Replication Genome-wide Association Studies Research Articles

Genetic variants of LRRC8C, OAS2, and CCL25 in the T cell exhaustion-related genes are associated with non-small cell lung cancer survival.

T cell exhaustion is a state in which T cells become dysfunctional and is associated with a decreased efficacy of immune checkpoint inhibitors. Lung cancer has the highest mortality among all cancers. However, the roles of genetic variants of the T cell exhaustion-related genes in the prognosis of non-small cell lung cancer (NSCLC) patients has not been reported. We conducted a two-stage multivariable Cox proportional hazards regression analysis with two previous genome-wide association study (GWAS) datasets to explore associations between genetic variants in the T cell exhaustion-related genes and survival of NSCLC patients. We also performed expression quantitative trait loci analysis for functional validation of the identified variants. Of all the 52,103 single nucleotide polymorphisms (SNPs) in 672 T cell exhaustion-related genes, 1,721 SNPs were found to be associated with overall survival (OS) of 1185 NSCLC patients of the discovery GWAS dataset from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial, and 125 of these 1,721 SNPs remained significant after validation in an additional independent replication GWAS dataset of 984 patients from the Harvard Lung Cancer Susceptibility (HLCS) Study. In multivariable stepwise Cox model analysis, three independent SNPs (i.e., LRRC8C rs10493829 T>C, OAS2 rs2239193 A>G, and CCL25 rs3136651 T>A) remained significantly associated with OS with hazards ratios (HRs) of 0.86 (95% confidence interval (CI) = 0.77-0.96, P = 0.008), 1.48 (95% CI = 1.18-1.85, P < 0.0001) and 0.78 (95% CI = 0.66-0.91, P = 0.002), respectively. Further combined analysis for these three SNPs suggested that an unfavorable genotype score was associated with a poor OS and disease-specific survival. Expression quantitative trait loci analysis suggested that the LRRC8C rs10493829 C allele was associated with elevated LRRC8C mRNA expression levels in normal lymphoblastoid cells, lung tissue, and whole blood. Our findings suggested that these functional SNPs in the T cell exhaustion-related genes may be prognostic predictors for survival of NSCLC patients, possibly via a mechanism of modulating corresponding gene expression.

Unraveling the role of CTLA-4 variants in acute kidney injury after ICI treatments.

e14682 Background: Immune checkpoint inhibitors (ICIs) often result in various immune-related adverse events (irAEs), which limit their therapeutic application and pose challenges to clinical decision-making. Among these irAEs, the incidence rate of ICI-related acute kidney injury (ICI-AKI) is on the rise. Understanding the genetic predisposition to ICI-AKI can inform personalized treatment plans, thereby minimizing risks and optimizing outcomes. This study aims to interrogate risk loci for AKI patients to gain insights into ICI-related AKI in cancer patients and to support the design of more personalized cancer therapies. Methods: This study comprehensively integrates meta-analysis, replication genome-wide association study (GWAS), fine-mapping, and mendelian randomization (MR) to explore potential genetic variants related with ICI-AKI. We first conducted a meta-analysis of 6 ICI pharmacogenomics studies, aggregating effect sizes from these studies using both fixed-effect and random-effects models to address heterogeneity and identified 186 significant genotypes. Subsequently, a GWAS was carried out over the 186 candidate genotypes in an independent cohort from the NIH All of Us program (N = 230,013) using logistic regression, identifying14,773 patients who developed AKI. To identify causal variants, we implemented fine-mapping techniques to further refine our genotype selection. Results: Our study identified genetic variants associated with an increased risk of AKI. Among these, the variant with the strongest association was located at the cytotoxic T lymphocyte antigen 4 (CTLA-4) gene locus, rs3087243 (chr2: 203874196, G&gt;A,T). This genotype exhibited a significant inverse relationship with AKI risk (beta = -8.19e-2, P = 2e-11), suggesting that reduced activity of the CTLA-4 gene may be linked to an elevated risk of developing AKI. Our findings indicate that cancer patients with this genotype may have a lower risk of ICI-related AKI after immunotherapy. In our future study, we will continue investigating significant SNPs including rs3087243 in cancer patients for their ICI-AKI risk. Conclusions: We identified an AKI-tolerant genotype, rs3087243. Patients with this genotype may be safter from developing ICI-related AKI after immunotherapy treatment. This work also highlights the research potential of All of Us clinicogenomics data.

