genetic Variants ◽

Association Studies ◽

Risk Scores ◽

Polygenic Risk Score ◽

Genome Wide Association Studies ◽

Polygenic Risk ◽

European Americans ◽

Genome Wide ◽

Common Genetic Variants

1528 Background: The discovery of rare genetic variants associated with cancer have a tremendous impact on reducing cancer morbidity and mortality when identified; however, rare variants are found in less than 5% of cancer patients. Genome wide association studies (GWAS) have identified hundreds of common genetic variants significantly associated with a number of cancers, but the clinical utility of individual variants or a polygenic risk score (PRS) derived from multiple variants is still unclear. Methods: We tested the ability of polygenic risk score (PRS) models developed from genome-wide significant variants to differentiate cases versus controls in the Penn Medicine Biobank. Cases for 15 different cancers and cancer-free controls were identified using electronic health record billing codes for 11,524 European American and 5,994 African American individuals from the Penn Medicine Biobank. Results: The discriminatory ability of the 15 PRS models to distinguish their respective cancer cases versus controls ranged from 0.68-0.79 in European Americans and 0.74-0.93 in African Americans. Seven of the 15 cancer PRS trended towards an association with their cancer at a p<0.05 (Table), and PRS for prostate, thyroid and melanoma were significantly associated with their cancers at a bonferroni corrected p<0.003 with OR 1.3-1.6 in European Americans. Conclusions: Our data demonstrate that common variants with significant associations from GWAS studies can distinguish cancer cases versus controls for some cancers in an unselected biobank population. Given the small effects, future studies are needed to determine how best to incorporate PRS with other risk factors in the precision prediction of cancer risk. [Table: see text]

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Migraine, Human Genetics and a Passion for Science

Twin Research and Human Genetics ◽

10.1017/thg.2020.22 ◽

2020 ◽

Vol 23 (2) ◽

pp. 105-106

Author(s):

Dale R. Nyholt

Keyword(s):

Genetic Architecture ◽

Latent Class ◽

Human Genetics ◽

Polygenic Risk Score ◽

Association Analyses ◽

Polygenic Risk ◽

The Past ◽

Risk Variants ◽

Genome Wide ◽

Wide Range

AbstractThis note reflects on my collaborations with Nick Martin and the GenEpi group over the past 20 years. Over the past two decades, our work together has focused on gene mapping and understanding the genetic architecture of a wide range of traits with particular foci on migraine and common baldness. Our migraine research has included latent class and twin analyses cumulating in genome-wide association analyses which had identified 44 (34 new) risk variants for migraine. Leveraging these results through polygenic risk score analyses identified subgroups of patients likely to respond to triptans (an acute migraine drug), providing the first step toward precision medicine in migraine [Kogelman et al. (2019) Neurology Genetics, 5, e364].

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Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry

Molecular Psychiatry ◽

10.1038/s41380-019-0517-y ◽

2019 ◽

Vol 25 (10) ◽

pp. 2455-2467 ◽

Cited By ~ 12

Author(s):

Tim B. Bigdeli ◽

◽

Giulio Genovese ◽

Penelope Georgakopoulos ◽

Jacquelyn L. Meyers ◽

...

Keyword(s):

Genetic Variants ◽

Association Studies ◽

Large Fraction ◽

African Ancestry ◽

Common Variant ◽

Human Populations ◽

Polygenic Risk Score ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Common Genetic Variants

Abstract Schizophrenia is a common, chronic and debilitating neuropsychiatric syndrome affecting tens of millions of individuals worldwide. While rare genetic variants play a role in the etiology of schizophrenia, most of the currently explained liability is within common variation, suggesting that variation predating the human diaspora out of Africa harbors a large fraction of the common variant attributable heritability. However, common variant association studies in schizophrenia have concentrated mainly on cohorts of European descent. We describe genome-wide association studies of 6152 cases and 3918 controls of admixed African ancestry, and of 1234 cases and 3090 controls of Latino ancestry, representing the largest such study in these populations to date. Combining results from the samples with African ancestry with summary statistics from the Psychiatric Genomics Consortium (PGC) study of schizophrenia yielded seven newly genome-wide significant loci, and we identified an additional eight loci by incorporating the results from samples with Latino ancestry. Leveraging population differences in patterns of linkage disequilibrium, we achieve improved fine-mapping resolution at 22 previously reported and 4 newly significant loci. Polygenic risk score profiling revealed improved prediction based on trans-ancestry meta-analysis results for admixed African (Nagelkerke’s R2 = 0.032; liability R2 = 0.017; P < 10−52), Latino (Nagelkerke’s R2 = 0.089; liability R2 = 0.021; P < 10−58), and European individuals (Nagelkerke’s R2 = 0.089; liability R2 = 0.037; P < 10−113), further highlighting the advantages of incorporating data from diverse human populations.

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A polygenic risk score for multiple myeloma risk prediction

European Journal of Human Genetics ◽

10.1038/s41431-021-00986-8 ◽

2021 ◽

Author(s):

Federico Canzian ◽

Chiara Piredda ◽

Angelica Macauda ◽

Daria Zawirska ◽

Niels Frost Andersen ◽

...

