scholarly journals Common schizophrenia alleles are enriched in mutation-intolerant genes and maintained by background selection

2016 ◽  
Author(s):  
Antonio F Pardiñas ◽  
Peter Holmans ◽  
Andrew J Pocklington ◽  
Valentina Escott-Price ◽  
Stephan Ripke ◽  
...  
Keyword(s):  
Large Scale ◽  
Genome Wide Association Study ◽  
Rare Variants ◽  
Meta Analysis ◽  
Single Gene ◽  
Poor Quality ◽  
Background Selection ◽  
Loss Of Function ◽  
Risk Variants ◽  
Genomic Studies

Schizophrenia is a debilitating psychiatric condition often associated with poor quality of life and decreased life expectancy. Lack of progress in improving treatment outcomes has been attributed to limited knowledge of the underlying biology, although large-scale genomic studies have begun to provide such insight. We report the largest single cohort genome-wide association study of schizophrenia (11,260 cases and 24,542 controls) and through meta-analysis with existing data we identify 50 novel GWAS loci. Using gene-wide association statistics we implicate an additional set of 22 novel associations that map onto a single gene. We show for the first time that the common variant association signal is highly enriched among genes that are intolerant to loss of function mutations and that variants in these genes persist in the population despite the low fecundity associated with the disorder through the process of background selection. Associations point to novel areas of biology (e.g. metabotropic GABA-B signalling and acetyl cholinesterase), reinforce those implicated in earlier GWAS studies (e.g. calcium channel function), converge with earlier rare variants studies (e.g. NRXN1, GABAergic signalling), identify novel overlaps with autism (e.g. RBFOX1, FOXP1, FOXG1), and support early controversial candidate gene hypotheses (e.g. ERBB4 implicating neuregulin signalling). We also demonstrate the involvement of six independent central nervous system functional gene sets in schizophrenia pathophysiology. These findings provide novel insights into the biology and genetic architecture of schizophrenia, highlight the importance of mutation intolerant genes and suggest a mechanism by which common risk variants are maintained in the population.

Abstract P054: Rare Variants in and Near IRS1 are Associated with Fasting Insulin in CHARGE-S Cohorts

Circulation ◽  
2013 ◽  
Vol 127 (suppl_12) ◽  
Author(s):  
Belinda K Cornes ◽  
Jennifer Brody ◽  
Alanna C Morrison ◽  
David Siscovick ◽  
James B Meigs ◽  
...  
Keyword(s):  
Large Scale ◽  
Rare Variants ◽  
Meta Analysis ◽  
Weighted Sum ◽  
Fasting Insulin ◽  
Loss Of Function ◽  
Gene Encoding ◽  
Annotation Information ◽  
Heart Study ◽  
Meta Analyses

Introduction: Common variants in the gene encoding insulin receptor substrate 1 ( IRS1 ) and nearby on 2q36.3 have been associated with levels of fasting insulin (FI). We hypothesized that a greater burden of rare variants in these regions is associated with higher FI. Methods: CHARGE-S sequenced (average coverage >60x) the IRS1 and 2q36.6 regions (totaling 185 kb) in 3,539 individuals on the SOLiD platform. FI information among non-diabetics was available in 3 studies: Framingham Heart Study ( N =811), Cardiovascular Heart Study ( N =967) and Atherosclerosis Risk in Communities Study ( N =1761). We analyzed rare variants (MAF < 1%) using a weighted sum test, similar to Madsen-Browning (powerful to detect an association if effects of casual rare variants are in the same direction), and the SKAT test (preferred method if variant effects are in opposite directions). Meta-analyses of weighted rare variants results used the inverse-variance method while SKAT results used a similar approach. For multi-variant tests, the threshold for significance was considered to be α = 0.05. Coding annotation predictions were obtained from the dbNSFP database which includes functional predictions from SIFT, MutationTaster, Polyphen-2, Phylo-P and LRT. Non-coding annotation information (protein binding regions, transcription factor binding sites, DNase hypersensitivity sites, conservation scores) was obtained from ENCODE and ORegAnno databases. From these annotations, we grouped different types of variants together (possible loss of function; possibly regulatory) in order to determine specific variants contributing most to the effect. Results: Sequencing found 4,534 variants in two regions, 86.7% of which were rare and novel, not seen in 1000 genomes or dbSNP. Approximately 20% of variants had annotation information available; of these, 34 variants were possibly damaging. We found suggestive association with FI ( p =0.03) for all rare variants in the meta-analysis of weighted-sum tests at 2q36.3 but not at IRS1 . At IRS1 (but not at 2q36.3), SKAT meta-analysis tests showed evidence for all rare variants associated with FI ( p =0.03). SKAT tests restricted to N =365 possibly damaging variants at IRS1 suggested an association with FI in coding ( p =0.06) and in non-coding ( p =0.02) variants. Conclusion: Large scale deep sequencing in the IRS1 and 2q36.3 regions found very large numbers of new, rare variants. Multi-variant tests suggest that rare variation in these regions influence FI levels, with individuals with more and rarer variants having higher FI. Further investigation is warranted to address why weighted sum and SKAT tests provide different levels of evidence for association in the two regions. Also, conditional analyses will test whether new rare variants at IRS1 or 2q36 explain observed GWAS associations.