A novel application of data-consistent inversion to overcome spurious inference in genome-wide association studies.

The genome-wide association studies (GWAS) typically use linear or logistic regression models to identify associations between phenotypes (traits) and genotypes (genetic variants) of interest. However, the use of regression with the additive assumption has potential limitations. First, the normality assumption of residuals is the one that is rarely seen in practice, and deviation from normality increases the Type-I error rate. Second, building a model based on such an assumption ignores genetic structures, like, dominant, recessive, and protective-risk cases. Ignoring genetic variants may result in spurious conclusions about the associations between a variant and a trait. We propose an assumption-free model built upon data-consistent inversion (DCI), which is a recently developed measure-theoretic framework utilized for uncertainty quantification. This proposed DCI-derived model builds a nonparametric distribution on model inputs that propagates to the distribution of observed data without the required normality assumption of residuals in the regression model. This characteristic enables the proposed DCI-derived model to cover all genetic variants without emphasizing on additivity of the classic-GWAS model. Simulations and a replication GWAS with data from the COPDGene demonstrate the ability of this model to control the Type-I error rate at least as well as the classic-GWAS (additive linear model) approach while having similar or greater power to discover variants in different genetic modes of transmission.

The causal effect of two occupational factors on osteoarthritis and rheumatoid arthritis: a Mendelian randomization study.

Osteoarthritis (OA) and rheumatoid arthritis (RA) are two common types of arthritis. We conducted a two-sample Mendelian randomization (MR) study to estimate the causal effects of two common occupational factors-job involves heavy manual or physical work and job involves mainly walking or standing-on OA and RA in individuals of European ancestry. Instruments were chosen from genome-wide association studies (GWASs) that identified independent single nucleotide polymorphisms (SNPs) robustly linked to job involves heavy manual or physical work (N = 263,615) as well as job involves mainly walking or standing (N = 263,556). Summary statistics for OA and RA were taken from the Integrative Epidemiology Unit (IEU) GWAS database; both discovery and replication GWAS datasets were considered. The primary analysis utilized the inverse variance weighted (IVW) MR method supplemented by various sensitivity MR analyses. In the IVW model, we found that genetically predicted job involves heavy manual or physical work was significantly associated with OA in both the discovery [odds ratio (OR) = 1.034, 95% confidence interval (CI): 1.016-1.053, P = 2.257 × 10-4] and replication (OR = 1.857, 95% CI: 1.223-2.822, P = 0.004) analyses. The causal associations were supported in diverse sensitivity analyses. MR analyses suggested no causal effect of genetically predicted job involves heavy manual or physical work on RA. Similarly, our data provided no evidence that genetically predicted job involves mainly walking or standing was related to OA and RA. Our MR study suggests that job involves heavy manual or physical work is a risk factor for OA. It is of utmost importance to create preventive strategies aimed at reducing its impact on OA at such work sites.

Mendelian-randomization study revealed causal relationship between nonalcoholic fatty liver disease and osteoporosis/fractures.

Patients with nonalcoholic fatty liver disease (NAFLD) are reported to have a higher risk of osteoporosis/fractures; however, the causal relationship remains unclear. Publicly available genome-wide association studies (GWASs) were used for Mendelian randomization (MR) analysis. GWASs of NAFLD and fractures were obtained from the FinnGen Consortium. GWASs of bone mineral density (BMD) were derived from a meta-analysis. GWASs of obesity, diabetes, liver function, and serum lipid-related metrics were used to clarify whether the accompanying NAFLD symptoms contributed to fractures. Moreover, two additional GWASs of NAFLD were applied. A causal association was not observed between NAFLD and BMD using GWASs from the FinnGen Consortium. However, a causal relationship between NAFLD and femoral neck-BMD (FN-BMD), a suggestive relationship between fibrosis and FN-BMD, and between NAFLD and osteoporosis were identified in replication GWASs. Genetically proxied body mass index (BMI), high-density lipoprotein (HDL), and hip circumference increased the likelihood of lower limb fractures. The waist-to-hip ratio decreased, whereas glycated hemoglobin (HbA1C) and homeostasis model assessment of β-cell function (HOMA-B) increased the risk of forearm fractures. Low-density lipoprotein (LDL) reduced, whereas HbA1C increased the incidence of femoral fractures. Alkaline phosphatase (ALP) raised the risk of foot fractures. However, after a multivariate MR analysis (adjusted for BMI), all the relationships became insignificant. NAFLD caused reduced BMD, and genetically predicted HDL, LDL, HbA1C, HOMA-B, ALP, hip circumference, and waist-to-hip ratio causally increased the risk of fractures. BMI may mediate causal relationships. Larger GWASs are required to verify this finding.

