Suggestive Evidence Of Association Research Articles

Biomarkers for Psychosis: Are We There Yet? Umbrella Review of 1478 Biomarkers.

This umbrella review aims to comprehensively synthesize the evidence of association between peripheral, electrophysiological, neuroimaging, neuropathological, and other biomarkers and diagnosis of psychotic disorders. We selected systematic reviews and meta-analyses of observational studies on diagnostic biomarkers for psychotic disorders, published until February 1, 2018. Data extraction was conducted according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines. Evidence of association between biomarkers and psychotic disorders was classified as convincing, highly suggestive, suggestive, weak, or non-significant, using a standardized classification. Quality analyses used the Assessment of Multiple Systematic Reviews (AMSTAR) tool. The umbrella review included 110 meta-analyses or systematic reviews corresponding to 3892 individual studies, 1478 biomarkers, and 392210 participants. No factor showed a convincing level of evidence. Highly suggestive evidence was observed for transglutaminase autoantibodies levels (odds ratio [OR] = 7.32; 95% CI: 3.36, 15.94), mismatch negativity in auditory event-related potentials (standardized mean difference [SMD] = 0.73; 95% CI: 0.5, 0.96), P300 component latency (SMD = -0.6; 95% CI: -0.83, -0.38), ventricle-brain ratio (SMD = 0.61; 95% CI: 0.5, 0.71), and minor physical anomalies (SMD = 0.99; 95% CI: 0.64, 1.34). Suggestive evidence was observed for folate, malondialdehyde, brain-derived neurotrophic factor, homocysteine, P50 sensory gating (P50 S2/S1 ratio), frontal N-acetyl-aspartate, and high-frequency heart rate variability. Among the remaining biomarkers, weak evidence was found for 626 and a non-significant association for 833 factors. While several biomarkers present highly suggestive or suggestive evidence of association with psychotic disorders, methodological biases, and underpowered studies call for future higher-quality research.

Causal associations of Sjögren’s syndrome with cancers: a two-sample Mendelian randomization study

BackgroundSeveral observational studies have explored the associations between Sjögren’s syndrome (SS) and certain cancers. Nevertheless, the causal relationships remain unclear. Mendelian randomization (MR) method was used to investigate the causality between SS and different types of cancers.MethodsWe conducted the two-sample Mendelian randomization with the public genome-wide association studies (GWASs) summary statistics in European population to evaluate the causality between SS and nine types of cancers. The sample size varies from 1080 to 372,373. The inverse variance weighted (IVW) method was used to estimate the causal effects. A Bonferroni-corrected threshold of P < 0.0031 was considered significant, and P value between 0.0031 and 0.05 was considered to be suggestive of an association. Sensitivity analysis was performed to validate the causality. Moreover, additional analysis was used to assess the associations between SS and well-accepted risk factors of cancers.ResultsAfter correcting the heterogeneity and horizontal pleiotropy, the results indicated that patients with SS were significantly associated with an increased risk of lymphomas (odds ratio [OR] = 1.0010, 95% confidence interval [CI]: 1.0005–1.0015, P = 0.0002) and reduced risks of prostate cancer (OR = 0.9972, 95% CI: 0.9960–0.9985, P = 2.45 × 10−5) and endometrial cancer (OR = 0.9414, 95% CI: 0.9158–0.9676, P = 1.65 × 10−5). Suggestive associations were found in liver and bile duct cancer (OR = 0.9999, 95% CI: 0.9997–1.0000, P = 0.0291) and cancer of urinary tract (OR = 0.9996, 95% CI: 0.9992–1.0000, P = 0.0281). No causal effect of SS on other cancer types was detected. Additional MR analysis indicated that causal effects between SS and cancers were not mediated by the well-accepted risk factors of cancers. No evidence of the causal relationship was observed for cancers on SS.ConclusionsSS had significant causal relationships with lymphomas, prostate cancer, and endometrial cancer, and suggestive evidence of association was found in liver and bile duct cancer and cancer of urinary tract, indicating that SS may play a vital role in the incidence of these malignancies.

