Intergenic Single Nucleotide Polymorphisms Research Articles

Genetics of facial telangiectasia in the Rotterdam Study: a genome-wide association study and candidate gene approach.

The severity of facial telangiectasia or red veins is associated with many lifestyle factors. However, the genetic predisposition remains unclear. We performed a genome-wide association study (GWAS) on facial telangiectasia in the Rotterdam Study (RS) and tested for replication in two independent cohorts. Additionally, a candidate gene approach with known pigmentation genes was performed. Facial telangiectasia were extracted from standardized facial photographs (collected from 2010-2013) of 2842 northwestern European participants (median age 66.9, 56.8% female) from the RS. Our GWAS top hits (P-value <10-6 ) were tested for replication in 460 elderly women of the SALIA cohort and in 576 additional men and women of the RS. Associations of top single nucleotide polymorphisms (SNPs) with expression quantitative trait loci (eQTL) in various tissues were reviewed (GTEx database) alongside phenotype associations in the UK biobank database. SNP-based associations between known pigmentation genes and facial telangiectasia were tested. Conditional analysis on skin colour was additionally performed. Our most significant GWAS signal was rs4417318 (P-value 5.38*10-7 ), an intergenic SNP on chromosome 12 mapping to the SLC16A7 gene. Other suggestive SNPs tagged genes ZNF211, ZSCAN4, ICOS and KCNN3; SNP eQTLs and phenotype associations tagged links to the vascular system. However, the top signals did not pass significance in the two replication cohorts. The pigmentation genes KIAA0930, SLCA45A2 and MC1R, were significantly associated with telangiectasia in a candidate gene approach but not independently of skin colour. In this GWAS on telangiectasia in a northwestern European population, no genome-wide significant SNPs were found, although suggestive signals indicate genes involved in the vascular system might be involved in telangiectasia. Significantly associated pigmentation genes underline the link between skin colour and telangiectasia.

Identification of Genetic Susceptibility Factors Associated with Canine Gastric Dilatation-Volvulus.

Canine gastric dilatation-volvulus (GDV) is a common life-threatening condition occurring primarily in large and giant breeds with a 3.9% to 36.7% lifetime risk. The genetic correlates of GDV have not previously been systematically explored. We undertook an inter-breed genome-wide association analysis (GWAS) of 253 dogs from ten breeds including 106 healthy dogs and 147 dogs with at least one GDV episode. SNP array genotyping followed by imputation was conducted on 241 samples to identify GDV-associated single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs). A subset of 33 dogs (15 healthy dogs and 18 GDV patients from the three most represented breeds) was characterized by whole genome sequencing (WGS). After genome-wide Bonferroni correction, we identified a significant putatively protective intergenic SNP (rs851737064) across all breeds. The signal was most significant in Collies, German Shorthaired Pointers, and Great Danes. Subsequent focused analysis across these three breeds identified 12 significant additional putatively protective or deleterious SNPs. Notable significant SNPs included those occurring in genes involved in gastric tone and motility including VHL, NALCN, and PRKCZ. These data provide important new clues to canine GDV risk factors and facilitate generation of hypotheses regarding the genetic and molecular underpinnings this syndrome.

Effect of plasma polyunsaturated fatty acid levels on leukocyte telomere lengths in the Singaporean Chinese population

BackgroundShorter telomere length (TL) has been associated with poor health behaviors, increased risks of chronic diseases and early mortality. Excessive shortening of telomere is a marker of accelerated aging and can be influenced by oxidative stress and nutritional deficiency. Plasma n6:n3 polyunsaturated fatty acid (PUFA) ratio may impact cell aging. Increased dietary intake of marine n-3 PUFA is associated with reduced telomere attrition. However, the effect of plasma PUFA on leukocyte telomere length (LTL) and its interaction with genetic variants are not well established.MethodsA nested coronary artery disease (CAD) case-control study comprising 711 cases and 638 controls was conducted within the Singapore Chinese Health Study (SCHS). Samples genotyped with the Illumina ZhongHua-8 array. Plasma n-3 and n-6 PUFA were quantified using mass spectrometry (MS). LTL was measured with quantitative PCR method. Linear regression was used to test the association between PUFA and LTL. The interaction between plasma PUFAs and genetic variants was assessed by introducing an additional term (PUFA×genetic variant) in the regression model. Analysis was carried out in cases and controls separately and subsequently meta-analyzed using the inverse-variance weighted method. We further assessed the association of PUFA and LTL with CAD risk by Cox Proportional-Hazards model and whether the effect of PUFA on CAD was mediated through LTL by using structural equation modeling.ResultsHigher n6:n3 ratio was significantly associated with shorter LTL (p = 0.018) and increased CAD risk (p = 0.005). These associations were mainly driven by elevated plasma total n-3 PUFAs, especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) (p < 0.05). There was a statistically significant interaction for an intergenic single nucleotide polymorphism (SNP) rs529143 with plasma total n-3 PUFA and DHA on LTL beyond the genome-wide threshold (p < 5 × 10− 8). Mediation analysis showed that PUFA and LTL affected CAD risk independently.ConclusionsHigher plasma n6:n3 PUFA ratio, and lower EPA and DHA n-3 PUFAs were associated with shorter LTL and increased CAD risk in this Chinese population. Furthermore, genetic variants may modify the effect of PUFAs on LTL. PUFA and LTL had independent effect on CAD risk in our study population.

