SNPs In Linkage Disequilibrium Research Articles

From GWAS to functional variants: ARL14 cis-regulatory variants are associated with severe malaria.

GWAS have identified several non-functional tagSNPs associated with severe malaria. We hypothesized that causal SNPs could play a significant role in severe malaria by altering promoter or enhancer activity. Here, we sought to identify such regulatory SNPs. SNPs in linkage disequilibrium with tagSNPs associated with severe malaria were identified and were further annotated using FUMA. Then, SNPs were prioritized using IW-scoring method to identify regulatory ones. Gene reporter assays were performed to assess the regulatory effect of a region containing candidates. The association between SNPs and severe malaria was assessed using logistic regression models in a Senegalese cohort. Among 418 SNPs, the best candidates were rs116525449 and rs79644959, which were in full disequilibrium between them, and located within the ARL14 promoter. Our gene reporter assay results revealed that the region containing the SNPs exhibited cell-specific promoter or enhancer activity, while the SNPs influenced promoter activity. We detected an association between severe malaria and those two SNPs using the overdominance model and we replicated the association of severe malaria with the tagSNP rs116423146. We suggest that these SNPs regulate ARL14 expression in immune cells and the presentation of antigens to T lymphocytes, thus influencing severe malaria development.

O-251 LIN28B gene expression is downregulated in spermatozoa of oligozoospermic men and associates with genetic variants previously linked to pubertal onset

Abstract Study question Is there an association between genetic polymorphisms in LIN28B with LIN28B expression and semen quality in spermatozoa from oligozoospermic men? Summary answer LIN28B is downregulated in spermatozoa of oligozoospermic men and explains 39% of sperm count variability. One SNP (rs314280) was associated with low LIN28B mRNA expression. What is known already Large-scale genomic studies have identified genetic variants in or near LIN28B to be robustly associated with pubertal traits such as age at menarche and age at voice break. The LIN28 family of genes are known to control cell division, growth and differentiation. The LIN28B orthologue is exclusively expressed at high levels in the testis and placenta; however, we have limited knowledge about the role of LIN28B in relationship to testicular function. Interestingly, other studies have showed that later onset of puberty is associated with poor semen quality, suggesting that pubertal development may influence adult testicular function. Study design, size, duration Twenty-nine oligozoospermic (cases) and fifty-four men with normal sperm concentration (controls) were recruited from patients seeking andrological work-up for male/couple infertility at a University Hospital. Subjects with abnormal karyotype, Yq-microdeletions, varicocele GIII-IV, hypogonadotropic hypogonadism, seminal infection, diabetes, BMI>35, excessive consumption of alcohol/drugs, testicular cancer, chemotherapy/radiotherapy were excluded. Semen samples were obtained for analysis (WHO, 2010) and sperm isolation by density gradient (PureSperm40®). Peripheral blood samples were analysed for reproductive hormones and used for DNA extraction. Participants/materials, setting, methods LIN28B and GAPDH-S mRNA abundance were measured by qRT-PCR (2-ΔCT method) in RNA isolated from purified sperm using SYBR® MasterMix (Takyon). Five SNPs in linkage disequilibrium (rs7759938, rs395962, rs314268, rs314277 and rs314280) were genotyped (TaqMan™ SNP Genotyping Assay). Statistical differences between groups were assessed by Mann-Whitney test and genetic association was analysed using “SNPassoc” package in R. Values are showed as median, Q1-Q3. Main results and the role of chance Cases and controls had similar age and BMI but as expected sperm concentration, morphology and vitality were differed between groups (9.9, 4.9-13.1 vs 82.8, 46.0-146.5 mill/ml; 1, 1-2 vs 3, 1-4% normal forms and 83%, 76-89 vs 86%, 82-90, respectively) (p < 0.05). No differences were observed in progressive motility, semen volume and days of abstinence. FSH and LH serum levels were higher in cases compared with controls (4.6, 2.6-7.8 vs 3.2, 2.5-4 mIU/ml and 4.2, 2.9-5.2 vs 3.1, 2.1-4.2 mIU/ml, respectively; p = 0.019 and p = 0.017). Relative expression of LIN28B was significantly diminished in cases compared with controls (0.0034, 0.0015-0.0103 vs 0.0446, 0.0122-0.1026; p < 0.001), while expression of the internal housekeeping control GAPDH-S was similar between groups. Linear regression model showed significant association of sperm concentration and total sperm count with LIN28B relative expression adjusted by age, abstinence time, % progressive motility and % normal morphology (beta=0.408, R2=0.241, p < 0.001 and beta=0.461, R2=0.393, p < 0.001). LIN28B rs314280 was associated with mRNA expression in the dominant model (p = 0.025) and two other SNPs (rs7759938, rs314268) showed the same trend (p = 0.09). Men with at least one minor allele of these 3 SNPs had a lower LIN28B mRNA abundance (p = 0.006; p = 0.07; p = 0.055). Limitations, reasons for caution Genotype frequency comparisons between cases and control were not conducted because of the small sample size. A larger cohort will be studied to address this assumption and association of genotypes with parameters of semen quality. Wider implications of the findings To our knowledge this study represents the first report on LIN28B expression and human testicular function. The significant direct association of LIN28B mRNA expression with sperm concentration suggests that LIN28B may be involved in spermatogonial proliferation. Trial registration number not applicable