X chromosome associations with chronic obstructive pulmonary disease and related phenotypes: an X chromosome-wide association study

BackgroundThe association between genetic variants on the X chromosome to risk of COPD has not been fully explored. We hypothesize that the X chromosome harbors variants important in determining risk of COPD related phenotypes and may drive sex differences in COPD manifestations.MethodsUsing X chromosome data from three COPD-enriched cohorts of adult smokers, we performed X chromosome specific quality control, imputation, and testing for association with COPD case–control status, lung function, and quantitative emphysema. Analyses were performed among all subjects, then stratified by sex, and subsequently combined in meta-analyses.ResultsAmong 10,193 subjects of non-Hispanic white or European ancestry, a variant near TMSB4X, rs5979771, reached genome-wide significance for association with lung function measured by FEV1/FVC (beta 0.020, SE 0.004, p 4.97 × 10–08), with suggestive evidence of association with FEV1 (beta 0.092, SE 0.018, p 3.40 × 10–07). Sex-stratified analyses revealed X chromosome variants that were differentially trending in one sex, with significantly different effect sizes or directions.ConclusionsThis investigation identified loci influencing lung function, COPD, and emphysema in a comprehensive genetic association meta-analysis of X chromosome genetic markers from multiple COPD-related datasets. Sex differences play an important role in the pathobiology of complex lung disease, including X chromosome variants that demonstrate differential effects by sex and variants that may be relevant through escape from X chromosome inactivation. Comprehensive interrogation of the X chromosome to better understand genetic control of COPD and lung function is important to further understanding of disease pathology.Trial registration Genetic Epidemiology of COPD Study (COPDGene) is registered at ClinicalTrials.gov, NCT00608764 (Active since January 28, 2008). Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints Study (ECLIPSE), GlaxoSmithKline study code SCO104960, is registered at ClinicalTrials.gov, NCT00292552 (Active since February 16, 2006). Genetics of COPD in Norway Study (GenKOLS) holds GlaxoSmithKline study code RES11080, Genetics of Chronic Obstructive Lung Disease.

Association of Reported Candidate Monogenic Genes With Lung Cancer Risk

Introduction/BackgroundPublished studies on association of germline monogenic genes and lung cancer risk were inconsistent. Our objective is to assess the validity of reported candidate monogenic genes for their association with lung cancer. Materials and MethodsA systematic review of published papers prior to August 2022 was performed first to identify all genes where germline mutations were associated with lung cancer risk. We then performed a confirmation study in 2,050 lung cancer cases and 198,553 controls in the UK Biobank (UKB). Germline mutations of these genes were identified from sequencing data and annotated using The American College of Medical Genetics criteria. The robust SKAT-O, a gene-based analysis that properly controls for false positives due to unbalanced case-control ratio, was used for association tests adjusting for age at recruitment, gender, and genetic background. ResultsThe systematic review identified 12 genes that were statistically significantly associated with lung cancer risk in at least one study (P < .05), including ATM, BLM, BRCA2, BRIP1, CHEK2, FANCA, FANCD2, MSH6, PMS1, RAD51C, RAD51D, and TP53. When pathogenic/likely pathogenic mutations were aggregated within each gene, the association was confirmed for ATM (P = 4.47E-4) at the study-wise significance level (P < .0042, Bonferroni correction for 12 tests). Suggestive evidence of association was found for 2 other genes, BRCA2 (P = .007) and TP53 (P = .03). Among these 3 genes, the lung cancer risks range from 1.95 (BRCA2) to 5.28 (TP53). ConclusionThis study provides statistical evidence for association of previously reported genes and lung cancer risk and has clinical utility for risk assessment and genetic counseling.

Systematic review of reported association studies of monogenic genes and bladder cancer risk and confirmation analysis in a large population cohort.