Effects of germline DHFR and FPGS variants on methotrexate metabolism and relapse of leukemia

AbstractMethotrexate (MTX) during maintenance therapy is essential for curing acute lymphoblastic leukemia (ALL), but dosing strategies aiming at adequate treatment intensity are challenged by interindividual differences in drug disposition. To evaluate genetic factors associated with MTX metabolism, we performed a genome-wide association study in 447 ALL cases from the Nordic Society for Pediatric Haematology and Oncology ALL2008 study, validating results in an independent set of 196 patients. The intergenic single-nucleotide polymorphism rs1382539, located in a regulatory element of DHFR, was associated with increased levels of short-chain MTX polyglutamates (P = 1.1 × 10−8) related to suppression of enhancer activity, whereas rs35789560 in FPGS (p.R466C, P = 5.6 × 10−9) was associated with decreased levels of long-chain MTX polyglutamates through reduced catalytic activity. Furthermore, the FPGS variant was linked with increased relapse risk (P = .044). These findings show a genetic basis for interpatient variability in MTX response and could be used to improve future dosing algorithms.

Abstract B15: Bladder cancer susceptibility polymorphisms and mortality from non-muscle and muscle-invasive bladder cancer

Abstract Introduction: Genome-wide association studies (GWAS) have identified several common germline single-nucleotide polymorphisms (SNPs) associated with increased risk of bladder cancer. Little is known about whether these variants are also associated with overall and bladder cancer-specific mortality. We examined the association between 13 GWAS-identified bladder cancer risk SNPs and overall and bladder cancer-specific survival in 316 bladder cancer cases recruited as part of a population-based case-control study. Methods: Residents of New Hampshire with primary bladder cancer diagnosed between 2002-2004 were identified from the New Hampshire State Cancer Registry. Medical history and lifestyle factors were collected via in-person interviews at time of enrollment. DNA was isolated from peripheral blood or buccal specimens and genotyping was performed using the Illumina Human610-Quad BeadChip. Date and cause of death were ascertained from the National Death Index with follow-up through December 31, 2013. Non-muscle invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC) were examined separately. We used Cox proportional hazards models to estimate adjusted hazard ratios (HR) and 95% confidence intervals (CI) for overall and bladder cancer-specific survival, assuming a log-additive genetic model. HR estimates for MIBC individuals were adjusted for age at diagnosis, sex, smoking status, American Joint Committee on Cancer stage, initial treatment (including extent of resection, cystectomy, and use of chemotherapy or radiation), and three principal components for genetic ancestry. HR estimates for NMIBC were additionally adjusted for 2004 World Health Organization/International Society of Urologic Pathologists classification. An alpha of 0.05 was used to determine statistical significance. Results: Among 43 participants with MIBC, 30 deaths occurred over a median follow-up of 6.4 years, including 19 from bladder cancer. Among 273 participants with NMIBC, 94 deaths occurred over a median follow-up of 10.3 years, including 23 from bladder cancer. The risk allele [A] of enhancer-associated intergenic SNP rs710521 near TP63 was associated with poorer overall survival after MIBC diagnosis (HR=3.21, 95% CI=1.26-8.16). The risk allele [C] of synonymous SNP rs10936599 of MYNN/TERC was associated with better overall survival after NMIBC diagnosis (HR=0.66, 95% CI=0.46-0.94). No associations with bladder cancer-specific survival were identified. Conclusions: Common bladder cancer susceptibility variants rs710521 and rs10936599 may be associated with overall survival after diagnosis of MIBC and NMIBC, respectively. Citation Format: Reno C. Leeming, Michael S. Zens, John D. Seigne, Brock C. Christensen, Diane Gilbert-Diamond, Margaret R. Karagas, Michael N. Passarelli. Bladder cancer susceptibility polymorphisms and mortality from non-muscle and muscle-invasive bladder cancer [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2019 May 18-21; Denver, CO. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(15_Suppl):Abstract nr B15.

