Disease Genetics Consortium Research Articles

Causal effect of Lipoprotein-associated phospholipase A2 activity on coronary artery disease and myocardial Infarction: A Two-Sample Mendelian Randomization study

BackgroundLipoprotein-associated phospholipase A2 (Lp-PLA2) activity has been reported to be associated with coronary artery disease (CAD) and myocardial infarction (MI). However, whether Lp-PLA2 is a causal risk factor for CAD and MI remains unclear. Herein, we performed a two-sample mendelian randomization (MR) study to assess the causal effect of Lp-PLA2 activity on CAD and MI. MethodsWe selected 7 single-nucleotide polymorphisms (SNPs) associated with Lp-PLA2 activity as instrumental variables based on the data from Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium with 13,664 European individuals. Summary data about CAD and MI were obtained from Coronary Artery Disease Genome-wide Replication and Meta-analysis plus the Coronary Artery Disease Genetics (CARDIOGRAMPLUSC4D) consortium with 60,801 CAD cases and 43,676 MI cases (mostly European). The inverse-variance weighted method was applied to assess the causal associations of Lp-PLA2 activity with CAD and MI in the main analysis. ResultsThe main inverse-variance weighted (IVW) MR analysis showed that 1-SD increment in genetically determined LP-PLA2 activity was associated with increased risks of CAD (odds ratio, 5.93; 95% CI, 2.91–12.07; p value = 9.43 × 10-7) and MI (odds ratio, 4.71; 95% CI, 2.49–8.90; p value = 1.86 × 10-6). MR-Egger regression showed no evidence of pleiotropic bias. The causal associations were consistent in sensitivity analyses with multiple MR methods, in which showed Lp-PLA2 activity was causally associated with an increased risk of CAD and MI. ConclusionsIn this two-sample MR study, high Lp-PLA2 activity was a causal risk factor for CAD and MI, indicating that Lp-PLA2 activity may be a promising intervention target in reducing the risk of CAD and MI.

Disentangling the association between kidney function and atrial fibrillation: a bidirectional Mendelian randomization study

Abstract Background Observational studies suggest that kidney function and atrial fibrillation (AF) are bidirectionally associated. Whether this bidirectional association is causal remains unclear. Purpose To investigate the causality of the bidirectional association between kidney function and AF. Methods Genetic variants associated with different measures of kidney function including estimated glomerular filtration rate (eGFR) based on creatinine (eGFRcreat), blood urea nitrogen (BUN), chronic kidney disease (CKD, eGFR <60ml/min/1.73m2), eGFR based on cystatin (eGFRcys), urine albumin-to-creatinine ratio (UACR) and microalbuminuria (MA, UACR >30mg/g) were retrieved from multiple Genome-Wide Association Studies (GWAS). These GWAS were all part of the Chronic Kidney Disease Genetics (CKDGen) Consortium (n=24,063–1,040,070). Genetic variants associated with AF were retrieved from a GWAS on AF (n=1,030,836). We used two-sample MR analyses to assess the potential causality of the bidirectional association between kidney function and AF. Results MR analyses supported a causal effect of genetically predicted BUN, CKD and MA on AF risk (for BUN: n=18 SNPs, outlier corrected odds ratio (OR): 2.05, per 1 unit increase of BUN (mg/dL), 95% CI: 1.30–3.25, p-value = 2.13E-03. For CKD: n=9 SNPs, outlier corrected OR: 1.10, 95% CI: 1.04–1.17, p-value = 1.97E-03. For MA: n=5 SNPs, outlier corrected OR: 1.26, 95% CI: 1.10–1.46, p-value = 1.38E-03). MR analyses also supported a causal effect of genetically predicted AF on eGFRcreat (n=97 SNPs, outlier corrected OR: 0.998, per 1 unit increase of log transformed eGFRcreat (ml/min/1.73m2), 95% CI: 0.997–0.999, p-value = 6.78E-03), CKD risk (n=107 SNPs, outlier corrected OR: 1.06, 95% CI: 1.03–1.09, p-value = 2.97E-04) and MA risk (n=83 SNPs, outlier corrected OR: 1.07, 95% CI: 1.04–1.09, p-value = 2.49E-08). A suggestive causal effect of genetically predicted AF on eGFRcys was found (n=103 SNPs, outlier corrected OR: 0.993, per 1 unit increase of log transformed eGFRcys (ml/min/1.73m2), 95% CI: 0.986–0.999, p-value = 4.60E-02). MR analyses did not support a significant causal effect of the other kidney function measures on AF risk and vice versa. Moreover, sensitivity analyses, including weighted median estimator (WME), MR-Egger and the MR pleiotropy residual sum and outlier test (MR-PRESSO) indicated that these findings were robust. Furthermore, the associations did not change when genetic variants associated with coronary artery disease and heart failure were excluded. Conclusions MR analyses supported a bidirectional causal association between kidney function and AF. Our findings carry the potential for identification of important therapeutic targets for both conditions with implications for secondary prevention. Funding Acknowledgement Type of funding sources: Public Institution(s). Main funding source(s): Erasmus Medical Center and Erasmus University, Rotterdam Forest plot with the MR effect estimatesBidirectional MR: Kidney function and AF