To evaluate which of previously reported monogenic genes are associated with increased bladder cancer risk, we reviewed published papers on associations of genes and bladder cancer risk and performed a confirmation study of these genes in a large population-based cohort. A systematic review of published papers prior to June 2022 was performed first to identify all genes where germline mutations were associated with bladder cancer risk. The associations of these candidate genes with bladder cancer risk were then tested among 1695 bladder cancer cases and 186 271 controls in the UK Biobank (UKB). The robust SKAT-O, a gene-based analysis that properly controls for type I error rates due to unbalanced case-control ratio, was used for association tests adjusting for age at recruitment, gender, smoking status, and genetic background. The systematic review identified nine genes that were significantly associated with bladder cancer risk in at least one study (p< 0.05), including MUTYH, MSH2, MSH6, MLH1, ATM, BRCA2, ERCC5, TGFB1 and CHEK2. When pathogenic/likely pathogenic mutations were aggregated within each gene, the association was confirmed for three genes in the UKB at p< 0.0056 (Bonferroni correction for nine tests), including CHEK2, ATM and BRCA2, all also known to be associated with hereditary breast cancer. Suggestive evidence of association was found for two other genes, including MLH1 (p= 0.006) and MSH2 (p= 0.007), both known to be associated with Lynch syndrome. Among these five genes, the bladder cancer risks range from 1.60 (ATM) to 4.88 (MLH1), and mutation carrier rates in cases range from 0.06% (MSH2) to 2.01% (CHEK2). This study provides statistical evidence for association of previously reported genes and bladder cancer risk and has clinical utility for risk assessment and genetic counselling.

A Million Veteran Program GWAS of Alzheimer’s Disease and Related Dementias in African Americans Identifies Multiple Genome‐Wide Significant Dementia Risk Loci

AbstractBackgroundWhile genome wide association studies (GWASs) of Alzheimer’s Disease (AD) in European ancestry cohorts (EUR) have identified &gt;70 potentially independent AD risk loci, progress in non‐European populations has lagged. In this study, data from US Veterans of African ancestry (AFR) from the Million Veteran Program (MVP) biorepository were used to identify genetic factors associated with AD and related dementias (ADRD).MethodUsing the VA electronic medical record, 4,012 AFR ADRD cases (algorithm includes codes for AD and dementias such as vascular dementia) and 18,435 dementia‐free AFR controls were identified for inclusion in the GWAS. A GWAS was also performed using proxy dementia based on survey‐reported AFR participant parental history of AD or other dementia that included 4,385 maternal cases, 2,256 paternal cases, and 45,970 controls. Meta‐analysis of the case control and proxy results for was performed and then subsequently combined with results from a AFR AD GWAS conducted by the Alzheimer Disease Genetics Consortium (ADGC; Kunkle et al., 2021).ResultThe AFR MVP GWAS (case‐control + proxy) yielded genome‐wide significant associations with several loci including APOE (p=2.48x10‐101), ROBO1 (rs11919682, p=1.63x10‐8), and RP11‐340A13.2 (rs148433063, p=8.56x10‐9. The ROBO1 and RP11‐240A13.2 SNPs were not replicated in the ADGC sample (missing or not significant). The meta‐analysis of MVP and ADGC GWAS results (Table 1) additionally identified genome significant SNPs near known AD risk genes TREM2 (rs73427293, p=2.95x10‐9), CD2AP (rs7738720, p=1.14x10‐9), and ABCA7 (rs73505251, p=3.26x10‐10). Comparison of expression of genes near variants with suggestive evidence of association (p&lt;5x10‐7) in the brains of EUR AD cases and controls from Framingham Heart Study, Religious Orders Study/Rush Memory and Aging Project, Mayo‐Mount Sinai Brain Bank, and Boston University Brain Bank (Panitch et al.) identified several differentially expressed genes including EML6.ConclusionThe AFR dementia GWAS presented here is the largest to date. It increased the number of genome wide significant common‐variant dementia loci reported in AFR cohorts from two to six, including genes previously implicated in EUR cohorts. Increasing representation of AFRs is an important priority in genetic studies and may lead to increased insight into AD pathophysiology and reduce health disparities.

Juvenile idiopathic arthritis polygenic risk scores are associated with cardiovascular phenotypes in early adulthood: a phenome-wide association study