scholarly journals Trans-ancestry genome-wide analysis of atrial fibrillation provides new insights into disease biology and enables polygenic prediction of cardioembolic risk

2021 ◽  
Author(s):  
Kazuo Miyazawa ◽  
Kaoru Ito ◽  
Zhaonan Zou ◽  
Hiroshi Matsunaga ◽  
Satoshi Koyama ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Rare Variants ◽  
Meta Analysis ◽  
Polygenic Risk Score ◽  
Disease Biology ◽  
Genome Wide ◽  
Increased Risk ◽  
Causal Genes

To understand the genetic underpinnings of atrial fibrillation (AF) in the Japanese population, we performed a large-scale genome-wide association study comprising 9,826 cases of AF among 150,272 individuals and identified five new susceptibility loci, including East Asian-specific rare variants. A trans-ancestry meta-analysis of >1 million individuals, including 77,690 cases, identified 35 novel loci. Leveraging gene expression and epigenomic datasets to prioritize putative causal genes and their transcription factors revealed the involvement of IL6R gene and transcription factor ERG besides the known ones. Further, we constructed a polygenic risk score (PRS) for AF, using the trans-ancestry meta-analysis. PRS was associated with an increased risk of long-term cardiovascular and stroke mortality, and segregated individuals with cardioembolic stroke in undiagnosed AF patients. Our results provide novel biological and clinical insights into AF genetics and suggest their potential for clinical applications.

scholarly journals Examining the effect of mitochondrial DNA variants on blood pressure in two Finnish cohorts

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jaakko Laaksonen ◽  
Pashupati P. Mishra ◽  
Ilkka Seppälä ◽  
Leo-Pekka Lyytikäinen ◽  
Emma Raitoharju ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Mitochondrial Dna ◽  
Genome Wide Association Study ◽  
Rare Variants ◽  
Meta Analysis ◽  
Noncommunicable Diseases ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Genome Wide ◽  
Mitochondrial Dna Variants

AbstractHigh blood pressure (BP) is a major risk factor for many noncommunicable diseases. The effect of mitochondrial DNA single-nucleotide polymorphisms (mtSNPs) on BP is less known than that of nuclear SNPs. We investigated the mitochondrial genetic determinants of systolic, diastolic, and mean arterial BP. MtSNPs were determined from peripheral blood by sequencing or with genome-wide association study SNP arrays in two independent Finnish cohorts, the Young Finns Study and the Finnish Cardiovascular Study, respectively. In total, over 4200 individuals were included. The effects of individual common mtSNPs, with an additional focus on sex-specificity, and aggregates of rare mtSNPs grouped by mitochondrial genes were evaluated by meta-analysis of linear regression and a sequence kernel association test, respectively. We accounted for the predicted pathogenicity of the rare variants within protein-encoding and the tRNA regions. In the meta-analysis of 87 common mtSNPs, we did not observe significant associations with any of the BP traits. Sex-specific and rare-variant analyses did not pinpoint any significant associations either. Our results are in agreement with several previous studies suggesting that mtDNA variation does not have a significant role in the regulation of BP. Future studies might need to reconsider the mechanisms thought to link mtDNA with hypertension.

scholarly journals Rare variants in KDR, encoding VEGF Receptor 2, are associated with tetralogy of Fallot