Genetically determined risk of mood swings and cardiometabolic diseases: mendelian randomization study

Abstract Background Mood swings is believed to associated with increased risk of Cardiometabolic Diseases (CMD). However, the roles of mood swings on CMD are controversial because of the bias of reverse causation and/or confounding in epidemiological studies. Hence, we use a two-sample MR approach to identify the causal association between genetically determined mood swings and CMD. Methods We obtained 33 independent single-nucleotide polymorphisms (SNPs) with genome-wide significant (P<5×10–8) associated with mood swings as instrumental variable in UK Biobank. Summary data of outcomes were extracted from the Coronary Artery Disease Genome-wide Replication and Meta-analysis plus the Coronary Artery Disease Genetics consortium, the Diabetes Genetics Replication and Meta-analysis consortium, the CKDGen consortium, and the International Stroke Genetics Consortium. Results The genetic instrument of 33 SNPs explained 4.8% of the variance in mood swings. Genetically determined mood swings was associated with an increased risk of coronary artery disease (CAD) (odds ratio 3.12, 95% confidence interval 1.92 to 5.08; P=4.32×10–6). However, mood swings had no effect on the other cardiometabolic outcomes. The above estimates were consistent across all three MR methods without significant heterogeneity. Also, there was no evidence of directional pleiotropy for each outcome except for large artery stroke. Conclusions Using MR approaches that are able draw causal inference, our results suggest that interventions aimed at improving mood swings in the population would lead to a reduction risk of CAD, which highlights the importance of mood management in high-risk CAD population. Funding Acknowledgement Type of funding sources: None.

Definitive roles of TOMM40-APOE-APOC1 variants in the Alzheimer's risk

Despite advances, the roles of genetic variants from the APOE-harboring 19q13.32 region in Alzheimer's disease (AD) remain controversial. We leverage a comprehensive approach to gain insights into a more homogeneous genetic architecture of AD in this region. We use a sample of 2,673 AD-affected and 16,246 unaffected subjects from 4 studies and validate our main findings in the landmark Alzheimer's Disease Genetics Consortium cohort (3,662 AD-cases and 1,541 controls). We report the remarkably high excesses of the AD risk for carriers of the ε4 allele who also carry minor alleles of rs2075650 (TOMM40) and rs12721046 (APOC1) polymorphisms compared to carriers of their major alleles. The exceptionally high 4.37-fold (p=1.34 × 10−3) excess was particularly identified for the minor allele homozygotes. The beneficial and adverse variants were significantly depleted and enriched, respectively, in the AD-affected families. This study provides compelling evidence for the definitive roles of the APOE-TOMM40-APOC1 variants in the AD risk.

Discovery and prioritization of variants and genes for kidney function in >1.2 million individuals

Genes underneath signals from genome-wide association studies (GWAS) for kidney function are promising targets for functional studies, but prioritizing variants and genes is challenging. By GWAS meta-analysis for creatinine-based estimated glomerular filtration rate (eGFR) from the Chronic Kidney Disease Genetics Consortium and UK Biobank (n = 1,201,909), we expand the number of eGFRcrea loci (424 loci, 201 novel; 9.8% eGFRcrea variance explained by 634 independent signal variants). Our increased sample size in fine-mapping (n = 1,004,040, European) more than doubles the number of signals with resolved fine-mapping (99% credible sets down to 1 variant for 44 signals, ≤5 variants for 138 signals). Cystatin-based eGFR and/or blood urea nitrogen association support 348 loci (n = 460,826 and 852,678, respectively). Our customizable tool for Gene PrioritiSation reveals 23 compelling genes including mechanistic insights and enables navigation through genes and variants likely relevant for kidney function in human to help select targets for experimental follow-up.

Integration of a polygenic risk score of kidney function with cumulative cisplatin dose and time variables for the prediction of serum platinum levels.