BackgroundThere is growing concern about the long-term cardiovascular health of patients with juvenile idiopathic arthritis (JIA). In this study we assessed the association between JIA polygenic risk and cardiovascular phenotypes (cardiovascular risk factors, early atherosclerosis/arteriosclerosis markers, and cardiac structure and function measures) early in life.MethodsJIA polygenic risk scores (PRSs) were constructed for 2,815 participants from the Avon Longitudinal Study of Parents and Children, using the single nucleotide polymorphism (SNP) weights from the most recent JIA genome wide association study. The association between JIA PRSs and cardiovascular phenotypes at age 24 years was assessed using linear and logistic regression. For outcomes with strong evidence of association, further analysis was undertaken to examine how early in life (from age seven onwards) these associations manifest.ResultsThe JIA PRS was associated with diastolic blood pressure (β 0.062, 95% CI 0.026 to 0.099, P = 0.001), insulin (β 0.050, 95% CI 0.011 to 0.090, P = 0.013), insulin resistance index (HOMA2_IR, β 0.054, 95% CI 0.014 to 0.095, P = 0.009), log hsCRP (β 0.053, 95% CI 0.011 to 0.095, P = 0.014), waist circumference (β 0.041, 95% CI 0.007 to 0.075, P = 0.017), fat mass index (β 0.049, 95% CI 0.016 to 0.083, P = 0.004) and body mass index (β 0.046, 95% CI 0.011 to 0.081, P = 0.010). For anthropometric measures and diastolic blood pressure, there was suggestive evidence of association with JIA PRS from age seven years. The findings were consistent across multiple sensitivity analyses.ConclusionsGenetic liability to JIA is associated with multiple cardiovascular risk factors, supporting the hypothesis of increased cardiovascular risk in JIA. Our findings suggest that cardiovascular risk is a core feature of JIA, rather than secondary to the disease activity/treatment, and that cardiovascular risk counselling should form part of patient care.

Genome-wide association study of SNP- and gene-based approaches to identify susceptibility candidates for lupus nephritis in the Han Chinese population.

BackgroundLupus nephritis (LN) is one of the most common and serious complications of systemic lupus erythaematosus (SLE). Genetic factors play important roles in the pathogenesis of LN and could be used to predict who might develop LN. The purpose of this study was to screen for susceptible candidates of LN across the whole genome in the Han Chinese population.Methods592 LN patients and 453 SLE patients without renal damage were genotyped at 492,970 single nucleotide polymorphisms (SNPs) in the genome-wide association study (GWAS). Fifty-six SNPs were selected for replication in an independent cohort of 188 LN and 171 SLE without LN patients. Further quantitative real-time (qRT) PCR was carried out in 6 LN patients and 6 healthy controls. Gene-based analysis was conducted using the versatile gene-based test for GWAS. Subsequently, enrichment and pathway analyses were performed in the DAVID database.ResultsThe GWAS analysis and the following replication research identified 9 SNPs showing suggestive correlation with LN (P<10-4). The most significant SNP was rs12606116 (18p11.32), at P=8.72×10−6. The qRT-PCR results verified the mRNA levels of LINC00470 and ADCYAP1, the closest genes to rs12606116, were significantly lower in LN patients. From the gene-based analysis, 690 genes had suggestive evidence of association (P<0.05), including LINC00470. The enrichment analysis identified the involvement of transforming growth factor beta (TGF-β) signalings in the development of LN. Lower plasma level of TGF-β1 (P<0.05) in LN patients and lower expression of transforming growth factor beta receptor 2 in lupus mice kidney (P<0.05) futher indicate the involvement of TGF-β in LN.ConclusionsOur analyses identified several promising susceptibility candidates involved in LN, and further verification of these candidates was necessary.

Circulating vascular endothelial growth factor and cancer risk: A bidirectional mendelian randomization.

In observational studies, circulating vascular endothelial growth factor (VEGF) has been reported to be associated with certain types of cancer. The purpose of this study was to verify whether there is a causal relationship between circulating VEGF and different types of cancer and the direction of the causal relationship. Summary statistical data were obtained from the corresponding genome-wide association studies (GWASs) to investigate the causal relationship between circulating VEGF and the risk of several cancers, including breast cancer, ovarian cancer, lung cancer, colorectal cancer, anus and anal canal cancer, prostate cancer, esophageal cancer, kidney cancer, bladder cancer, thyroid cancer, malignant neoplasm of the brain and malignant neoplasm of the liver and intrahepatic bile ducts. A two-sample bidirectional Mendelian randomization (MR) analysis and sensitivity tests were used to evaluate the validity of causality. A causal relationship was detected between circulating VEGF and colorectal cancer (OR 1.21, 95% CI 1.11–1.32, p < 0.000) and colon adenocarcinoma (OR 1.245, 95% CI 1.10–1.412, p < 0.000). Suggestive evidence of association was detected in VEGF on malignant neoplasms of the rectum (OR 1.16, 95% CI 1.00–1.34, p = 0.049). No causal relationship was found between circulating VEGF and other types of cancer, nor was there a reverse causal relationship from tumors to VEGF (p > 0.05). Circulating VEGF has a causal relationship with specific types of cancer. Our findings highlight and confirm the importance of circulating VEGF in the prevention and treatment of colorectal cancer.