Genome-wide screen to identify genetic loci associated with cognitive decline in late-life depression.

This study sought to conduct a comprehensive search for genetic risk of cognitive decline in the context of geriatric depression. A genome-wide association study (GWAS) analysis in the Neurocognitive Outcomes of Depression in the Elderly (NCODE) study. Longitudinal, naturalistic follow-up study. Older depressed adults, both outpatients and inpatients, receiving care at an academic medical center. The Consortium to Establish a Registry for Alzheimer's Disease (CERAD) neuropsychological battery was administered to the study participants at baseline and a minimum of twice within a subsequent 3-year period in order to measure cognitive decline. A GWAS analysis was conducted to identify genetic variation that is associated with baseline and change in the CERAD Total Score (CERAD-TS) in NCODE. The GWAS of baseline CERAD-TS revealed a significant association with an intergenic single-nucleotide polymorphism (SNP) on chromosome 6, rs17662598, that surpassed adjustment for multiple testing (p = 3.7 × 10-7; false discovery rate q = 0.0371). For each additional G allele, average baseline CERAD-TS decreased by 8.656 points. The most significant SNP that lies within a gene was rs11666579 in SLC27A1 (p = 1.1 × 10-5). Each additional copy of the G allele was associated with an average decrease of baseline CERAD-TS of 4.829 points. SLC27A1 is involved with processing docosahexaenoic acid (DHA), an endogenous neuroprotective compound in the brain. Decreased levels of DHA have been associated with the development of Alzheimer's disease. The most significant SNP associated with CERAD-TS decline over time was rs73240021 in GRXCR1 (p = 1.1 × 10-6), a gene previously linked with deafness. However, none of the associations within genes survived adjustment for multiple testing. Our GWAS of cognitive function and decline among individuals with late-life depression (LLD) has identified promising candidate genes that, upon replication in other cohorts of LLD, may be potential biomarkers for cognitive decline and suggests DHA supplementation as a possible therapy of interest.

2071-P: C2CD4A, Pancreatic Beta-Cell Function, and Type 2 Diabetes Susceptibility

To this day, intergenic single nucleotide polymorphisms (SNPs) identified from genome-wide association studies (GWAS) are still a geneticist’s nightmare, because these SNPs are steps away from revealing the disease causative gene, relevant tissue(s), and mechanism of action. For instance, fine mapping and validation of genes causing β cell failure from susceptibility loci identified in type 2 diabetes GWAS poses a significant challenge. The VPS13C-C2CD4A-C2CD4B locus on chromosome 15 confers diabetes susceptibility in every ethnic group studied to date. However, the causative gene is unknown. FoxO1, a transcription factor, is involved in the pathogenesis of β cell dysfunction, but its link to human diabetes GWAS has not been explored. To this end, we generated a genome-wide map of FoxO1 super-enhancers in chemically identified β cells using 2-photon live-cell imaging to monitor FoxO1 localization. Super-enhancers mark genes underpinning β cell identity, and comparing super-enhancers in mouse and human bridge the mouse data to human relevance. When parsed against human super-enhancers and GWAS-derived diabetes susceptibility alleles, this map revealed a conserved super-enhancer in C2CD4A, a gene encoding a β cell/stomach-enriched nuclear protein of unknown function. Genetic ablation of C2cd4a in β cells of mice phenocopied the metabolic abnormalities of human carriers of C2CD4A-linked polymorphisms, resulting in impaired insulin secretion during glucose tolerance tests as well as hyperglycemic clamps. C2cd4a regulates glycolytic genes, and notably represses key β cell “disallowed” genes, such as lactate dehydrogenase A, Aldolase B, and monocarboxylate transporter. We propose that C2CD4A is a transcriptional coregulator of the glycolytic pathway whose dysfunction accounts for the diabetes susceptibility associated with the chromosome 15 GWAS locus. Disclosure T. Kuo: None. D. Accili: Board Member; Self; Lilly Diabetes. Other Relationship; Self; Forkhead BioTherapeutics Inc. Funding National Institutes of Health (K01DK114372)

Association between metformin medication, genetic variation and prostate cancer risk.