12063 Background: Platinum levels are measurable in the serum for decades after cisplatin therapy and higher levels may be related to chemotherapy-induced toxicities. Since cisplatin is cleared exclusively by the kidney, we hypothesized that a genetic predictor of kidney function, an estimated glomerular filtration rate polygenic risk score (eGFR PRS), would significantly associate with serum platinum levels and could improve prediction models. Methods: Within a large well-characterized, multicenter clinical cohort of cisplatin-treated testicular cancer survivors (TCS), we conducted analyses on all patients with genetic data and serum platinum levels. Genotyping was performed on the HumanOmniExpressExome chip and standard QC measures were included. Serum platinum concentrations were quantified by inductively coupled plasma mass spectrometry. For all TCS, time since therapy (TIME) and cumulative cisplatin dose were collected. The eGFR PRS was developed from the Chronic Kidney Disease Genetics (CKDGen) consortium meta-analysis summary statistics using PRS-CS. Using principal component analysis, we restricted the analysis to TCS of genetically determined European ancestry, then calculated the genome-wide PRS for all participants. We performed Cox regression analyses to evaluate prediction models of serum platinum that included cumulative dose and TIME, as well as a model including eGFR PRS. Data are presented as median(interquartile range). Results: 901 patients were included in our analysis with a median diagnosis age of 31 (26 - 38) years, cumulative cisplatin dose of 400 (300-400) mg/m2, and time since first cisplatin dose of 4.6 (2.3-9.5) years. The median serum platinum level for all TCS was 305 (121-981) ng/L. When stratified into quartiles by eGFR PRS, TCS in the lowest quartile had a median serum platinum level of 316 (139-1014) ng/L while TCS in the highest had a median of 268 (106-731) ng/L. Comparison of two Cox regression models for serum platinum prediction, one including only cumulative dose and TIME as predictors and a second including dose, TIME, eGFR PRS, and an eGFR PRS*TIME interaction term, we determined the model including eGFR PRS had a lower AIC (14350 vs 16180) suggesting a more parsimonious model. Further, eGFR PRS was a significant independent predictor of serum platinum levels (p = 0.02) and the impact of eGFR PRS varies over time (eGFR PRS*TIME, p = 0.05). Conclusions: The genetic predictor of kidney function circumvents the use of renal function measures that may have been impaired by initial cisplatin administration. It is a significant independent predictor of serum platinum levels and consistent with expectation: TCS with higher genetically predicted kidney function had lower serum platinum levels. Our results suggest kidney function inferred by genetics may improve the prediction of serum platinum levels.

Genome‐wide interaction study of smoking in Alzheimer’s disease

AbstractBackgroundGenome‐wide association studies (GWAS) have identified approximately 40 risk loci associated with Alzheimer’s disease (AD). However, only a fraction of heritability has been explained. In large meta‐analysis, smoking was associated with AD dementia. In this study, we sought to identify interactions between smoking and single‐nucleotide polymorphisms (SNPs) to further characterize AD genetic architecture.MethodWe used a subset of datasets of individuals of European ancestry from the Alzheimer’s Disease Genetic Consortium (ADGC) that had smoking information available from parent studies. The presence of any past or current smoking habit was considered to be positive smoking exposure. In each dataset, we ran a genome‐wide case‐control analysis including SNP and smoking main terms, and a SNP‐smoking interaction term. Models were adjusted for age, sex, and principal components of population substructure. Results from each dataset were meta‐analyzed using the inverse variance method. Pathway analysis of top SNPs was run using Ingenuity.ResultThe sample included 6,916 total individuals, including 2,862 AD cases and 4,054 controls. Although no interaction terms reached genome‐wide significance, there were two suggestive loci: top SNP rs3734416 [minor (C) allele frequency (MAF) = 0.27; interaction P = 7.2 × 10−6; OR for C allele in smokers = 1.23; OR for C allele in non‐smokers = 0.86] on chromosome 6 within the gene MTHFD1L and 95kb downstream of PLEKHG1, and top SNP rs693951 [MAF (G) = 0.27; interaction P = 1.3 × 10−6; OR for major A allele in smokers = 1.31; OR for A allele in non‐smokers = 0.83] on chromosome 8, 70kb upstream of ANGPT1. Pathway analysis implicated cellular development, cellular growth and proliferation and nervous system development and function. MTHFD1L has been implicated in candidate gene studies of AD and PLEKHG1 has been implicated in a GWAS of white matter hyperintensities. ANGPT1 has been implicated in recovery after ischemic stroke in candidate gene, transcriptomic and blood‐based biomarker studies.ConclusionWe found suggestive evidence of a smoking‐SNP interaction associated with AD risk at 2 loci previously linked with AD and cerebrovascular disease, but that were not identified in the largest AD GWAS to date. Expansion of the sample and replication are underway.

Genome‐wide association analyses identify genes modifying age‐at‐onset of Alzheimer’s disease