Connecting Genomics and Proteomics to Identify Protein Biomarkers for Adult and Youth-Onset Type 2 Diabetes: A Two-Sample Mendelian Randomization Study

Type 2 diabetes shows an increasing prevalence in both adults and children. Identification of biomarkers for both youth and adult-onset type 2 diabetes is crucial for development of screening tools or drug targets. In this study, using two-sample Mendelian randomization (MR), we identified 22 circulating proteins causally linked to adult type 2 diabetes and 11 proteins with suggestive evidence for association with youth-onset type 2 diabetes. Among these, colocalization analysis further supported a role in type 2 diabetes for C-type mannose receptor 2 (MR odds ratio [OR] 0.85 [95% CI 0.79-0.92] per genetically predicted SD increase in protein level), MANS domain containing 4 (MR OR 0.90 [95% CI 0.88-0.92]), sodium/potassium-transporting ATPase subunit β2 (MR OR 1.10 [95% CI 1.06-1.15]), endoplasmic reticulum oxidoreductase 1β (MR OR 1.09 [95% CI 1.05-1.14]), spermatogenesis-associated protein 20 (MR OR 1.12 [95% CI 1.06-1.18]), haptoglobin (MR OR 0.96 [95% CI 0.94-0.98]), and α1-3-N-acetylgalactosaminyltransferase and α1-3-galactosyltransferase (MR OR 1.04 [95% CI 1.03-1.05]). Our findings support a causal role in type 2 diabetes for a set of circulating proteins, which represent promising type 2 diabetes drug targets.

Abstract 154: Sex-specific Genome Wide Association Study Of Early-onset Ischemic Stroke

Introduction: Genetic studies of early-onset disease have been an effective strategy to identify novel pathways and drug targets generalizable also to later-onset disease. Few studies have investigated the sex-specific genetic associations with early-onset ischemic stroke even though several features of ischemic stroke differ between males and females. We hypothesized that stratifying the GWAS by sex would reveal novel stroke loci. Methods: We performed a transethnic ischemic stroke GWAS of 3,056 female cases and 4,462 male cases &lt; 60 years-old and 16,192 and 16,048 sex-matched controls, respectively, from the Early Onset Stroke Genetics Consortium. Results: We identified a significant association in women with a locus in close proximity to TMX1 , a transmembrane platelet protein that inhibits platelet function. Additionally, we identified 2 other suggestive (P &lt; 5 x 10 -6 ) loci in females (see Table), i.e., at APOH , which encodes beta2-glycoprotein I, an established GWAS locus for lipoprotein(a), and LRFN2 which has been previously reported to associate with obesity-related measures and type II diabetes. We observed suggestive evidence for association in males with MMP3/MMP12 , a known stroke susceptibility locus. Conclusions: Despite a very modest sample size, sex-specific analyses identified suggestive associations at biologically important novel loci in females and a known stroke locus in males. Further studies of sex-specific associations in both early- and later-onset ischemic stroke are needed.

Abstract WP205: Trans-ethnic Genome-wide Association Studies Meta-analysis Of Large Brain Arterial Diameters Identifies Two Novel Genetic Loci