The relationship between metformin use and prostate cancer risk remains controversial. Genetic variation in metformin metabolism pathways appears to modify metformin glycemic control and the protective association with some cancers. However, no studies to date have examined this pharmacogenetic interaction and prostate cancer chemoprevention. Clinical data and germline DNA were collected from our prostate biopsy database between 1996 and 2014. In addition to a genome-wide association study (GWAS), 27 single nucleotide polymorphisms (SNPs) implicated in metformin metabolism were included on a custom SNP array. Associations between metformin use and risk of high-grade (Grade Group ≥ 2) and overall prostate cancer were explored using a case-control design. Interaction between the candidate/GWAS SNPs and the metformin-cancer association was explored using a case-only design. Among 3481 men, 132 (4%) were taking metformin at diagnosis. Metformin users were older, more likely non-Caucasian, and had higher body mass index, Gleason score, and number of positive cores. Overall, 2061 (59%) were diagnosed with prostate cancer, of which 922 (45%) were high-grade. After adjusting for baseline characteristics, metformin use was associated with higher risk of high-grade prostate cancer (OR = 1.76, 95% CI 1.1-2.9, p = 0.02) and overall prostate cancer (OR = 1.77, 95% CI 1.1-2.9, p = 0.03). None of the 27 candidate SNPs in metformin metabolic pathways had significant interaction with the metformin-cancer association. Among the GWAS SNPs, one SNP (rs149137006) had genome-wide significant interaction with metformin for high-grade prostate cancer, and another, rs115071742, for overall prostate cancer. They were intronic and intergenic SNPs, respectively, with largely uncharacterized roles in prostate cancer chemoprevention. In our cohort, metformin use was associated with increased risk of being diagnosed with prostate cancer. While SNPs involved in metformin metabolism did not have modifying effects on the association with disease risk, one intronic and one intergenic SNP from the GWAS study did, and these require further study.

Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis

Homoplastic mutations are mutations independently occurring in different clades of an organism. The homoplastic changes may be a result of convergence evolution due to selective pressures. Reports on the analysis of homoplastic mutations in Mycobacterium tuberculosis have been limited. Here we characterized the distribution of homoplastic single nucleotide polymorphisms (SNPs) among genomes of 1,170 clinical M. tuberculosis isolates. They were present in all functional categories of genes, with pe/ppe gene family having the highest ratio of homoplastic SNPs compared to the total SNPs identified in the same functional category. Among the pe/ppe genes, the homoplastic SNPs were common in a relatively small number of homologous genes, including ppe18, the protein of which is a component of a promising candidate vaccine, M72/AS01E. The homoplastic SNPs in ppe18 were particularly common among M. tuberculosis Lineage 1 isolates, suggesting the need for caution in extrapolating the results of the vaccine trial to the population where L1 is endemic in Asia. As expected, homoplastic SNPs strongly associated with drug resistance. Most of these mutations are already well known. However, a number of novel mutations associated with streptomycin resistance were identified, which warrants further investigation. A SNP in the intergenic region upstream of Rv0079 (DATIN) was experimentally shown to increase transcriptional activity of the downstream gene, suggesting that intergenic homoplastic SNPs should have effects on the physiology of the bacterial cells. Our study highlights the potential of homoplastic mutations to produce phenotypic changes. Under selective pressure and during interaction with the host, homoplastic mutations may confer advantages to M. tuberculosis and deserve further characterization.

Association of SNP-SNP Interactions of Surfactant Protein Genes with Pediatric Acute Respiratory Failure.

The hallmarks of pediatric acute respiratory failure (ARF) are dysregulated inflammation and surfactant dysfunction. The objective is to study association of surfactant protein (SP) genes’ single nucleotide polymorphisms (SNPs) with ARF and its morbidity: pulmonary dysfunction at discharge (PDAD), employing a single-, two-, and three-SNP interaction model. We enrolled 468 newborn controls and 248 children aged ≤ 24 months with ARF; 86 developed PDAD. Using quantitative genetic principles, we tested the association of SP genes SNPs with ARF and PDAD. We observed a dominant effect of rs4715 of the SFTPC on ARF risk. In a three-SNP model, we found (a) 34 significant interactions among SNPs of SFTPA1, SFTPA2, and SFTPC associated with ARF (p = 0.000000002–0.05); 15 and 19 of those interactions were associated with increased and decreased risk for ARF, respectively; (b) intergenic SNP–SNP interactions of both hydrophobic and hydrophilic SP genes associated with PDAD (p = 0.00002–0.03). The majority of intra- and intergenic interactions associated with ARF involve the SFTPA2 SNPs, whereas most of the intra- and intergenic interactions associated with PDAD are of SFTPA1 SNPs. We also observed a dominant effect of haplotypes GG of SFTPA1 associated with increased and AA of SFTPC associated with decreased ARF risk (p = 0.02). To the best of our knowledge, this is the first study showing an association of complex interactions of SP genes with ARF and PDAD. Our data indicate that SP genes polymorphisms may contribute to ARF pathogenesis and subsequent PDAD and/or may serve as markers for disease susceptibility in healthy children.