Integrating genome-wide association study with regulatory SNP annotations identified novel candidate genes for osteoporosis.

Osteoporosis (OP) is a metabolic bone disease, characterized by a decrease in bone mineral density (BMD). However, the research of regulatory variants has been limited for BMD. In this study, we aimed to explore novel regulatory genetic variants associated with BMD. We conducted an integrative analysis of BMD genome-wide association study (GWAS) and regulatory single nucleotide polymorphism (rSNP) annotation information. Firstly, the discovery GWAS dataset and replication GWAS dataset were integrated with rSNP annotation database to obtain BMD associated SNP regulatory elements and SNP regulatory element-target gene (E-G) pairs, respectively. Then, the common genes were further subjected to HumanNet v2 to explore the biological effects. Through discovery and replication integrative analysis for BMD GWAS and rSNP annotation database, we identified 36 common BMD-associated genes for BMD irrespective of regulatory elements, such as FAM3C (pdiscovery GWAS = 1.21 × 10-25, preplication GWAS = 1.80 × 10-12), CCDC170 (pdiscovery GWAS = 1.23 × 10-11, preplication GWAS = 3.22 × 10-9), and SOX6 (pdiscovery GWAS = 4.41 × 10-15, preplication GWAS = 6.57 × 10-14). Then, for the 36 common target genes, multiple gene ontology (GO) terms were detected for BMD such as positive regulation of cartilage development (p = 9.27 × 10-3) and positive regulation of chondrocyte differentiation (p = 9.27 × 10-3). We explored the potential roles of rSNP in the genetic mechanisms of BMD and identified multiple candidate genes. Our study results support the implication of regulatory genetic variants in the development of OP.

Mapping the gene network landscape of Alzheimer’s disease through integrating genomics and transcriptomics

Integration of multi-omics data with molecular interaction networks enables elucidation of the pathophysiology of Alzheimer's disease (AD). Using the latest genome-wide association studies (GWAS) including proxy cases and the STRING interactome, we identified an AD network of 142 risk genes and 646 network-proximal genes, many of which were linked to synaptic functions annotated by mouse knockout data. The proximal genes were confirmed to be enriched in a replication GWAS of autopsy-documented cases. By integrating the AD gene network with transcriptomic data of AD and healthy temporal cortices, we identified 17 gene clusters of pathways, such as up-regulated complement activation and lipid metabolism, down-regulated cholinergic activity, and dysregulated RNA metabolism and proteostasis. The relationships among these pathways were further organized by a hierarchy of the AD network pinpointing major parent nodes in graph structure including endocytosis and immune reaction. Control analyses were performed using transcriptomics from cerebellum and a brain-specific interactome. Further integration with cell-specific RNA sequencing data demonstrated genes in our clusters of immunoregulation and complement activation were highly expressed in microglia.

Genome-wide Association Study Identified Chromosome 8 Locus Associated with Medication-Related Osteonecrosis of the Jaw.

Medication‐related osteonecrosis of the jaw (MRONJ) is a rare but serious drug‐related adverse event. To identify pharmacogenomic markers of MRONJ associated with bisphosphonate therapy, we conducted a genomewide association study (GWAS) meta‐analysis followed by functional analysis of 5,008 individuals of European ancestry treated with bisphosphonates, which includes the largest number of MRONJ cases to date (444 cases and 4,564 controls). Discovery GWAS was performed in randomly selected 70% of the patients with cancer and replication GWAS was performed in the remaining 30% of the patients with cancer treated with intravenous bisphosphonates followed by meta‐analysis of all 3,639 patients with cancer. GWAS was also performed in 1,369 patients with osteoporosis treated with oral bisphosphonates. The lead single‐nucleotide polymorphism (SNP), rs2736308 on chromosome 8, was associated with an increased risk of MRONJ with an odds ratio (OR) of 2.71 and 95% confidence interval (CI) of 1.90–3.86 (P = 3.57*10−8) in the meta‐analysis of patients with cancer. This SNP was validated in the MRONJ GWAS in patients with osteoporosis (OR: 2.82, 95% CI: 1.55–4.09, P = 6.84*10−4). The meta‐analysis combining patients with cancer and patients with osteoporosis yielded the same lead SNP rs2736308 on chromosome 8 as the top SNP (OR: 2.74, 95% CI: 2.09–3.39, P = 9.65*10−11). This locus is associated with regulation of the BLK, CTSB, and FDFT1 genes, which had been associated with bone mineral density. FDFT1 encodes a membrane‐associated enzyme, which is implicated in the bisphosphonate pathway. This study provides insights into the potential mechanism of MRONJ.