Keyword(s):

Multiple Myeloma ◽

Risk Score ◽

Association Studies ◽

Polygenic Risk Score ◽

Genome Wide Association Studies ◽

Polygenic Risk ◽

Epidemiologic Evidence ◽

Risk Variants ◽

Genome Wide ◽

Weighted Score

AbstractThere is overwhelming epidemiologic evidence that the risk of multiple myeloma (MM) has a solid genetic background. Genome-wide association studies (GWAS) have identified 23 risk loci that contribute to the genetic susceptibility of MM, but have low individual penetrance. Combining the SNPs in a polygenic risk score (PRS) is a possible approach to improve their usefulness. Using 2361 MM cases and 1415 controls from the International Multiple Myeloma rESEarch (IMMEnSE) consortium, we computed a weighted and an unweighted PRS. We observed associations with MM risk with OR = 3.44, 95% CI 2.53–4.69, p = 3.55 × 10−15 for the highest vs. lowest quintile of the weighted score, and OR = 3.18, 95% CI 2.1 = 34–4.33, p = 1.62 × 10−13 for the highest vs. lowest quintile of the unweighted score. We found a convincing association of a PRS generated with 23 SNPs and risk of MM. Our work provides additional validation of previously discovered MM risk variants and of their combination into a PRS, which is a first step towards the use of genetics for risk stratification in the general population.

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Abstract 16685: Shared Genetic Pathways Contribute to Risk of Hypertrophic and Dilated Cardiomyopathies With Opposite Directions of Effect

Circulation ◽

10.1161/circ.142.suppl_3.16685 ◽

2020 ◽

Vol 142 (Suppl_3) ◽

Author(s):

Rafik Tadros ◽

Catherine Francis ◽

Xiao Xu ◽

Alexa M Vermeer ◽

Andrew R Harper ◽

...

Keyword(s):

Risk Score ◽

Genetic Variants ◽

Rare Variants ◽

Genetic Correlations ◽

Left Ventricular ◽

Polygenic Risk Score ◽

Polygenic Risk ◽

Clinical Events ◽

Mutation Carriers ◽

Common Genetic Variants

Introduction: Hypertrophic (HCM) and dilated (DCM) cardiomyopathies are leading causes of sudden death and heart failure requiring transplantation in young individuals. While some cases have a monogenic underlying cause, the majority remain unexplained. Objective: To better understand the contribution of common genetic variants in susceptibility and severity of cardiomyopathy. Methods: We conducted three genome-wide association studies (GWAS) and multi-trait analyses in European-ancestry individuals, including a HCM (1,733 cases) and DCM meta-analyses (5,521 cases), and a GWAS of 9 left ventricular (LV) traits in 19,260 healthy participants from the UK Biobank that underwent cardiac magnetic resonance imaging. We investigated genetic correlations between LV traits, HCM and DCM using LD score regression. We used two-sample mendelian randomization (MR) to assess the causal relationship of increased LV contractility with HCM risk. Lastly, we derived a polygenic risk score and assessed whether it modulates maximal LV wall thickness (maxLVWT) and clinical events in 368 sarcomeric mutation carriers, using linear and Cox mixed effects models, respectively. Results: We identified 16 genetic loci (15 novel) associated with HCM, 13 loci (7 novel) associated with DCM, and 23 loci associated with LV traits. We showed strong genetic correlations between LV volumes and contractility traits in the general population and cardiomyopathies, with opposing effects in HCM and DCM. Using MR, we demonstrated a causal association linking increased LV contractility with HCM risk and estimated that each unit (1%) increase in LV ejection fraction increases the risk of HCM by 37% (95% CI 10%-69%, P=0.004). Lastly, a polygenic risk score (PRS HCM ) derived from the HCM GWAS was associated with maxLVWT (P=0.0001) and clinical events (P=0.009) in carriers of HCM-causing rare variants. Conclusion: Our findings highlight the contribution of common genetic variants in susceptibility for HCM and DCM, and in severity in sarcomeric mutation carriers. Our data also point to increased LV contractility as an important mechanism of HCM independently of sarcomere activating rare variants, and highlight the potential clinical relevance of PRS for risk stratification in HCM.

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Polygenic risk for schizophrenia is associated with social cognition across development

10.1101/034512 ◽

2015 ◽

Author(s):

Laura Germine ◽

Elise B Robinson ◽

Jordan W Smoller ◽

Monica E Calkins ◽

Tyler M Moore ◽

...