Abstract 162: Multiancestry GWAS And Functional Genomics Analysis Of HNF1A Locus To Define Novel Pathogenic Mechanism For Ischemic Stroke

Background: Ischemic stroke (IS) disproportionately affects populations of African descent due to genetic predispositions. A multiancestry Genome-wide Association Study (GWAS) identified non-coding SNPs in HNF1A locus highly associated with IS, exclusively to African ancestry. Analysis of this ancestry-specific genomic architecture can reveal novel pathogenic mechanism for IS. Methods: The IS-associated SNPs in HNF1A locus were analysed. Electrophoretic Mobility Shift Assay (EMSA) identified functional SNPs (fSNP) that allele-specifically bind to nuclear proteins from human vascular endothelial cells (ECs). Proteomics identified transcription factors (TFs) binding to fSNPs. siRNA knockdown was conducted to determine the function of TFs on HNF1A expression. The effects of stroke-like condition hypoxia on TFs and HNF1A were studied in various vascular cells. Results: GWAS-revealed non-coding tag SNP rs55931441 in HNF1A locus was associated with IS risk exclusively in African population. The frequency of risk allele A of tag SNP was 3.8% in African but absent in other races, supporting the causative role of this locus in determining the genetic risk of IS. EMSA revealed no nuclear protein binding to rs55931441, suggesting it is unlikely an fSNP with TF-mediated regulation on target genes. We expanded the screening to 7 haplotype SNPs in linkage disequilibrium with R 2 >0.8. Among them, rs144534697 presented with allele-imbalanced nuclear protein binding. Proteomics revealed ILF3, a vascular function-related TF, binds preferentially to non-risk allele C. Functional studies showed that ILF3 regulates HNF1A as a repressor. Less binding of ILF3 to risk allele A results in a loss of repression to HNF1A and augments its function as vascular pathogenic factor. Furthermore, vascular stressor hypoxia downregulated ILF3 and upregulated HNF1A in vascular ECs, smooth muscle cells and fibroblasts. Conclusion: Our functional genomics analysis of disease-associated SNPs identified by multiancestry GWAS offers a novel mechanistic approach for diseases with ancestry prominence. The newly identified ILF3-HNF1A pathway may serve as a general mechanistic explanation for the pathogenesis of IS, given their response to vascular stressor hypoxia.

Abstract B003: Causal effect of type II diabetes on prostate cancer in the East Asian population: A two-sample Mendelian randomization study

Abstract Type II diabetes, a metabolic disease, and prostate cancer are prevalent diseases in the elderly population. Whether type II diabetes has an association with prostate cancer has not been thoroughly studied. Limited research has been performed from a perspective of genetic level, especially among non-European populations. In this study, we used a two-sample Mendelian randomization (MR) approach to evaluate the causal effect between type II diabetes as an exposure and prostate cancer as an outcome in the East Asian population. For type II diabetes, we used 174 risk loci identified in a meta-analysis of 77,418 cases and 356,122 controls from 23 East Asian Genome-wide Association Studies (GWAS). For prostate cancer, summary statistics were extracted from the GWAS from BioBank Japan using 5,408 cases and 103,939 controls. We performed two-sample Mendelian randomization with the inverse variance weighted method while using MR Egger and weighted median methods as sensitivity analysis. For type II diabetes risk SNPs not directly present in the prostate cancer GWAS, we identified proxy SNPs in linkage disequilibrium (LD, r2 > 0.8) using the 1000 genome project. We used P-value < 0.05 as a threshold to determine statistical significance. Based on 152 out of 174 SNPs of type II diabetes in the East Asian population, we found that type II diabetes had a significant negative causal effect on prostate cancer [Odds Ratio (OR) = 0.76, 95% Confidence Interval (CI): 0.76 - 0.89, P = 2.26 x 10-6]. Results from sensitivity analysis using other weighting methods provided similar results. In conclusion, we observed an inverse relationship between type II diabetes and prostate cancer among the East Asian population. Patients with diabetes may have a lower risk of prostate cancer due to a reduced level of insulin and testosterone. To validate this association, further research is needed on those hormones and prostate cancer risk at the metabolic level. Citation Format: Zhongyi Guo. Causal effect of type II diabetes on prostate cancer in the East Asian population: A two-sample Mendelian randomization study [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr B003.