Genetic Variants Associated With Corneal Biomechanical Properties and Potentially Conferring Susceptibility to Keratoconus in a Genome-Wide Association Study

Keratoconus is an important cause of visual loss in young adults, but little is known about its genetic causes. Understanding the genetic determinants of corneal biomechanical factors may in turn teach us about keratoconus etiology. To identify genetic associations with corneal biomechanical properties and to examine whether these genetic variants are associated with keratoconus. A stage 1 discovery and replication genome-wide association study (GWAS) of corneal biomechanical properties was performed in 2 cross-sectional populations (6645 participants from the European Prospective Investigation into Cancer and Nutrition [EPIC]-Norfolk Eye Study and 2384 participants from the TwinsUK study). In stage 2, the association of genetic determinants identified in stage 1 with keratoconus was examined in a case-control study. A total of 752 patients with keratoconus were compared with 974 TwinsUK participants (undergoing direct sequencing) or 13 828 EPIC-Norfolk participants (undergoing genotyping and imputation) who were not part of the stage 1 analysis. Data were collected from March 1, 1993, through March 13, 2017, and analyzed from November 1, 2015, through February 1, 2018. In stage 1, allele dosage at genome-wide single-nucleotide polymorphisms (SNPs); in stage 2, allele dosage at SNPs with genome-wide significance (P < 5 × 10-8) in stage 1 and not previously reported as associated with corneal disease. In stage 1, corneal hysteresis (CH) and corneal resistance factor (CRF), measured with the Ocular Response Analyzer (ORA); in stage 2, association with keratoconus compared with controls. Among 6645 participants in the discovery cohort (3635 women (54.7%); mean age, 69 years [range, 48-92 years]), 7 genome-wide significant loci associated with CH or CRF were identified that were independently replicated. Two further suggestive loci were identified after meta-analysis. To date, 5 of the identified loci, at ANAPC1, ADAMTS8, ADAMTS17, ABCA6, and COL6A1, have not previously been reported as associated with corneal disease. The ABCA6 locus (rs77542162) was associated with keratoconus using the TwinsUK (odds ratio [OR], 0.50; 95% CI, 0.27-0.92; P = .03) and EPIC-Norfolk controls (OR, 0.39; 95% CI, 0.22-0.70; P = .002). The other loci were associated with keratoconus using TwinsUK (OR per effect allele for ADAMTS8, 0.51 [95% CI, 0.37-0.71; P = 7.9 × 10-5]; for COL6A1, 1.65 [95% CI, 1.05-2.59; P = .03]) or EPIC-Norfolk (OR per effect allele for ANAPC1, 0.78 [95% CI, 0.68-0.89; P = 3.7 × 10-4]; for ADAMTS17, 0.82 [95% CI, 0.68-0.99; P = .04]) controls. Five loci that are associated with corneal biomechanical properties and that have suggestive associations with keratoconus were reported. These findings suggest the role of type VI collagen, extracellular matrix, and connective-tissue development for corneal biomechanics and keratoconus and the role of CH and CRF as biomarkers for keratoconus.

ASAFE: ancestry-specific allele frequency estimation.

In a genome-wide association study (GWAS) of an admixed population, such as Hispanic Americans, ancestry-specific allele frequencies can inform the design of a replication GWAS. We derive an EM algorithm to estimate ancestry-specific allele frequencies for a bi-allelic marker given genotypes and local ancestries on a 3-way admixed population, when the phase of each admixed individual's genotype relative to the pair of local ancestries is unknown. We call our algorithm Ancestry Specific Allele Frequency Estimation (ASAFE). We demonstrate that ASAFE has low error on simulated data. The R source code for ASAFE is available for download at https://github.com/BiostatQian/ASAFE CONTACT: qszhang@uw.edu Supplementary data are available at Bioinformatics online.