AbstractBackgroundSeveral studies have attempted to identify genes for age‐at‐onset (AAO) of dementia symptoms in Alzheimer’s disease (AD) through genome‐wide linkage (Daw et al. 1999, Li et al. 2002, Choi et al. 2011) and genome‐wide association studies (Kamboh et al. 2012, Naj et al. 2014). Naj et al. conducted a meta‐analysis of 14 datasets from the Alzheimer’s Disease Genetics Consortium (ADGC) with genotype imputation to HapMap2. Using an expanded set of ADGC cohorts, we re‐examined AAO using higher‐quality genome‐wide imputation data and pooled‐data analysis instead of meta‐analysis to identify novel genetic contributors to AAO of AD.MethodsWe combined data from 20 non‐Hispanic white prospective and case‐control ADGC datasets, excluding family‐based datasets. Genotype data were imputed to the Haplotype Reference Consortium (HRC) r1.1 reference panel using the Michigan Imputation Server and consistent quality control applied to each dataset, after which genotype data were merged across datasets using QCTOOL and GTOOL. We performed case‐only association analyses for log10(AAO) using multivariable linear regression with covariate adjustment for sex, cohort, and principal components capturing population substructure, and then conducted analyses conditioning on dosage of APOE ε4 alleles. Variants with P < 10−5 from conditional analyses were re‐analyzed using linear mixed modeling treating cohort as a random effect.ResultsWe used 9,228 AD cases, including 5,307 females (57.4%) with mean (SD) AAO of 74.2(7.7) years. In addition to the APOE region, which reached genome‐wide significance (P < 5 × 10−8), we observed strong novel associations with variants in NTM (encoding neurotrimin) on chr11q25 (rs117589002, P = 1.24 × 10−7) and in an intergenic region on chr3p22.3 (Pmin = 1.89 × 10−7). Other AAO loci previously identified in the smaller ADGC dataset (Naj et al 2014) remained nominally significant. After adjusting for APOE ε4, thirty‐two regions showed suggestive association (P < 10−5), with chr3p22.3 and NTM remaining the top loci. Chromosome 11q25 includes a known AD linkage region (Blacker et al. 2003). In addition, NTM variation has been found to be correlated with cognitive function tests (Liu et al. 2007) and intelligence (Pan et al. 2010).ConclusionsIn an expanded ADGC dataset, we confirmed AAO associations in the APOE region and observed evidence for potential novel AD AAO loci including NTM.

NIA genetics of Alzheimer’s disease data storage site (NIAGADS): Update 2020

AbstractBackgroundNIAGADS is a national genetics data repository that facilitates access of genotypic data to qualified investigators for the study of the genetics of late‐onset Alzheimer’s disease (AD) and other neurological diseases. Collaborations with large consortia and centers such as the Alzheimer’s Disease Genetics Consortium (ADGC), Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, the Alzheimer’s Disease Genome Sequencing Project (ADSP), and the Genome Center for Alzheimer’s Disease (GCAD) allow NIAGADS to lead the effort in managing large AD datasets that can be easily accessed by the research community and utilized to their fullest extent.MethodNIAGADS is supported by National Institute on Aging (NIA) under a cooperative agreement (U24 AG041689). All data derived from NIA funded AD genetics studies are expected to be deposited in NIAGADS or another NIA approved site. NIAGADS manages a Data Sharing Service (DSS) that facilitates the deposition and sharing of genomic data and association results with approved users in the neurodegenerative research community. In addition, researchers are able to freely use the NIAGADS Genomics Database to search annotation resources that link published AD studies to AD‐relevant sequence features and genome‐wide annotations.ResultAs of January 2020, NIAGADS houses 67 datasets (23 added in 2019) with >59,000 samples and nearly 34 billion genotypes. Qualified investigators can retrieve ADSP sequencing data with ease and flexibility through the NIAGADS DSS. The ADSP and other contributing studies have completed whole exome sequencing (WES) of 20,630 subjects and whole‐genome sequencing (WGS) of 4,750 subjects. Raw WES and WGS files, quality controlled VCF files, and phenotype data files are available via qualified access. The next planned dataset release will occur in late 2020 and will contain an additional 13,136 genomes jointly genotype called with the first release of 4,750 genomes, totaling about 17,886 genomes.ConclusionNIAGADS is a rich resource for AD researchers, with the goal of facilitating advances in Alzheimer’s genetics research. By housing datasets from multiple projects and institutions, NIAGADS enables AD researchers to be more efficient in meeting their research goals. Datasets, guidelines, and new features are available on our website at https://www.niagads.org.

Mechanism for the protective effect of APOE ε2 against Alzheimer disease is linked to tau and the classical complement pathway

AbstractBackgroundRecent reports suggest that the rare APOE Christchurch mutation and APOE2 allele protect against Alzheimer’s disease (AD) pathology by reducing the burden of tau pathology. However, the mechanism(s) underlying the APOE2 protective effect linking to tau is largely unknown.MethodWe conducted a genome‐wide association study (GWAS) for AD among 2,120 APOE2 carriers from the Alzheimer Disease Genetics Consortium (ADGC), and prioritized by gene network analysis and methylation profiling of CpG sites in the locus using the Religious Orders Study and Memory and Aging Project (ROSMAP) data. We also performed differential gene expression analysis among APOE2/3 subjects in prefrontal cortex tissue from 44 AD and 75 control brains of the Framingham Heart Study (FHS), Boston University Alzheimer’s Disease Center (BUADC), and ROSMAP. We validated the relationships between protein levels of the top‐ranked genes and levels of tau and amyloid beta proteins in prefrontal cortex area of 193 FHS/BUADC brains.ResultOf the significant genetic associations with AD (P < 10−6), PPP2CB was the key node in APOE2‐related gene networks and contained the most significant CpG site (P = 5.2 × 10−4) located 2,814 bp upstream of the top‐ranked GWAS variant. The complement genes C4A and C4B were the top‐ranked differentially expressed genes (P < 2 × 10−4) with reduced expression in APOE2/3 controls compared in APOE2/3 cases or other carriers. Furthermore, the level of PPP2CB protein was significantly associated with increased levels of C4B protein (P = 8.2 × 10−7), and the C4A level was associated with increased pTau231/tTau ratio (P = 0.006). Protein levels of C4A, C4B, and PPP2CB were not associated with amyloid beta 42 (Aβ42) or pTau181/tTau ratio. We were unable to confirm previous reports on the role of C1q, since the C1q level was not associated with any of these phenotypes.ConclusionThis is the first to report the molecular link between a tau phosphatase and the classical complement pathway, especially C4, as a mechanism for the ε2 protective effect against AD. Our findings may lead to the development of novel therapeutic targets for AD by mimicking the neuroprotective effect of APOE2.