CFDP1 is a neuroblastoma susceptibility gene that regulates transcription factors of the noradrenergic cell identity.

Pleiotropic genetic factors (e.g., DNA polymorphisms) may be involved in the initiation of neuroblastoma (NB) and coronary artery disease (CAD) given their common origin from defects in neural crest development. To discover novel NB susceptibility genes, we conducted a three-stage survey including a meta-analysis of NB and CAD genome-wide association data, prioritization of NB causal variants, and validation in an independent cohort of affected individuals-control subjects. The lead SNP, rs13337397 at the 16q23.1 locus, associated with both diseases in the meta-analysis and with NB in the validation study. All the SNPs in linkage disequilibrium with rs13337397 were annotated using the H3K27ac epigenetic marker of neural crest cells (NCC) and NB cell lines. Indeed, we identified the functional SNP rs13337017, mapping within an enhancer of NCCs and NB cell lines and showing long-range interactions with CFDP1 by Hi-C analysis. Luciferase assays indicated that the risk allele of rs13337017 increased CFDP1 expression in NB cell lines. Of note, CFDP1 high expression associated with unfavorable prognostic markers in an analysis including 498 NB transcriptomes. Moreover, depletion of CFDP1 markedly decreased viability and migration and increased apoptotic rates in NB cell lines. Finally, transcriptome and qPCR analyses revealed that the depletion of CFDP1 may affect noradrenergic neuron differentiation by downregulating master regulators of sympathetic noradrenergic identity, including PHOX2B, HAND2, and GATA3. Our data strongly suggest that CFDP1 acts as oncogene in NB. In addition, we provide evidence that genetic predisposition to NB can be mediated by the alteration of noradrenergic lineage-specific gene expression.

Genotyping of UGT1A1*80 as an Alternative to UGT1A1*28 Genotyping in Spain.

Background: The variant rs34983651 (UGT1A1*28) and its genotyping are used to prevent irinotecan-induced toxicity. Several variants are in close linkage disequilibrium. Our objective was to evaluate the potential correlation of genotyping UGT1A1*80 instead of UGT1A1*28 in different populations. Methods: We studied SNPs in linkage disequilibrium with UGT1A1*28 in several populations and selected rs887829 to develop an inexpensive and rapid genotyping method and compare it with the one we currently use for UGT1A1*28 genotyping. Samples from cancer patients (n = 701) already tested using PCR and electrophoresis prior to treatment with irinotecan for rs34983651 (UGT1A1*28) in a Spanish hospital were genotyped for rs887829 (UGT1A1*80) using real-time PCR with a TaqMan probe. Results: We observed a complete match for both genotypes, except in one sample. This method was 100% efficient in correctly genotyping *28/*28 patients, 99.68% efficient for *1/*28, and 100% efficient for *1/*1. Linkage disequilibrium between populations showed the Iberian population to be the most suitable for the clinical use of UGT1A1*80. This method is less expensive and the time to decision is shorter. Conclusion: Genotyping of rs887829 using the proposed method may be used to substitute genotyping of rs34983651 as a pharmacogenetics test in cancer patients prior to starting irinotecan-based treatments, mainly in the Iberian population. In addition, it is less expensive than other conventional methods and easy to implement, with a shorter time to decision than UGT1A1*28.

Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3.

TNFAIP3/A20 is a prominent autoimmune disease risk locus that is correlated with hypomorphic TNFAIP3 expression and exhibits complex chromatin architecture with over 30 predicted enhancers. This study aimed to functionally characterize an enhancer ∼55 kb upstream of the TNFAIP3 promoter marked by the systemic lupus erythematosus (SLE) risk haplotype index SNP, rs10499197. Allele effects of rs10499197, rs58905141, and rs9494868 were tested by EMSA and/or luciferase reporter assays in immune cell types. Co-immunoprecipitation, ChIP-qPCR, and 3C-qPCR were performed on patient-derived EBV B cells homozygous for the non-risk or SLE risk TNFAIP3 haplotype to assess haplotype-specific effects on transcription factor binding and chromatin regulation at the TNFAIP3 locus. This study found that the TNFAIP3 locus has a complex chromatin regulatory network that spans ∼1M bp from the promoter region of IL20RA to the 3′ untranslated region of TNFAIP3. Functional dissection of the enhancer demonstrated co-dependency of the RelA/p65 and CEBPB binding motifs that, together, increase IL20RA and IFNGR1 expression and decreased TNFAIP3 expression in the context of the TNFAIP3 SLE risk haplotype through dynamic long-range interactions up- and downstream. Examination of SNPs in linkage disequilibrium (D’ = 1.0) with rs10499197 identified rs9494868 as a functional SNP with risk allele-specific increase in nuclear factor binding and enhancer activation in vitro. In summary, this study demonstrates that SNPs carried on the ∼109 kb SLE risk haplotype facilitate hypermorphic IL20RA and IFNGR1 expression, while suppressing TNFAIP3 expression, adding to the mechanistic potency of this critically important locus in autoimmune disease pathology.