Genetic Risk Factors for the Development of Osteonecrosis in Children Under Age 10 Treated for Acute Lymphoblastic Leukemia

▪Background: Therapy induced osteonecrosis has become a limiting toxicity in the intensification of treatment for pediatric acute lymphoblastic leukemia (ALL), particularly among patients 10 to 20 years of age. Prior studies on the genetic determinants of osteonecrosis have focused primarily on patients older than 10 years, leaving the genetic risk factors for the larger group of children with ALL less than 10 years old incompletely understood. It is hypothesized that genetic risk factors may account for a greater proportion of risk of osteonecrosis or involve differing mechanisms in younger than in older patients.Methods: We performed the first evaluation of genetic risk factors for osteonecrosis in children less than 10 years old using a discovery cohort of 82 cases of osteonecrosis and 287 controls treated on Children's Oncology Group (COG) protocol AALL0331 (NCI standard risk ALL) and tested for replication in 817 children less than 10 treated on COG protocol AALL0232 (high risk ALL). Genotyping was performed using the Affymetrix Gene Chip Human Mapping Array 6.0 and the Illumina Human Exome BeadChip v1.1. A subset of 15 cases in the discovery cohort had coding variant calls verified by whole exome sequencing. Both discovery and replication genome-wide association studies (GWAS) adjusted for demographic and therapy variables known to modify the risk of osteonecrosis. Enhancer enrichment analysis using HaploReg identified tissues affected by the identified single nucleotide polymorphisms (SNPs). Genes associated with the identified SNPs were evaluated using Ingenuity Pathway Analysis for enrichment in biologically relevant pathways.Results: Within the discovery cohort, top ranked variants were rs76599360 and rs77556622 which were in full linkage disequilibrium [P =1.13x10-9, odds ratio (OR) 22.0, 95% confidence interval (95%CI) 8.15-59.6] located near bone morphogenic protein 7 (BMP7). The top replicated SNPs were located near BMP7 [rs75161997, P =5.34x10-8 (OR 15.0; 95%CI 5.64-39.7) and P =0.0498 (OR 8.44; 95%CI 1.002-71.1) in the discovery and replication cohorts, respectively] and PROX1-antisense RNA1 [PROX1-AS1:rs1891059, P =2.28x10-7 (OR 6.48; 95%CI 3.19-13.1) and P =0.0077 (OR 3.78; 95%CI 1.42-10.1) for the discovery and replication cohorts, respectively]. The top replicated non-synonymous SNP, rs34144324, was in a glutamate receptor gene [GRID2, P=8.65x10-6 (OR 3.46; 95%CI 2.00-5.98) and 0.0136 (OR 10.8; 95%CI 1.63-71.4) in the discovery and replication cohorts, respectively], and the genotyping of this variant was verified in the whole exome sequencing data. In a meta-analysis of both cohorts, the replicated BMP7 and PROX1-AS1 variants (rs75161997 and rs1891059, respectively) and a variant in NCRNA00251 (rs141059755) met the genome-wide significance threshold of <5x10-8 (Figure 1). In a meta-analysis of both cohorts, replicated SNPs with meta-analysis P<1 x10-5 showed enrichment in enhancers active in mesenchymal stem cells. Pathway analysis of genes linked to top SNPs (meta-analysis P <0.001) demonstrated enrichment in glutamate receptor signaling and adipogenesis pathways.Conclusions: Variants in genes important to bone and fat differentiation from mesenchymal stem cells were associated with osteonecrosis in children less than 10 years old. The importance of variants in glutamate receptor signaling in children less than 10 also confirms the findings of a recently completed GWAS of osteonecrosis in AALL0232 (Blood 2014 124:367; 2014) including patients of all ages and in which osteonecrosis occurred primarily in older children. These data provide new insights into osteonecrosis with implications for patients of all ages. [Display omitted] DisclosuresHunger:Sigma Tau: Consultancy; Jazz Pharmaceuticals: Consultancy; Merck: Equity Ownership; Spectrum Pharmaceuticals: Consultancy.