Association of Uncommon, Noncoding Variants in the APOE Region With Risk of Alzheimer Disease in Adults of European Ancestry

The ε2 and ε4 alleles of the apolipoprotein E (APOE) gene are associated with Alzheimer disease (AD) risk. Although nearby genetic variants have also been shown to be associated with AD, including rs2075650 in the TOMM40 gene and rs4420638 near the APOC1 gene, it is unknown whether these associations are independent of the ε2 and ε4 alleles. To assess whether variants near APOE are associated with AD independently of the ε2/ε3/ε4 genotype. In this genetic association study of the Alzheimer's Disease Genetics Consortium imputed genotype at data, 14 415 variants near APOE (±500 kilobase) for 18 795 individuals with European ancestry were tested for association with AD using 4 logistic mixed models adjusting for sex, cohort, population structure, and relatedness. Model 1 had no APOE adjustment, and model 2 adjusted for the count of ε2 and ε4 alleles. Model 3 was restricted to ε3 homozygotes, and model 4 was restricted to ε4 homozygotes. Data were downloaded from May 31, 2018, to June 3, 2018, and analyzed from November 1, 2018, to June 24, 2020. Alzheimer disease affectation status was defined by clinicians using standard National Institute of Neurological and Communicative Disorders and Stroke and Alzheimer Disease and Related Disorders Association criteria. Association was evaluated using Score tests; results with P < .05 divided by the number of independent tests per model were considered statistically significant. Among the 18 795 individuals in the study, 9704 were affected by AD and 9066 were control individuals; the median age at onset/evaluation was 76 (interquartile range, 70-82) years; and 11 167 were female (59.4%). Associations with AD were found for rs2075650 (odds ratio [OR], 2.59; 95% CI, 2.45-2.75; P = 3.19 × 10-228) and rs4420638 (OR, 2.77; 95% CI, 2.62-2.94; P = 2.99 × 10-254) without APOE adjustment. Although rs2075650 was nominally associated with AD among the ε4 homozygotes (OR, 1.33; 95% CI, 1.00-1.77; P = .047), the association between rs4420638 and AD was eliminated by APOE adjustment (model 2 OR, 1.06 [95% CI, 0.96-1.18; P = .24]; model 3 OR, 1.13 [95% CI, 0.95-1.34; P = .18]; model 4 OR, 0.90 [95% CI, 0.56-1.45; P = .66]). There was a significant association between rs192879175 and AD among ε3 homozygotes (OR, 0.50; 95% CI, 0.37-0.68; P = 8.30 × 10-6). The results of this genetic association study suggest that ε2/ε3/ε4 alleles are not the only variants in the APOE region that are associated with AD risk. Additional work with independent data is needed to replicate these results.

Novel Alzheimer Disease Risk Loci and Pathways in African American Individuals Using the African Genome Resources Panel