Obesity status modifies the association between rs7556897T>C in the intergenic region SLC19A3-CCL20 and blood pressure in French children.

Background Growing evidence reports an association between inflammatory markers, obesity and blood pressure (BP). Specifically, the intergenic single nucleotide polymorphism (SNP) rs7556897T > C (MAF = 0.34) located between SLC19A3 and the CCL20 was shown to be associated with chronic inflammatory diseases. In addition, CCL20 expression was found increased in pancreatic islets of obese rodents and human pancreatic β cells under the influence of inflammation. In this study, we hypothesized that SNP rs7556897 could affect BP levels, thus providing a link between inflammation, BP and obesity. Methods BP was measured under supine position with a manual sphygmomanometer; values reported were the means of three readings. We analyzed rs7556897 in 577 normal weight and 689 obese French children. Using real-time polymerase chain reaction (PCR), we quantified CCL20 and SLC19A3 expression in adipose tissue and peripheral blood mononuclear cells (PBMCs) of normal weight and overweight children. Results The rs7556897C allele was negatively associated with diastolic BP in normal weight children (β = -0.012 ± 0.004, p = 0.006) but positively associated in obese children (β = 2.178 ± 0.71, p = 0.002). A significant interaction between rs7556897T > C and the obesity status (obese or normal weight) was detected (β = 3.49, p = 9.79 × 10-5) for BP in a combined population analysis. CCL20 mRNA was only expressed in the adipose tissue of overweight children, and its expression levels were 10.7× higher in PBMCs of overweight children than normal weight children. Finally, CCL20 mRNA levels were positively associated with rs7556897T > C in PBMCs of 58 normal weight children (β = 0.43, p = 0.002). SLC19A3 was not expressed in PBMCs, and in adipose tissue, it showed same levels of expression in normal weight and overweight children. The gene expression results may highlight a specific involvement of CCL20 via communicating obesity/inflammation pathways that regulate BP. Conclusions Childhood obesity reverses the effect of rs7556897T > C on diastolic BP, possibly via the modulation of CCL20 expression levels.

An Intergenic rs9275596 Polymorphism on Chr. 6p21 Is Associated with Multiple Sclerosis in Latvians.

Background and objectives: Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system, leading to demyelination of neurons and potentially debilitating physical and mental symptoms. The disease is more prevalent in women than in men. The major histocompatibility complex (MHC) region has been identified as a major genetic determinant for autoimmune diseases, and its role in some neurological disorders including MS was evaluated. An intergenic single-nucleotide polymorphism (SNP), rs9275596, located between the HLA-DQB1 and HLA-DQA2 genes, is in significant association with various autoimmune diseases according to genome-wide association studies (GWASs). A cumulative effect of this SNP with other polymorphisms from this region was revealed. The aim of the study was to verify the data on rs9275596 association in multiple sclerosis in a case/control study of the Latvian population and to evaluate eventual functional significance of allele substitutions. Materials and Methods: rs9275596 (chr6:32713854; GRCh38.p12) was genotyped in 273 MS patients and 208 controls on main and sex-specific associations. Eventual functional significance of allele substitutions was evaluated in silico using publicly available tools. Results: The rs9275596 rare alleles were identified as a disease susceptibility factor in association with the MS main group and in affected females (p < 0.001 and p < 0.01, respectively). Risk factor genotypes with rare alleles included were associated with the MS common cohort (p < 0.002) and female cohort (odds ratio, OR = 2.24) and were identified as disease susceptible in males (OR = 2.41). It was shown that structural changes of rs9275596 affect the secondary structure of DNA. Functional significance of allele substitutions was evaluated on the eventual sequence affinity to transcription factors (TFs) and splicing signals similarity. A possible impact of the particular polymorphisms on the transcription and splicing efficiency is discussed. Conclusions: Our results suggest susceptibility of rs9275596 to multiple sclerosis in Latvians.