Evaluation of GWAS candidate susceptibility loci for uterine leiomyoma in the multi-ethnic NIEHS uterine fibroid study.

We evaluated the association of 56 candidate SNPs identified in two published genome-wide association studies (GWAS) of uterine leiomyoma (UL), or fibroids, with the risk and tumor size in the multi-ethnic uterine fibroid study (NIEHS-UFS). The selected SNPs were genotyped in 916 premenopausal women of African American (AA) and European American (EA) descents and their association with the outcomes was evaluated in race-stratified models and in meta-analysis of risk in NIEHS-UFS and discovery and replication GWAS in the Japanese population. We report moderate associations of variant rs4954368 in THSD7B (thrombospondin, type I, domain containing 7B) with tumor size in pooled analysis of AA and EA samples (P = 0.004), and at TNRC6B (trinucleotide repeat containing 6B) variants rs138039 and rs139909 in EA (P = 0.001 and 0.008, respectively). The most significant associations with risk in meta-analysis were observed at TNRC6B variants rs739182 (P = 3.7 × 10−10) and rs2072858 (P = 1.1 × 10−9) and were stronger than those reported in the discovery GWAS (P = 2.01 × 10−8 and 2.58 × 10−8, respectively). The present study failed to replicate the associations reported for CCDC57 and FASN in a discovery GWAS in populations of European descent. Consistent with previous replication studies in the Right From the Start Study (RFTS) and the BioVU DNA repository, we provide independent evidence for association of TNRC6B with both risk and size of UL. The present study is the first to report a replicated association of THSD7B with UL, albeit with tumor size and not with risk.

Converging Evidence for Epistasis between ANK3 and Potassium Channel Gene KCNQ2 in Bipolar Disorder.

Genome-wide association studies (GWAS) have implicated ANK3 as a susceptibility gene for bipolar disorder (BP). We examined whether epistasis with ANK3 may contribute to the “missing heritability” in BP. We first identified via the STRING database 14 genes encoding proteins with prior biological evidence that they interact molecularly with ANK3. We then tested for statistical evidence of interactions between SNPs in these genes in association with BP in a discovery GWAS dataset and two replication GWAS datasets. The most significant interaction in the discovery GWAS was between SNPs in ANK3 and KCNQ2 (p = 3.18 × 10−8). A total of 31 pair-wise interactions involving combinations between two SNPs from KCNQ2 and 16 different SNPs in ANK3 were significant after permutation. Of these, 28 pair-wise interactions were significant in the first replication GWAS. None were significant in the second replication GWAS, but the two SNPs from KCNQ2 were found to significantly interact with five other SNPs in ANK3, suggesting possible allelic heterogeneity. KCNQ2 forms homo- and hetero-meric complexes with KCNQ3 that constitute voltage-gated potassium channels in neurons. ANK3 is an adaptor protein that, through its interaction with KCNQ2 and KCNQ3, directs the localization of this channel in the axon initial segment (AIS). At the AIS, the KCNQ2/3 complex gives rise to the M-current, which stabilizes the neuronal resting potential and inhibits repetitive firing of action potentials. Thus, these channels act as “dampening” components and prevent neuronal hyperactivity. The interactions between ANK3 and KCNQ2 merit further investigation, and if confirmed, may motivate a new line of research into a novel therapeutic target for BP.

Identification of novel candidate genes for Alzheimer's disease by autozygosity mapping using genome wide SNP data.

Alzheimer's disease (AD) is highly prevalent in Wadi Ara despite the low frequency of apolipoprotein E ε4 in this genetically isolated Arab community in northern Israel. We hypothesized that the reduced genetic variability in combination with increased homozygosity would facilitate identification of genetic variants that contribute to the high rate of AD in this community. AD cases (n = 124) and controls (n = 142) from Wadi Ara were genotyped for a genome-wide set of more than 300,000 single nucleotides polymorphisms (SNPs) which were used to calculate measures of population stratification and inbreeding, and to identify regions of autozygosity. Although a high degree of relatedness was evident in both AD cases and controls, controls were significantly more related and contained more autozygous regions than AD cases (p = 0.004). Eight autozygous regions on seven different chromosomes were more frequent in controls than the AD cases, and 116 SNPs in these regions, primarily on chromosomes 2, 6, and 9, were nominally associated with AD. The association with rs3130283 in AGPAT1 on chromosome 6 was observed in a meta-analysis of seven genome-wide association study (GWAS) datasets. Analysis of the full Wadi Ara GWAS dataset revealed 220 SNP associations with AD at p ≤ 10⁻⁵, and seven of these were confirmed in the replication GWAS datasets (p < 0.05). The unique population structure of Wadi Ara enhanced efforts to identify genetic variants that might partially explain the high prevalence of AD in the region. Several of these variants show modest evidence for association in other Caucasian populations.