Introduction: Larger brain arterial diameters, which may be a consequence of connective tissue disorders or hypertension, are associated with mortality, cognitive decline and risk of dementia. Whether there may be genetic determinants of large brain arterial diameters is unknown, but identifying such traits may shed light into possible mechanistic links between large brain arterial diameters and the observed outcomes. Methods: We studied 3654 participants from four ethnically diverse population-based cohorts: The Atherosclerosis Risk in Communities study (n=1565: 74.3% white, 25.7% black), The Northern Manhattan Study (n=1092: 13.8% white, 16.6% black, 69.6% Hispanic), Epidemiology of Dementia in Singapore (n=647: 31.7% Chinese, 35.7% Malay, 32.6% Indian), and Memory Clinic Cohort in Singapore (n=350: 84.9% Chinese, 7.8% Malay, 7.3% Indian). We measured brain arterial diameters for 13 segments and normalized the averaged diameter per participant to obtain global brain arterial diameter as dependent variable. Genome-wide association studies (GWAS) was performed in each study using linear regression, adjusted for sex, age, head size, number of missing arteries and population substructure. Meta-analysis of association statistics was performed using the METAL to generate combined trait-specific effect estimates. We also performed trans-ethnic meta-regression by MR-MEGA to account for the heterogeneity in allelic effect that is correlated with ancestry. Results: Genome-wide significant (P&lt;5x10 -8 ) associations were observed for global brain arterial diameter with three SNPs: rs7921574(P=1.2x10 -8 ) mapping to an intron of CNNM2; rs2075858(P=2.47x10 -8 ) and rs2075857 (P=2.37x10 -8 ) mapping to introns of MUC5B. MR-MEGA analysis showed suggestive evidence of association (P=5.05x10 -8 ) for rs7921574. These loci comprise genes involved in response to magnesium transport, neuronal transmission, hypertension, mucociliary clearance and host defense. Conclusion: Our study reveals two novel risk loci for large brain arterial diameters. We have begun to replicate these associations and to identify functional causal variants in independent studies. Identifying these loci may help us to elucidate underlying disease mechanisms.

Eye disease and mortality, cognition, disease, and modifiable risk factors: an umbrella review of meta-analyses of observational studies.

Globally, 2.2 billion people live with some form of vision impairment and/or eye disease. To date, most systematic reviews examining associations have focused on a single eye disease and there is no systematic evaluation of the relationships between eye diseases and diverse physical and mental health outcomes. Moreover, the strength and reliability of the literature is unclear. We performed an umbrella review of observational studies with meta analyses for any physical and/or mental comorbidities associated with eye disease. For each association, random-effects summary effect size, heterogeneity, small-study effect, excess significance bias and 95% prediction intervals were calculated, and used to grade significant evidence from convincing to weak. 34 studies were included covering 58 outcomes. No outcomes yielded convincing evidence, six outcomes yielded highly suggestive results (cataract positively associated with type 2 diabetes, open-angled glaucoma positively associated with myopia and diabetes, diabetic retinopathy positively associated with cardiovascular disease and cardiovascular mortality, and retinopathy of prematurity positively associated with chorioamnionitis), eight outcomes yielded suggestive results (diabetic retinopathy positively associated with all-cause mortality and depression, diabetic macular oedema positively associated with dyslipidaemia, cataract positively associated with gout, nuclear sclerosis positively associated with all-cause mortality, open angled glaucoma positively associated with migraine and hypertension, and age-related macular degeneration positively associated with diabetes), and 18 outcomes yielded weak evidence. Results show highly suggestive or suggestive evidence for associations between several types of eye diseases with several comorbid outcomes. Practitioners and public health policies should note these findings when developing healthcare policies.

Genome-Wide Association Studies of Conotruncal Heart Defects with Normally Related Great Vessels in the United States.

Conotruncal defects with normally related great vessels (CTD-NRGVs) occur in both patients with and without 22q11.2 deletion syndrome (22q11.2DS), but it is unclear to what extent the genetically complex etiologies of these heart defects may overlap across these two groups, potentially involving variation within and/or outside of the 22q11.2 region. To explore this potential overlap, we conducted genome-wide SNP-level, gene-level, and gene set analyses using common variants, separately in each of five cohorts, including two with 22q11.2DS (N = 1472 total cases) and three without 22q11.2DS (N = 935 total cases). Results from the SNP-level analyses were combined in meta-analyses, and summary statistics from these analyses were also used in gene and gene set analyses. Across all these analyses, no association was significant after correction for multiple comparisons. However, several SNPs, genes, and gene sets with suggestive evidence of association were identified. For common inherited variants, we did not identify strong evidence for shared genomic mechanisms for CTD-NRGVs across individuals with and without 22q11.2 deletions. Nevertheless, several of our top gene-level and gene set results have been linked to cardiogenesis and may represent candidates for future work.

Solitary choroidal granuloma

<h3>Background and objectives</h3> Chronic widespread pain (CWP) is a common disorder affecting ∼10% of the general population and has an estimated heritability of 48–52%. In the first large-scale genome-wide association...

Genetic Variants in the Regulatory T cell-Related Pathway and Colorectal Cancer Prognosis.