Development of powdery mildew race 5-specific SNP markers in Cucumis melo L. using whole-genome resequencing

Melon (Cucumis melo L.), belonging to the Cucurbitaceae family, is cultivated worldwide and is highly valued for its fruit quality. However, this important crop is negatively affected by several races of powdery mildew (PM) fungus, Podosphaera xanthii. Hence, exploration of PM race-specific resistant markers would be an effective strategy to develop race-specific melon cultivars. Young leaves from four melon genotypes, including susceptible SCNU1154 and race-specific-resistant Edisto47, PMR5, and MR1 lines, were sequenced by next-generation sequencing, specifically whole-genome resequencing (WGR), to detect race-specific single nucleotide polymorphism (SNP) markers. Including putative resistance gene (R-gene) SNPs, 168, 83, and 122 race 5-specific SNPs with the exact variation were identified on PM-related chromosome 2, 5, and 12, respectively, for distinguishing race-specific lines by comparing the WGR data in the C. melo genome. Based on proximity to the PM resistance quantitative trait loci (QTLs) in physical maps, 43, 37, and 48 SNPs were screened on chromosome 2, 5, and 12, respectively. Using a derived cleaved amplified polymorphic sequence (dCAPS) method, polymorphisms were only found in three SNPs (SNPR5_119, SNPR5_120, and SNPR5_121) out of 48 against race 5 on chromosome 12. Among these three, a putative R-gene, an NBS-LRR-type SNP, SNPR5_119, displayed similar genotypic and phenotypic variation to race 5-specific susceptible (SCNU1154, PMR45, WMR29, and Edisto47) and resistant (PI414723, PMR5, and MR1) lines in C. melo except for PI124112. Importantly, two other intergenic SNPs, SNPR5_120 and SNPR5_121, showed genotypic and phenotypic variation between susceptible and resistant lines tested. High-resolution melting (HRM) analysis was used to further validate the same expression patterns of SNPR5_120 as a dCAPS method in all lines tested. Therefore, the identified PM race 5-specific candidate markers described here might be useful for a marker-assisted selection breeding program in C. melo.

Statistical methods for testing X chromosome variant associations: application to sex-specific characteristics of bipolar disorder

BackgroundBipolar disorder (BD) affects both sexes, but important sex differences exist with respect to its symptoms and comorbidities. For example, rapid cycling (RC) is more prevalent in females, and alcohol use disorder (AUD) is more prevalent in males. We hypothesize that X chromosome variants may be associated with sex-specific characteristics of BD. Few studies have explored the role of the X chromosome in BD, which is complicated by X chromosome inactivation (XCI). This process achieves “dosage compensation” for many X chromosome genes by silencing one of the two copies in females, and most statistical methods either ignore that XCI occurs or falsely assume that one copy is inactivated at all loci. We introduce new statistical methods that do not make these assumptions.MethodsWe investigated this hypothesis in 1001 BD patients from the Genetic Association Information Network (GAIN) and 957 BD patients from the Mayo Clinic Bipolar Disorder Biobank. We examined the association of over 14,000 X chromosome single nucleotide polymorphisms (SNPs) with sex-associated BD traits using two statistical approaches that account for whether a SNP may be undergoing or escaping XCI. In the “XCI-informed approach,” we fit a sex-adjusted logistic regression model assuming additive genetic effects where we coded the SNP either assuming one copy is expressed or two copies are expressed based on prior knowledge about which regions are inactivated. In the “XCI-robust approach,” we fit a logistic regression model with sex, SNP, and SNP-sex interaction effects that is flexible to whether the region is inactivated or escaping XCI.ResultsUsing the “XCI-informed approach,” which considers only the main effect of SNP and does not allow the SNP effect to differ by sex, no significant associations were identified for any of the phenotypes. Using the “XCI-robust approach,” intergenic SNP rs5932307 was associated with BD (P = 8.3 × 10−8), with a stronger effect in females (odds ratio in males (ORM) = 1.13, odds ratio in females for a change of two allele copies (ORW2) = 3.86).ConclusionX chromosome association studies should employ methods which account for its unique biology. Future work is needed to validate the identified associations with BD, to formally assess the performance of both approaches under different true genetic architectures, and to apply these approaches to study sex differences in other conditions.

Genome-wide association study identifies SIAH3 locus influencing the rate of ventricular enlargement in non-demented elders.

Ventricular enlargement occurs in several neurodegenerative and psychiatric diseases. A large genome-wide association study (GWAS) has identified seven loci associated with ventricular volume. The rate of ventricular enlargement increased in the progression of disease from normal cognition to dementia. Here, we aimed to use the rate of ventricular enlargement as an endophenotype for the development and progression of neurodegenerative diseases to discover more common genetic variants. We performed a GWAS of the rate of ventricular enlargement using 507 nondemented non-Hispanic white participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. Linear regression model was used to identify the association of the rate of ventricular enlargement with single nucleotide polymorphisms (SNPs) in PLINK software. The associations of genome-wide significant SNPs with other four phenotypes were further discussed. Two SNPs (rs11620312, P = 4.04×10−8; rs79174114, P = 4.28×10−8) within SIAH3 gene in linkage disequilibrium (LD) reached genome-wide significance for association with increased rate of ventricular enlargement. Some intergenic SNPs and SNPs within NKAIN2, TBC1D2, GALNT18, ABCC1 and SRCIN1 genes were identified as potential candidates. SIAH3 rs11620312-C carriers were associated with poor cognition and brain hypometabolism longitudinally. Our findings indicated that SIAH3 gene may have potential influence on the pathogenesis of neurodegenerative diseases.