Compared with non-Hispanic White individuals, African American individuals from the same community are approximately twice as likely to develop Alzheimer disease. Despite this disparity, the largest Alzheimer disease genome-wide association studies to date have been conducted in non-Hispanic White individuals. In the largest association analyses of Alzheimer disease in African American individuals, ABCA7, TREM2, and an intergenic locus at 5q35 were previously implicated. To identify additional risk loci in African American individuals by increasing the sample size and using the African Genome Resource panel. This genome-wide association meta-analysis used case-control and family-based data sets from the Alzheimer Disease Genetics Consortium. There were multiple recruitment sites throughout the United States that included individuals with Alzheimer disease and controls of African American ancestry. Analysis began October 2018 and ended September 2019. Diagnosis of Alzheimer disease. A total of 2784 individuals with Alzheimer disease (1944 female [69.8%]) and 5222 controls (3743 female [71.7%]) were analyzed (mean [SD] age at last evaluation, 74.2 [13.6] years). Associations with 4 novel common loci centered near the intracellular glycoprotein trafficking gene EDEM1 (3p26; P = 8.9 × 10-7), near the immune response gene ALCAM (3q13; P = 9.3 × 10-7), within GPC6 (13q31; P = 4.1 × 10-7), a gene critical for recruitment of glutamatergic receptors to the neuronal membrane, and within VRK3 (19q13.33; P = 3.5 × 10-7), a gene involved in glutamate neurotoxicity, were identified. In addition, several loci associated with rare variants, including a genome-wide significant intergenic locus near IGF1R at 15q26 (P = 1.7 × 10-9) and 6 additional loci with suggestive significance (P ≤ 5 × 10-7) such as API5 at 11p12 (P = 8.8 × 10-8) and RBFOX1 at 16p13 (P = 5.4 × 10-7) were identified. Gene expression data from brain tissue demonstrate association of ALCAM, ARAP1, GPC6, and RBFOX1 with brain β-amyloid load. Of 25 known loci associated with Alzheimer disease in non-Hispanic White individuals, only APOE, ABCA7, TREM2, BIN1, CD2AP, FERMT2, and WWOX were implicated at a nominal significance level or stronger in African American individuals. Pathway analyses strongly support the notion that immunity, lipid processing, and intracellular trafficking pathways underlying Alzheimer disease in African American individuals overlap with those observed in non-Hispanic White individuals. A new pathway emerging from these analyses is the kidney system, suggesting a novel mechanism for Alzheimer disease that needs further exploration. While the major pathways involved in Alzheimer disease etiology in African American individuals are similar to those in non-Hispanic White individuals, the disease-associated loci within these pathways differ.

Characterizing Clinical and Neuropathological Traits of APOE Haplotypes in African Americans and Europeans.

The APOEɛ4 allele is the largest genetic risk factor for late-onset Alzheimer's disease (AD). Recent literature suggested that the contribution of APOEɛ4 to AD risk could be population-specific, with ɛ4 conferring a lower risk to Blacks or African Americans. To investigate the effect of APOE haplotypes on AD risk in individuals with European ancestry (EU) and Blacks or African Americans (AA). We selected data from 1) the National Alzheimer's Coordinating Center: a total of 3,486 AD cases and 4,511 controls (N = 7,997, 60% female) with genotypes from the Alzheimer's Disease Genetics Consortium (ADGC), and 2) the Rush University Religious Orders Study and Memory and Aging Project (ROSMAP) cohort with 578 AD and 670 controls (N = 1,248, 60% female). Using ɛ3 homozygotes as the reference, we compared the association of various APOE haplotypes with the clinical and neuropathological correlates of dementia in AA and EU. In both cohorts, we find no difference in the odds or age of onset of AD among the ɛ4-linked haplotypes defined by rs769449 within either AA or EU. Additionally, while APOEɛ4 was associated with a faster rate of decline, no differences were found in rate of decline, clinical or neuropathological features among the ɛ4-linked haplotypes. Further analysis with other variants near the APOE locus failed to identify any effect modification. Our study finds similar effects of the ɛ4-linked haplotypes defined by rs769449 on AD as compared to ɛ3 in both AA and EU. Future studies are required to understand the heterogeneity of APOE conferred risk of AD among various genotypes and populations.

Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease

Polygenic inheritance plays a central role in Parkinson disease (PD). A priority in elucidating PD etiology lies in defining the biological basis of genetic risk. Unraveling how risk leads to disruption will yield disease-modifying therapeutic targets that may be effective. Here, we utilized a high-throughput and hypothesis-free approach to determine biological processes underlying PD using the largest currently available cohorts of genetic and gene expression data from International Parkinson’s Disease Genetics Consortium (IPDGC) and the Accelerating Medicines Partnership-Parkinson’s disease initiative (AMP-PD), among other sources. We applied large-scale gene-set specific polygenic risk score (PRS) analyses to assess the role of common variation on PD risk focusing on publicly annotated gene sets representative of curated pathways. We nominated specific molecular sub-processes underlying protein misfolding and aggregation, post-translational protein modification, immune response, membrane and intracellular trafficking, lipid and vitamin metabolism, synaptic transmission, endosomal–lysosomal dysfunction, chromatin remodeling and apoptosis mediated by caspases among the main contributors to PD etiology. We assessed the impact of rare variation on PD risk in an independent cohort of whole-genome sequencing data and found evidence for a burden of rare damaging alleles in a range of processes, including neuronal transmission-related pathways and immune response. We explored enrichment linked to expression cell specificity patterns using single-cell gene expression data and demonstrated a significant risk pattern for dopaminergic neurons, serotonergic neurons, hypothalamic GABAergic neurons, and neural progenitors. Subsequently, we created a novel way of building de novo pathways by constructing a network expression community map using transcriptomic data derived from the blood of PD patients, which revealed functional enrichment in inflammatory signaling pathways, cell death machinery related processes, and dysregulation of mitochondrial homeostasis. Our analyses highlight several specific promising pathways and genes for functional prioritization and provide a cellular context in which such work should be done.