High numbers of lymphocytes in tumor tissue, including T regulatory cells (Treg), have been associated with better colorectal cancer survival. Tregs, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and therefore variants in genes related to Treg differentiation and function could be associated with colorectal cancer prognosis. In a prospective German cohort of 3,593 colorectal cancer patients, we assessed the association of 771 single-nucleotide polymorphisms (SNP) in 58 Treg-related genes with overall and colorectal cancer-specific survival using Cox regression models. Effect modification by microsatellite instability (MSI) status was also investigated because tumors with MSI show greater lymphocytic infiltration and have been associated with better prognosis. Replication of significant results was attempted in 2,047 colorectal cancer patients of the International Survival Analysis in Colorectal Cancer Consortium (ISACC). A significant association of the TGFBR3 SNP rs7524066 with more favorable colorectal cancer-specific survival [hazard ratio (HR) per minor allele: 0.83; 95% confidence interval (CI), 0.74-0.94; P value: 0.0033] was replicated in ISACC (HR: 0.82; 95% CI, 0.68-0.98; P value: 0.03). Suggestive evidence for association was found with two IL7 SNPs, rs16906568 and rs7845577. Thirteen SNPs with differential associations with overall survival according to MSI in the discovery analysis were not confirmed. Common genetic variation in the Treg pathway implicating genes such as TGFBR3 and IL7 was shown to be associated with prognosis of colorectal cancer patients. The implicated genes warrant further investigation.

Novel genetic risk factors influence progression of islet autoimmunity to type 1 diabetes

Type 1 diabetes arises from the autoimmune destruction of insulin-producing beta-cells of the pancreas, resulting in dependence on exogenously administered insulin to maintain glucose homeostasis. In this study, our aim was to identify genetic risk factors that contribute to progression from islet autoimmunity to clinical type 1 diabetes. We analyzed 6.8 million variants derived from whole genome sequencing of 160 islet autoantibody positive subjects, including 87 who had progressed to type 1 diabetes. The Cox proportional-hazard model for survival analysis was used to identify genetic variants associated with progression. We identified one novel region, 20p12.1 (TASP1; genome-wide P < 5 × 10–8) and three regions, 1q21.3 (MRPS21–PRPF3), 2p25.2 (NRIR), 3q22.1 (COL6A6), with suggestive evidence of association (P < 8.5 × 10–8) with progression from islet autoimmunity to type 1 diabetes. Once islet autoimmunity is initiated, functional mapping identified two critical pathways, response to viral infections and interferon signaling, as contributing to disease progression. These results provide evidence that genetic pathways involved in progression from islet autoimmunity differ from those pathways identified once disease has been established. These results support the need for further investigation of genetic risk factors that modulate initiation and progression of subclinical disease to inform efforts in development of novel strategies for prediction and intervention of type 1 diabetes.

Genome-Wide Association Study Meta-Analysis of Stroke in 22 000 Individuals of African Descent Identifies Novel Associations With Stroke.

Stroke is a complex disease with multiple genetic and environmental risk factors. Blacks endure a nearly 2-fold greater risk of stroke and are 2× to 3× more likely to die from stroke than European Americans. The COMPASS (Consortium of Minority Population Genome-Wide Association Studies of Stroke) has conducted a genome-wide association meta-analysis of stroke in >22 000 individuals of African ancestry (3734 cases, 18 317 controls) from 13 cohorts. In meta-analyses, we identified one single nucleotide polymorphism (rs55931441) near the HNF1A gene that reached genome-wide significance (P=4.62×10-8) and an additional 29 variants with suggestive evidence of association (P<1×10-6), representing 24 unique loci. For validation, a look-up analysis for a 100 kb region flanking the COMPASS single nucleotide polymorphism was performed in SiGN (Stroke Genetics Network) Europeans, SiGN Hispanics, and METASTROKE (Europeans). Using a stringent Bonferroni correction P value of 2.08×10-3 (0.05/24 unique loci), we were able to validate associations at the HNF1A locus in both SiGN (P=8.18×10-4) and METASTROKE (P=1.72×10-3) European populations. Overall, 16 of 24 loci showed evidence for validation across multiple populations. Previous studies have reported associations between variants in the HNF1A gene and lipids, C-reactive protein, and risk of coronary artery disease and stroke. Suggestive associations with variants in the SFXN4 and TMEM108 genes represent potential novel ischemic stroke loci. These findings represent the most thorough investigation of genetic determinants of stroke in individuals of African descent, to date.