Keyword(s):

Social Cognition ◽

Genetic Risk ◽

Neurocognitive Performance ◽

Verbal Reasoning ◽

Emotion Identification ◽

Polygenic Risk ◽

Risk Variants ◽

Genome Wide ◽

Common Genetic Variants ◽

The Relationship

Breakthroughs in genomics have begun to unravel the genetic architecture of schizophrenia risk, providing methods for quantifying schizophrenia polygenic risk based on common genetic variants. Our objective in the current study was to understand the relationship between schizophrenia genetic risk variants and neurocognitive development in healthy individuals. We first used combined genomic and neurocognitive data from the Philadelphia Neurodevelopmental Cohort (PNC; 4303 participants ages 8 - 21 years) to screen 26 neurocognitive phenotypes for their association with schizophrenia polygenic risk. Schizophrenia polygenic risk was estimated for each participant based on summary statistics from the most recent schizophrenia genome-wide association analysis (Psychiatric Genomics Consortium 2014). After correction for multiple comparisons, greater schizophrenia polygenic risk was significantly associated with reduced speed of emotion identification and verbal reasoning. These associations were significant by age 9 and there was no evidence of interaction between schizophrenia polygenic risk and age on neurocognitive performance. We then looked at the association between schizophrenia polygenic risk and emotion identification speed in the Harvard / MGH Brain Genomics Superstruct Project sample (GSP; 695 participants age 18-35 years), where we replicated the association between schizophrenia polygenic risk and emotion identification speed. These analyses provide evidence for a replicable association between polygenic risk for schizophrenia and specific aspects of neurocognitive performance. Our findings indicate that individual differences in genetic risk for schizophrenia are linked with the development of social cognition and potentially verbal reasoning, and that these associations emerge relatively early in development.

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Genome-wide Association Study of Pediatric Obsessive-Compulsive Traits: Shared Genetic Risk between Traits and Disorder

10.1101/858241 ◽

2019 ◽

Author(s):

Christie L. Burton ◽

Mathieu Lemire ◽

Bowei Xiao ◽

Elizabeth C. Corfield ◽

Lauren Erdman ◽

...

Keyword(s):

Genetic Variants ◽

Genetic Risk ◽

Meta Analysis ◽

Case Control ◽

Genome Wide Association ◽

Polygenic Risk Score ◽

Obsessive Compulsive ◽

Polygenic Risk ◽

Genome Wide ◽

Shared Genetic

AbstractObjectiveTo identify genetic variants associated with obsessive-compulsive (OC) traits and test for sharing of genetic risks between OC traits and obsessive-compulsive disorder (OCD).MethodsWe conducted a genome-wide association analysis of OC traits using the Toronto Obsessive-Compulsive Scale (TOCS) in 5018 unrelated Caucasian children and adolescents from the community (Spit for Science sample). We tested the hypothesis that genetic variants associated with OC traits from the community would be associated with clinical OCD using a meta-analysis of three OCD case-controls samples (cases=3384, controls=8363). Shared genetic risk was examined between OC traits and OCD in the respective samples using polygenic risk score and genetic correlation analyses.ResultsA locus tagged by rs7856850 in an intron of PTPRD (protein tyrosine phosphatase δ) was significantly associated with OC traits at the genome-wide significance level (p=2.48×10−8). The rs7856850 locus was also associated with OCD in a meta-analysis of three independent OCD case/control genome-wide datasets (p=0.0069). Polygenic risk scores derived from OC traits were significantly associated with OCD in a sample of childhood-onset OCD and vice versa (p’s<0.01). OC traits were highly but not significantly genetically correlated with OCD (rg=0.83, p=0.07).ConclusionsWe report the first validated genome-wide significant variant for OC traits. OC traits measured in the community sample shared genetic risk with OCD case/control status. Our results demonstrate the importance of the type of measure used to measure traits as well as the feasibility and power of using trait-based approaches in community samples for genetic discovery.

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Polygenic Risk Score of Sporadic late Onset Alzheimer Disease Reveals a Shared Architecture with the Familial and Early Onset Forms

10.1101/165209 ◽

2017 ◽

Cited By ~ 1

Author(s):

Jorge L Del-Aguila ◽

Benjamin Saef ◽

Kathleen Black ◽

Maria Victoria Fernandez ◽

John Budde ◽

...

Keyword(s):

Early Onset ◽

Genetic Architecture ◽

Late Onset ◽

Age At Onset ◽

Risk Scores ◽

Polygenic Risk Score ◽

Polygenic Risk ◽

Risk Variants ◽

Genome Wide ◽

Load Risk

AbstractObjective:To determine whether the genetic architecture of sporadic late-onset Alzheimer’s Disease (sLOAD) has an effect on familial late-onset AD (fLOAD), sporadic early-onset (sEOAD) and autosomal dominant early-onset (eADAD).Methods:Polygenic risk scores (PRS) were constructed using previously identified 21 genome-wide significant loci for LOAD risk.Results:We found that there is an overlap in the genetic architecture among sEOAD, fLOAD, and sLOAD. sEOAD showed the highest odds for the PRS (OR=2.27; p=1.29×10-7), followed by fLOAD (OR=1.75; p=1.12×10-7) and sLOAD (OR=1.40; p=1.21×10-3). PRS is associated with cerebrospinal fluid ptau181-Aβ42on eADAD.Conclusion:Our analysis confirms that the genetic factors identified for sLOAD also modulate risk in fLOAD and sEOAD cohorts. Furthermore, our results suggest that the burden of these risk variants is associated with familial clustering and earlier-onset of AD. Although these variants are not associated with risk in the eADAD, they may be modulating age at onset.

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