2021 ◽  
Author(s):  
Doris Škorić-Milosavljević ◽  
Najim Lahrouchi ◽  
Fernanda M. Bosada ◽  
Gregor Dombrowsky ◽  
Simon G. Williams ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Tetralogy Of Fallot ◽  
Large Scale ◽  
Rare Variants ◽  
Growth Factor Receptor ◽  
Vegf Receptor ◽  
Loss Of Function ◽  
Endothelial Growth Factor

Abstract Purpose Rare genetic variants in KDR, encoding the vascular endothelial growth factor receptor 2 (VEGFR2), have been reported in patients with tetralogy of Fallot (TOF). However, their role in disease causality and pathogenesis remains unclear. Methods We conducted exome sequencing in a familial case of TOF and large-scale genetic studies, including burden testing, in >1,500 patients with TOF. We studied gene-targeted mice and conducted cell-based assays to explore the role of KDR genetic variation in the etiology of TOF. Results Exome sequencing in a family with two siblings affected by TOF revealed biallelic missense variants in KDR. Studies in knock-in mice and in HEK 293T cells identified embryonic lethality for one variant when occurring in the homozygous state, and a significantly reduced VEGFR2 phosphorylation for both variants. Rare variant burden analysis conducted in a set of 1,569 patients of European descent with TOF identified a 46-fold enrichment of protein-truncating variants (PTVs) in TOF cases compared to controls (P = 7 × 10-11). Conclusion Rare KDR variants, in particular PTVs, strongly associate with TOF, likely in the setting of different inheritance patterns. Supported by genetic and in vivo and in vitro functional analysis, we propose loss-of-function of VEGFR2 as one of the mechanisms involved in the pathogenesis of TOF.

scholarly journals Using a Two-Sample Mendelian Randomization Method in Assessing the Causal Relationships Between Human Blood Metabolites and Heart Failure

2021 ◽  
Vol 8 ◽  
Author(s):  
Zixian Wang ◽  
Shiyu Chen ◽  
Qian Zhu ◽  
Yonglin Wu ◽  
Guifeng Xu ◽  
...  
Keyword(s):  
Heart Failure ◽  
Human Blood ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Mendelian Randomization ◽  
Causal Effect ◽  
Meta Analysis ◽  
Sensitivity Analyses ◽  
Blood Metabolites ◽  
Causal Relationships

Background: Heart failure (HF) is the main cause of morbidity and mortality worldwide, and metabolic dysfunction is an important factor related to HF pathogenesis and development. However, the causal effect of blood metabolites on HF remains unclear.Objectives: Our chief aim is to investigate the causal relationships between human blood metabolites and HF risk.Methods: We used an unbiased two-sample Mendelian randomization (MR) approach to assess the causal relationships between 486 human blood metabolites and HF risk. Exposure information was obtained from Sample 1, which is the largest metabolome-based genome-wide association study (mGWAS) data containing 7,824 Europeans. Outcome information was obtained from Sample 2, which is based on the results of a large-scale GWAS meta-analysis of HF and contains 47,309 cases and 930,014 controls of Europeans. The inverse variance weighted (IVW) model was used as the primary two-sample MR analysis method and followed the sensitivity analyses, including heterogeneity test, horizontal pleiotropy test, and leave-one-out analysis.Results: We observed that 11 known metabolites were potentially related to the risk of HF after using the IVW method (P &lt; 0.05). After adding another four MR models and performing sensitivity analyses, we found a 1-SD increase in the xenobiotics 4-vinylphenol sulfate was associated with ~22% higher risk of HF (OR [95%CI], 1.22 [1.07–1.38]).Conclusions: We revealed that the 4-vinylphenol sulfate may nominally increase the risk of HF by 22% after using a two-sample MR approach. Our findings may provide novel insights into the pathogenesis underlying HF and novel strategies for HF prevention.

scholarly journals Exome-Sequence Analyses of Four Multi-Incident Multiple Sclerosis Families

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 988
Author(s):  
Tobias Zrzavy ◽  
Fritz Leutmezer ◽  
Wolfgang Kristoferitsch ◽  
Barbara Kornek ◽  
Christine Schneider ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Genome Wide Association Study ◽  
Rare Variants ◽  
Demyelinating Disease ◽  
Phenotypic Variability ◽  
Convincing Evidence ◽  
Risk Variants ◽  
Unbiased Manner ◽  
The Central Nervous System ◽  
Reduced Penetrance