MAPT haplotype-stratified GWAS reveals differential association for AD risk variants.

Introduction MAPT H1 haplotype is implicated as a risk factor for neurodegenerative diseases including Alzheimer's disease (AD).MethodsUsing Alzheimer's Disease Genetics Consortium (ADGC) genome‐wide association study (GWAS) data (n = 18,841), we conducted a MAPT H1/H2 haplotype–stratified association to discover MAPT haplotype–specific AD risk loci.ResultsWe identified 11 loci—5 in H2‐non‐carriers and 6 in H2‐carriers—although none of the MAPT haplotype–specific associations achieved genome‐wide significance. The most significant H2 non‐carrier–specific association was with a NECTIN2 intronic (P = 1.33E‐07) variant, and that for H2 carriers was near NKX6‐1 (P = 1.99E‐06). The GABRG2 locus had the strongest epistasis with MAPT H1/H2 variant rs8070723 (P = 3.91E‐06). Eight of the 12 genes at these loci had transcriptome‐wide significant differential expression in AD versus control temporal cortex (q < 0.05). Six genes were members of the brain transcriptional co‐expression network implicated in “synaptic transmission” (P = 9.85E‐59), which is also enriched for neuronal genes (P = 1.0E‐164), including MAPT.DiscussionThis stratified GWAS identified loci that may confer AD risk in a MAPT haplotype–specific manner. This approach may preferentially enrich for neuronal genes implicated in synaptic transmission.

Waist circumference increases risk of coronary heart disease: Evidence from a Mendelian randomization study.

BackgroundThis study investigated whether expanding waist circumference (WC) is causally associated with an elevated risk of coronary heart disease (CHD), using a two‐sample Mendelian randomization (MR) study through integrating summarized data from genome‐wide association study.MethodsThe data included in this analysis were mainly from the Genetic Investigation of ANthropometric Traits (GIANT), Consortium and Coronary Artery Disease Genome wide Replication, and Meta‐analysis plus the Coronary Artery Disease (C4D) Genetics (CARDIoGRAMplusC4D) Consortium. Three statistical approaches, inverse‐variance weighted (IVW), weighted median, and MR‐Egger regression method were conducted to assess the casual relationship. The exposure was WC, measured by 46 single‐nucleotide polymorphisms from GIANT and the outcome was the risk of CHD. Then, we used the genetic data from Neale Lab and TAG to infer whether WC causally affected the established risk factors of CHD.ResultsThe IVW method presented that genetically predicted WC was positively casually associated with CHD (odds ratio [OR]: 1.57, 95% CI = 1.33–1.84; p = 4.81e‐08), which was consistent with the result of weighted median and MR‐Egger regression. MR‐Egger regression indicated that there was no directional horizontal pleiotropy to violate the MR assumption. Additionally, expanded WC was also associated with higher risk of hypertension and diabetes, higher cholesterol, more smoking intensity, and decreased frequency of physical activity.ConclusionOur analysis provided strong evidence to indicate a causal relationship between WC and increased risk of CHD.

Failure to detect synergy between variants in transferrin and hemochromatosis and Alzheimer's disease in large cohort

Alzheimer's disease (AD) is the most common cause of dementia and, despite decades of effort, there is no effective treatment. In the last decade, many association studies have identified genetic markers that are associated with AD status. Two of these studies suggest that an epistatic interaction between variants rs1049296 in the transferrin (TF) gene and rs1800562 in the homeostatic iron regulator (HFE) gene, commonly known as hemochromatosis, is in genetic association with AD. TF and HFE are involved in the transport and regulation of iron in the brain, and disrupting these processes exacerbates AD pathology through increased neurodegeneration and oxidative stress. However, by using a significantly larger data set from the Alzheimer's Disease Genetics Consortium, we fail to detect an association between TF rs1049296 or HFE rs1800562 with AD risk (TF rs1049296 p = 0.38 and HFE rs1800562 p = 0.40). In addition, logistic regression with an interaction term and a synergy factor analysis both failed to detect epistasis between TF rs1049296 and HFE rs1800562 (SF = 0.94; p = 0.48) in AD cases. Each of these analyses had sufficient statistical power (power > 0.99), suggesting that previously reported associations may be the result of more complex epistatic interactions, genetic heterogeneity, or false-positive associations because of limited sample sizes.

No causal effects of plasma homocysteine levels on the risk of coronary heart disease or acute myocardial infarction: A Mendelian randomization study.