Functional impact of a cellular Long non-coding RNA on CCR5 expression and HIV infection

Abstract An intergenic single nucleotide polymorphism (rs1015164 A/G) showed genome-wide significant association with HIV outcomes in previously published meta-analyses. We found that rs1015164 marks expression levels of an antisense long non-coding RNA, which we termed CCR5AS. CCR5AS interferes with the interaction between an RNA binding protein, RALY and the untranslated region of CCR5, and thus enhances CCR5 expression. Inhibition of CCR5AS decreased CCR5 mRNA as well as surface expression levels and reduced in vitro infection of CCR5-dependent HIV. Our data reveal a previously unknown mechanism by which a variation in a long non-coding RNA region affects HIV infection.

SA75 - ASSOCIATION OF SUICIDE MARKERS WITH COMPULSIVE SYMPTOMS IN HEALTHY SUBJECTS

Background Suicide is one of the leading causes of death worldwide. A complex interplay between various risk factors is assumed to ultimately trigger a suicide attempt. Among those, genetic variations and personality traits seem to be the most relevant predictors. Results from a genome-wide association study we participated in (Galfalvy et al. 2015) point to several variations associated with the condition. In order to elucidate their underlying function a closer look on the influence on personality traits as one of the main predictors seemed feasible. Among others, stressful life events have been known to increase the risk of suicidal behavior. Therefore, we investigated whether 23 susceptibility markers associated with suicidal behavior also affect obsessive- compulsive behavior (as a personality trait prone to show a high risk of coping problems under stress) in healthy individuals. Methods Unrelated healthy volunteers of German descent were screened for an absence of any psychiatric disorder in themselves or their first degree relatives. Obsessive and compulsive symptoms were elevated using the Maudsley Obsessive Compulsive Inventory (MOCI). Finally, 2104 subjects (52% female) were enrolled in the study. Genotype data was obtained using chip technology and imputation. After stringent quality controls 23 Single Nucleotide Polymorphisms (SNPs) were analyzed using an additive linear regression model. Benjamini-Hochberg procedure was used to correct for multiple testing. Results In females, significant associations with the MOCI total score were identified for two intergenic SNPs, localized near BRINP3 (associated with coronary heart disease and aggressive periodontitis) and LOC647132 (a processed pseudogene which is associated with antibody response to smallpox vaccine), both involved in inflammation processes. In males, significant associations could be detected for seven SNPs localized in the TBX20 gene linked to migration and development of brainstem motor neurons, cardiac development and multiple cardiac functions and pathologies. Discussion These results indicate a sex specific overlap of the genetic make-up between suicidality and obsessive-compulsive behavior, thereby emphasizing the relevance of personality traits for suicidal behavior. Further research approaches are necessary in order to replicate these findings and also to identify the underlying functional relevance of the associated variants.

Abstract 17134: Variation Within a Left Ventricle-Specific Hand1 Enhancer Impairs Gata Transcription Factor Binding and Disrupts Ventricular Conduction System Development

The ventricular conduction system (VCS), composed of the His bundle, the left and right bundle branches, and the Purkinje fiber network, rapidly propagates electrical impulses through the ventricles to coordinate chamber contraction. An ECG depicts VCS-mediated ventricular depolarization as the QRS interval. Disorders of the VCS may manifest as arrhythmias, and are associated with increased risk of sudden cardiac death and overall mortality. The genetic and developmental mechanisms underlying VCS dysfunction are poorly understood. Genome-wide association studies have identified multiple single nucleotide polymorphisms (SNPs) associated with VCS arrhythmias. A majority of these SNPs occur outside of coding domains, within intergenic or intronic regions. We hypothesize that such pathogenic SNPs may impact VCS development and function by altering the expression of critical genes. Two intergenic SNPs associated with QRS prolongation occur near the bHLH cardiac transcription factor HAND1 . We have identified a left ventricle (LV) enhancer, located between these two SNPs, that is necessary and sufficient for LV cis -regulatory activity. Two evolutionarily conserved GATA transcription factor consensus-binding sites within this enhancer are bound by GATA4 and necessary for cis -regulatory activity. CRISPR-mediated deletion of this enhancer dramatically reduced Hand1 expression solely within the LV. Mice homozygous for this deleted enhancer displayed dysregulated LV gene expression, morphologically abnormal His bundles and left bundle branches, and a VCS phenotype consistent with right bundle branch block. Genome-wide association analyses of human patients with QRS prolongation revealed additional, linked SNPs, one of which overlaps with a critical GATA cis -regulatory element within the LV-specific Hand1 enhancer. This SNP disrupts GATA4 binding. Ongoing studies of mice that genetically mimic these minor SNP variants will assess reduced Hand1 expression and impaired VCS function. We conclude that a LV-specific Hand1 enhancer is necessary for VCS development and a SNP associated with QRS prolongation directly influences GATA4 binding to a critical cis -regulatory element within this enhancer.