Multiple sclerosis (MS) is an inflammatory demyelinating disease of the Central Nervous System (CNS). Currently, it is estimated that 30–40% of the phenotypic variability of MS can be explained by genetic factors. However, low susceptibility variants identified through Genome Wide Association Study (GWAS) were calculated to explain about 50% of the heritability. Whether familial high-risk variants also contribute to heritability is a subject of controversy. In the last few years, several familial variants have been nominated, but none of them have been unequivocally confirmed. One reason for this may be that genetic heterogeneity and reduced penetrance are hindering detection. Sequencing a large number of MS families is needed to answer this question. In this study, we performed whole exome sequencing in four multi-case families, of which at least three affected individuals per family were analyzed. We identified a total of 138 rare variants segregating with disease in each of the families. Although no single variant showed convincing evidence for disease causation, some genes seemed particularly interesting based on their biological function. The main aim of this study was to provide a complete list of all rare segregating variants to provide the possibility for other researchers to cross-check familial candidate genes in an unbiased manner.

scholarly journals Population-scale analysis of common and rare genetic variation associated with hearing loss in adults

2021 ◽  
Author(s):  
Kavita Praveen ◽  
Lee Dobbyn ◽  
Lauren Gurski ◽  
Ariane H. Ayer ◽  
Jeffrey Staples ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Exome Sequencing ◽  
Large Scale ◽  
Meta Analysis ◽  
Adult Population ◽  
Loss Of Function ◽  
Common Coding ◽  
A Genome ◽  
Increased Risk ◽  
Coding Variants

ABSTRACTUnderstanding the genetic underpinnings of disabling hearing loss, which affects ∼466 million people worldwide, can provide avenues for new therapeutic target development. We performed a genome-wide association meta-analysis of hearing loss with 125,749 cases and 469,497 controls across five cohorts, including UK Biobank, Geisinger DiscovEHR, the Malmö Diet and Cancer Study, Mount Sinai’s BioMe Personalized Medicine Cohort, and FinnGen. We identified 53 loci affecting hearing loss risk, 15 of which are novel, including common coding variants in COL9A3 and TMPRSS3. Through exome-sequencing of 108,415 cases and 329,581 controls from the same cohorts, we identified hearing loss associations with burden of rare coding variants in FSCN2 (odds ratio [OR] = 1.14, P = 1.9 × 10−15) and burden of predicted loss-of-function variants in KLHDC7B (OR = 2.14, P = 5.2 × 10−30). We also observed single-variant and gene-burden associations with 11 genes known to cause Mendelian forms of hearing loss, including an increased risk in heterozygous carriers of mutations in the autosomal recessive hearing loss genes GJB2 (Gly12fs; OR = 1.21, P = 4.2 × 10−11) and SLC26A5 (gene burden; OR = 1.96, P = 2.8 × 10−17). Our results suggest that loss of KLHDC7B function increases risk for hearing loss, and show that Mendelian hearing loss genes contribute to the burden of hearing loss in the adult population, suggesting a shared etiology between common and rare forms of hearing loss. This work illustrates the potential of large-scale exome sequencing to elucidate the genetic architecture of common traits in which risk is modulated by both common and rare variation.

scholarly journals Exome Array Analysis of Early-Onset Ischemic Stroke

Stroke ◽  
2020 ◽  
Vol 51 (11) ◽  
pp. 3356-3360
Author(s):  
Thomas Jaworek ◽  
Kathleen A. Ryan ◽  
Brady J. Gaynor ◽  
Patrick F. McArdle ◽  
Oscar C. Stine ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Early Onset ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Population Level ◽  
Small Vessel ◽  
Stroke Treatment ◽  
Functional Variants ◽  
Individual Snps