Genome-Wide Association Study Identifies Multiple Genetic Loci for Activated Partial Thromboplastin Time and Prothrombin Time

AbstractAbstract 4222 Background:Activated partial thromboplastin time (aPTT) and prothrombin time (PT) are commonly used to screen for coagulation factor deficiencies. Shorter aPTT is also a risk marker for incident and recurrent venous thromboembolism (VTE). Genetic factors influencing aPTT and PT are not well understood. So far only one genome-wide association study (GWAS) has been reported for aPTT in 1,477 participants and none for PT. Methods:We conducted a GWAS for the aPTT in 9,240 European Americans (EAs) from the Atherosclerosis Risk in Communities (ARIC) study and for PT in 1,221 EAs from the Genetic Study of Three Population Microisolates in South Tyrol (MICROS). Replication was assessed by in silico analysis in MICROS (aPTT, n=1,215) and the Lothian Birth Cohorts (LBC) (LBC1936 (aPTT and PT, n=925-989), LBC1921 (aPTT, n=445)), and by de novo genotyping in the Caerphilly study (aPTT, n=882). Subjects on anticoagulants were excluded. Genotyping was conducted with the Affymetrix single nucleotide polymorphism (SNP) array 6.0 or Illumina HumanHap300/370 and imputed to ∼2.5 million HapMap SNPs. SNPs with imputation quality score < 0.3 or minor allele frequencies ≤1% were excluded from data analysis. The imputed SNP dosages were analyzed in linear regression adjusted for age, sex, and field center, where applicable. Results:Five loci were associated with aPTT at genome-wide significance of p<5×10-8 that have not been previously reported: F5 (1q23, top SNP rs9332701, missense, β (effect size associated with one copy increase in minor allele)=0.54, p=3.7×10-8), F11 (4q35, rs1593, intronic, β =0.54 and 0.36, p=1.25×10-17 and 2.0×10-8 before and after adjusting for known variants in F11), NSD1 (5q35.2-q35.3, rs11950938, intronic, β =1.00 and 1.21, p=1.11×10-15 and 1.5×10-22 before and after adjusting for known variants in F12 of the same region), C6orf10 (6p21.3, rs2050190, intronic, β =-0.25, p=1.3×10-8), and ABO (9q34.1-q34.2, rs8176704, intronic, tag for A2 group, β =0.19 and 0.89, p=0.02 and 4.3×10-24 before and after adjusting for O blood group). Three of the five loci replicated in at least one replication sample and the other two were directionally consistent in 3 replication samples. Furthermore, meta-analysis pooling the discovery and replication GWAS samples yielded two additional independent loci at chromosomes 1q23 (F5, best SNP rs6028, coding-synonymous, β =0.23, p=5.97×10-9) and 15q25.3 (AGBL1, rs2469184, intronic, β =0.16, p= 4.24×10-8), with consistent associations across studies. The signals at the F5 region were not due to FV Leiden (rs6025, p=0.46 in ARIC). We also confirmed previously reported loci in KNG1, HRG, F11, F12, and ABO (O group). For PT, novel associations from two gene regions reached genome-wide significance in MICROS: F7 (top SNP rs3093253, within an exon but not translated, β =-5.44, p=8.2×10-19) and PROCR (rs6060244, near PROCR, β =4.11, p=3.5×10-9). Both loci replicated in LBC1936. Conclusions:In this large GWAS, six of the nine novel loci associated with the aPTT and PT are coagulation-related and the other three (NSD1, C6orf10, and AGBL1) are new candidate genes not directly involved in coagulation. The C6orf10 gene interacts with TNF-a at the transcription level and was previously associated with inflammatory diseases. These findings may be relevant to the prevention and treatment of coagulation disorders including VTE. Disclosures:No relevant conflicts of interest to declare.