Although many observational studies have shown an association between plasma homocysteine levels and cardiovascular diseases, controversy remains. In this study, we estimated the role of increased plasma homocysteine levels on the etiology of coronary heart disease and acute myocardial infarction. A two-sample Mendelian randomization study on disease was conducted, i.e. "coronary heart disease" (n = 184,305) and "acute myocardial infarction" (n = 181,875). Nine single nucleotide polymorphisms, which were genome-wide significantly associated with plasma homocysteine levels in 57,644 subjects from the Coronary ARtery DIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) plus The Coronary Artery Disease (C4D) Genetics (CARDIoGRAMplusC4D) consortium genome-wide association study and were known to be associated at p < 5×10-8, were used as an instrumental variable. None of the nine single nucleotide polymorphisms were associated with coronary heart disease or acute myocardial infarction (p > 0.05 for all). Mendelian randomization analysis revealed no causal effects of plasma homocysteine levels, either on coronary heart disease (inverse variance weighted; odds ratio = 1.015, 95% confidence interval = 0.923-1.106, p = 0.752) or on acute myocardial infarction (inverse variance weighted; odds ratio = 1.037, 95% confidence interval = 0.932-1.142, p = 0.499). The results were consistent in sensitivity analyses using the weighted median and Mendelian randomization-Egger methods, and no directional pleiotropy (p = 0.213 for coronary heart disease and p = 0.343 for acute myocardial infarction) was observed. Sensitivity analyses confirmed that plasma homocysteine levels were not significantly associated with coronary heart disease or acute myocardial infarction. The findings from this Mendelian randomization study indicate no causal relationship between plasma homocysteine levels and coronary heart disease or acute myocardial infarction. Conflicting findings from observational studies might have resulted from residual confounding or reverse causation.

Negative Effects of Age at Menarche on Risk of Cardiometabolic Diseases in Adulthood: A Mendelian Randomization Study.

Observational studies have demonstrated that early menarche is associated with cardiometabolic diseases, but confounding factors make it difficult to infer causality. We used Mendelian randomization (MR) to examine whether age at menarche (AAM) is causally associated with type 2 diabetes (T2D), coronary artery disease (CAD) and cardiometabolic traits. A 2-sample MR analysis was conducted using genome-wide association study (GWAS) summary statistics from the Diabetes Genetics Replication and Meta-analysis (DIAGRAM) consortium (n = 159 208) for T2D and the Coronary Artery Disease Genome-wide Replication and Meta-analysis plus the Coronary Artery Disease Genetics (CARDIoGRAMplusC4D) consortium (n = 184 305) for CAD. We used 122 instrumental variables (IVs) extracted from a published GWAS meta-analysis incorporating 182 416 women to determine the causal effect of AAM on cardiometabolic diseases, treating childhood and adult body mass index (BMI) as the confounders. Sensitivity analyses were also performed to detect the pleiotropy of the IVs. Employing the MR approach, we found that later AAM was associated with decreased risk of CAD (OR, 0.92 [95% CI, 0.88-0.96]; P = 2.06 × 10-4) in adults, as well as lower blood levels of log fasting insulin, log homeostatic model assessment of insulin resistance (HOMA-IR), log HOMA of β-cell function (HOMA-B), triglycerides, and diastolic blood pressure, but higher blood level of high-density lipoprotein. However, the associations were substantially attenuated after excluding BMI-related variants. MR analyses provide little evidence on the causal effect between AAM and T2D. Our findings showed that AAM did not appear to have a causal effect on the risk of cardiometabolic diseases in adult life, as their associations observed in epidemiological studies might be largely mediated through excessive adiposity. We propose adiposity might be a primary target in future intervention strategy.

Circulating Vitamin E Levels and Risk of Coronary Artery Disease and Myocardial Infarction: A Mendelian Randomization Study.

Observational studies have reported a cardioprotective effect of vitamin E whereas intervention trials failed to confirm its beneficial effects, and even some reported adverse effects of vitamin E supplements on coronary artery disease (CAD). To clarify, we conducted a two-sample mendelian randomization study to investigate causal association of vitamin E with the risk of CAD. Three single nucleotide polymorphisms (SNPs) identified in a genome-wide analysis study including 7781 individuals of European descent, rs964184, rs2108622, and rs11057830 were used as the genetic instruments for vitamin E. Data for CAD/myocardial infarction (MI) were available from Coronary ARtery DIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) plus The Coronary Artery Disease (C4D) Genetics consortium. The effect of each SNP on CAD/myocardial infarction (MI) was weighted by its effect on serum vitamin E (mg/L), and results were pooled to give a summary estimates for the effect of increased vitamin E on risk of CAD/MI. Based on 3 SNPs each 1 mg/L increase in vitamin E was significantly associated with CAD (odds ratio (OR) 1.05, 95% confidence interval (CI) 1.03–1.06), MI (OR 1.04, 95% CI 1.03–1.05), elevated low-density lipoprotein cholesterol (0.021 standard deviations (SD), 95% CI 0.016, 0.027), triglycerides (0.026 SD, 95% CI 0.021, 0.031), and total cholesterol (0.043 SD, 95% CI 0.038, 0.048) and lower levels of high-density lipoprotein cholesterol (−0.019 SD 95% CI −0.024, −0.014). Our findings indicate that higher vitamin E may increase the risk of CAD/MI and the safety and efficacy of vitamin E supplementation use should be reevaluated.