Abstract LB-174: Genome-wide association meta-analysis identifies novel GP2 gene risk variants for pancreatic cancer in the Japanese population

Abstract Pancreatic cancer is one of the most challenging malignancies because of its dismal prognosis, largely unknown etiology, and absence of early detection method. Here we report the results of a meta-analysis of three genome-wide association studies (GWAS) involving 2039 pancreatic cancer cases and 32592 control subjects, which represent the largest sample size in the Japanese population. To complement the SNP-based GWAS, we performed a gene-based GWAS using MAGMA. Given the pleiotropic effects observed for the top variants, we performed a Mendelian randomization (MR) analysis to address the possible causal relationship between type-2 diabetes (T2D) and pancreatic cancer risk, using 82 T2D-related SNPs and 25 hemoglobin A1c (HbA1c)-related SNPs as instrumental variables. We identified 3 (13q12.2, 13q22.1, and 16p12.3) genome-wide significant loci (P&amp;lt;5.0×10-8), as well as 4 loci with suggestive evidence of association (P&amp;lt;1.0×10-6) for pancreatic cancer. Of the identified risk loci, 16p12.3 is novel; the lead SNP maps to rs78193826 (OR=1.46, 95%CI=1.29-1.66, P=4.28×10-9), an Asian-specific, non-synonymous variant of glycoprotein 2 (GP2) predicted to be highly deleterious. Additionally, gene-based GWAS identified a novel gene, KRT8, which is linked to exocrine pancreatic and liver diseases. The identified variants in the GP2 gene exhibited pleiotropic effects on multiple traits, including type 2 diabetes, Hemoglobin A1c (HbA1c) levels, and pancreatic cancer. MR analysis suggested that genetically increased HbA1c levels may be causally associated with increased pancreatic cancer risk. Further fine mapping and functional characterization are required to elucidate the effects of common GP2 gene variants on pancreatic cancer susceptibility. Moreover, our findings highlight genetic susceptibility factors shared between T2D and pancreatic cancer. Citation Format: Yingsong Lin, Masahiro Nakatochi, Hidemi Ito, Yoichiro Kamatani, Hiromi Sakamoto, Hiroshi Ishii, Naoki Sasahira, Makoto Ueno, Naoto Egawa, Mitsuru Mori, Haruhisa Nakao, Yasushi Adachi, Kenji Wakai, Shoichiro Tsugane, Masayuki Yamamoto, Atsushi Shimizu, Takashi Kadowaki, Teruhiko Yoshida, Fumihiko Matsuda, Michiaki Kubo, Shogo Kikuchi, Keitaro Matsuo. Genome-wide association meta-analysis identifies novel GP2 gene risk variants for pancreatic cancer in the Japanese population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-174.

Integrative Approach to Reveal Cell Type Specificity and Gene Candidates for Psoriatic Arthritis Outside the MHC.

We recently conducted a large association analysis to compare the genetic profiles between patients with psoriatic arthritis (PsA) and cutaneous-only psoriasis (PsC). Despite including over 7,000 genotyped patients, only the MHC achieved genome-wide significance. In this study, we hypothesized that appropriate epigenomic elements (H3K27ac marks for active enhancers) can guide us to reveal valuable information about the loci with suggestive evidence of association. Our aim is to investigate these loci and explore how they may lead to the development of PsA. We evaluated this potential by investigating the genes connected with these loci from the perspective of pharmacogenomics and gene expression. We illustrated that markers with suggestive evidence of association outside the MHC region are enriched in H3K27ac marks for osteoblast and chondrogenic differentiated cells; using pharmacogenomics resources, we showed that genes near these markers are targeted by existing drugs used to treat psoriatic arthritis. Significantly, six of the ten suggestive significant loci overlapping the regulatory elements encompass genes differentially expressed (FDR < 5%) in differentiated osteoblasts, including genes participating in the Wnt signaling such as RUNX1, FUT8, and CTNNAL1. Our approach shows that epigenomic information can be used as cost-effective approach to enhance the inferences for GWAS results, especially in situations when few genome-wide significant loci are available. Our results also point the way to more directed investigations comparing the genetics of PsA and PsC.