Synergistic triad epistasis of epigenetic H3K27me modifier genes, EZH2, KDM6A, and KDM6B, in gastric cancer susceptibility

For an epigenetic regulation of human genome, three enzymes write or erase methylation of lysine-27 residue on histone H3 (H3K27me). This methylation is catalyzed by EZH2 (KMT6A) methyltransferase and reversed by KDM6A (UTX) or KDM6B (JMJD3) demethylase. Genetic cancer risk association has been reported on EZH2, but not on KDM6A or KDM6B yet. A total of 23 tag single-nucleotide polymorphisms (SNPs) of the three genes were genotyped in 2349 Korean participants, and their gastric cancer risk associations and epistases were statistically examined by comparing the SNP genotypes of 1100 gastric cancer patients and 1249 healthy controls. All three genes are individually associated with gastric cancer susceptibility, as evident with the genotypes of KDM6A SNP rs5952279 (P = 0.00010) and rs144974719 (P = 0.00024), KDM6B rs78633955 (P = 0.0019) and rs11657063 (P = 0.0036), and EZH2 rs67648693 (P = 0.0028) and rs1061037 (P = 0.023). Furthermore, when odds ratio of interaction (ORint) is calculated for all intergenic SNP pairs, synergistic epistasis is evident among the three genes. Specifically, the interaction is synergistic between EZH2 rs58579167 and KDM6A rs5952279 (ORint = 3.2, P = 0.00066), between KDM6A rs2230018 and KDM6B rs78633955 (ORint = 1.9, P = 0.044), and between KDM6B rs78633955 and EZH2 rs73158295 (ORint = 1.7, P = 0.00030). These inter-SNP interactions together constitute a synergistic triad epistasis of ring-type topology. All three H3K27me modifier genes are individually associated with gastric cancer susceptibility with synergistic triad interaction. Not only two enzymes with the same function (KDM6A and KDM6B), but also those with opposite functions (EZH2 versus KDM6A or KDM6B) synergistically affect H3K27me consequences such as gastric cancer susceptibility.

A genome-wide association and admixture mapping study of bronchodilator drug response in African Americans with asthma.

Short-acting β2-adrenergic receptor agonists (SABAs) are the most commonly prescribed asthma medications worldwide. Response to SABAs is measured as bronchodilator drug response (BDR), which varies among racial/ethnic groups in the U.S1, 2. However, the genetic variation that contributes to BDR is largely undefined in African Americans with asthma3. To identify genetic variants that may contribute to differences in BDR in African Americans with asthma, we performed a genome-wide association study (GWAS) of BDR in 949 African American children with asthma, genotyped with the Axiom World Array 4 (Affymetrix, Santa Clara, CA) followed by imputation using 1000 Genomes phase III genotypes. We used linear regression models adjusting for age, sex, body mass index (BMI) and genetic ancestry to test for an association between BDR and genotype at single nucleotide polymorphisms (SNPs). To increase power and distinguish between shared vs. population-specific associations with BDR in children with asthma, we performed a meta-analysis across 949 African Americans and 1,830 Latinos (Total=2,779). Lastly, we performed genome-wide admixture mapping to identify regions whereby local African or European ancestry is associated with BDR in African Americans. We identified a population-specific association with an intergenic SNP on chromosome 9q21 that was significantly associated with BDR (rs73650726, p=7.69×10−9). A trans-ethnic meta-analysis across African Americans and Latinos identified three additional SNPs within the intron of PRKG1 that were significantly associated with BDR (rs7903366, rs7070958, and rs7081864, p≤5×10−8). Our results failed to replicate in three additional populations of 416 Latinos and 1,615 African Americans. Our findings indicate that both population specific and shared genetic variation contributes to differences in BDR in minority children with asthma, and that the genetic underpinnings of BDR may differ between racial/ethnic groups.