Background and Purpose: The genetic contribution to ischemic stroke may include rare- or low-frequency variants of high-penetrance and large-effect sizes. Analyses focusing on early-onset disease, an extreme-phenotype, and on the exome, the protein-coding portion of genes, may increase the likelihood of identifying such rare functional variants. To evaluate this hypothesis, we implemented a 2-stage discovery and replication design, and then addressed whether the identified variants also associated with older-onset disease. Methods: Discovery was performed in UMD-GEOS Study (University of Maryland-Genetics of Early-Onset Stroke), a biracial population-based study of first-ever ischemic stroke cases 15 to 49 years of age (n=723) and nonstroke controls (n=726). All participants had prior GWAS (Genome Wide Association Study) and underwent Illumina exome-chip genotyping. Logistic-regression was performed to test single-variant associations with all-ischemic stroke and TOAST (Trial of ORG 10172 in Acute Stroke Treatment) subtypes in Whites and Blacks. Population level results were combined using meta-analysis. Gene-based aggregation testing and meta-analysis were performed using seqMeta. Covariates included age and gender, and principal-components for population structure. Pathway analyses were performed across all nominally associated genes for each stroke outcome. Replication was attempted through lookups in a previously reported meta-analysis of early-onset stroke and a large-scale stroke genetics study consisting of primarily older-onset cases. Results: Gene burden tests identified a significant association with NAT10 in small-vessel stroke ( P =3.79×10 − 6 ). Pathway analysis of the top 517 genes ( P <0.05) from the gene-based analysis of small-vessel stroke identified several signaling and metabolism-related pathways related to neurotransmitter, neurodevelopmental notch-signaling, and lipid/glucose metabolism. While no individual SNPs reached chip-wide significance ( P <2.05×10 −7 ), several were near, including an intronic variant in LEXM (rs7549251; P =4.08×10 − 7 ) and an exonic variant in TRAPPC11 (rs67383011; P =5.19×10 − 6 ). Conclusions: Exome-based analysis in the setting of early-onset stroke is a promising strategy for identifying novel genetic risk variants, loci, and pathways.

scholarly journals A Further Comment on ‘Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets’ by Lam et al.

2018 ◽  
Vol 21 (6) ◽  
pp. 538-545 ◽  
Author(s):  
W. D. Hill
Keyword(s):  
Cognitive Ability ◽  
Drug Targets ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Tissue Specific ◽  
Nootropic Drug ◽  
Genome Wide ◽  
Quality Control Metrics

Lam et al. (2018) respond to a commentary of their paper entitled ‘Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets’ Lam et al. (2017). While Lam et al. (2018) have now provided the recommended quality control metrics for their paper, problems remain. Specifically, Lam et al. (2018) do not dispute that the results of their multi-trait analysis of genome-wide association study (MTAG) analysis has produced a phenotype with a genetic correlation of one with three measures of education, but do claim the associations found are specific to the trait of cognitive ability. In this brief paper, it is empirically demonstrated that the phenotype derived by Lam et al. (2017) is more genetically similar to education than cognitive ability. In addition, it is shown that of the genome-wide significant loci identified by Lam et al. (2017) are loci that are associated with education rather than with cognitive ability.

scholarly journals The Potential Role of Genomic Medicine in the Therapeutic Management of Rheumatoid Arthritis

2019 ◽  
Vol 8 (6) ◽  
pp. 826 ◽  
Author(s):  
Marialbert Acosta-Herrera ◽  
David González-Serna ◽  
Javier Martín
Keyword(s):  
Rheumatoid Arthritis ◽  
Large Scale ◽  
Rare Variants ◽  
Drug Repositioning ◽  
Genomic Medicine ◽  
Response To Therapy ◽  
Response To Treatment ◽  
Genomic Studies ◽  
The Right

During the last decade, important advances have occurred regarding understanding of the pathogenesis and treatment of rheumatoid arthritis (RA). Nevertheless, response to treatment is not universal, and choosing among different therapies is currently based on a trial and error approach. The specific patient’s genetic background influences the response to therapy for many drugs: In this sense, genomic studies on RA have produced promising insights that could help us find an effective therapy for each patient. On the other hand, despite the great knowledge generated regarding the genetics of RA, most of the investigations performed to date have focused on identifying common variants associated with RA, which cannot explain the complete heritability of the disease. In this regard, rare variants could also contribute to this missing heritability as well as act as biomarkers that help in choosing the right therapy. In the present article, different aspects of genetics in the pathogenesis and treatment of RA are reviewed, from large-scale genomic studies to specific rare variant analyses. We also discuss the shared genetic architecture existing among autoimmune diseases and its implications for RA therapy, such as drug repositioning.

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