Utilising Polygenic Risk Score Analysis for AD to Determine the “Sphere of Influence” of the APOE Isoform SNPs

The APOE gene and particularly the ε4 allele have been a long-established risk factor for Alzheimer’s disease (AD), demonstrating the largest genetic effect size in this complex disease. In light of the odds ratios observed for the risk allele, many studies disregard neighbouring association signals as merely “tagging” this effect. Polygenic risk score (PRS) analyses in this field regularly use low linkage disequilibrium parameters (r2≥0.1) when selecting SNPs for analysis across the genome and remove kilobases of data surrounding the APOE locus, preventing confounding factors influencing their results. This study investigated a 500kb region surrounding the APOE locus, utilising PRS analysis to explore whether additional SNPs in this region could be providing contributory effects to AD predictability. The data presented here suggest that the “sphere of influence” of the APOE isoform SNPs covers a region of around 92kb; SNPs in Linkage Disequilibrium (LD) at r2<0.4 with rs429358 potentially contribute independently to the PRS predictability for AD, and that there are additional independent SNPs in this region that have increased effects in an APOE ε4 negative sample. This study concludes that further consideration is required when selecting LD parameters for PRS analysis and that additional investigation into the region surrounding APOE may yield polymorphisms that may play a pivotal role in the development of AD.

Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes

Key MessageSeveral Fusarium wilt resistance genes were discovered, genetically and physically mapped, and rapidly deployed via marker-assisted selection to develop cultivars resistant toFusarium oxysporumf. sp.fragariae, a devastating soil-borne pathogen of strawberry.Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragariatimesananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen, and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here, we show that resistance to both races is widespread in natural and domesticated populations and that resistance to race 1 is conferred by partially to completely dominant alleles among loci (FW1, FW2, FW3, FW4, and FW5) found on three non-homoeologous chromosomes (1A, 2B, and 6B). The underlying genes have not yet been cloned and functionally characterized; however, plausible candidates were identified that encode pattern recognition receptors or other proteins known to confer gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.

Identification of ATP2B4 Regulatory Element Containing Functional Genetic Variants Associated with Severe Malaria

Genome-wide association studies for severe malaria (SM) have identified 30 genetic variants mostly located in non-coding regions. Here, we aimed to identify potential causal genetic variants located in these loci and demonstrate their functional activity. We systematically investigated the regulatory effect of the SNPs in linkage disequilibrium (LD) with the malaria-associated genetic variants. Annotating and prioritizing genetic variants led to the identification of a regulatory region containing five ATP2B4 SNPs in LD with rs10900585. We found significant associations between SM and rs10900585 and our candidate SNPs (rs11240734, rs1541252, rs1541253, rs1541254, and rs1541255) in a Senegalese population. Then, we demonstrated that both individual SNPs and the combination of SNPs had regulatory effects. Moreover, CRISPR/Cas9-mediated deletion of this region decreased ATP2B4 transcript and protein levels and increased Ca2+ intracellular concentration in the K562 cell line. Our data demonstrate that severe malaria-associated genetic variants alter the expression of ATP2B4 encoding a plasma membrane calcium-transporting ATPase 4 (PMCA4) expressed on red blood cells. Altering the activity of this regulatory element affects the risk of SM, likely through calcium concentration effect on parasitaemia.

Genetic associations with carotid intima-media thickness link to atherosclerosis with sex-specific effects in sub-Saharan Africans

Atherosclerosis precedes the onset of clinical manifestations of cardiovascular diseases (CVDs). We used carotid intima-media thickness (cIMT) to investigate genetic susceptibility to atherosclerosis in 7894 unrelated adults (3963 women, 3931 men; 40 to 60 years) resident in four sub-Saharan African countries. cIMT was measured by ultrasound and genotyping was performed on the H3Africa SNP Array. Two new African-specific genome-wide significant loci for mean-max cIMT, SIRPA (p = 4.7E-08), and FBXL17 (p = 2.5E-08), were identified. Sex-stratified analysis revealed associations with one male-specific locus, SNX29 (p = 6.3E-09), and two female-specific loci, LARP6 (p = 2.4E-09) and PROK1 (p = 1.0E-08). We replicate previous cIMT associations with different lead SNPs in linkage disequilibrium with SNPs primarily identified in European populations. Our study find significant enrichment for genes involved in oestrogen response from female-specific signals. The genes identified show biological relevance to atherosclerosis and/or CVDs, sex-differences and transferability of signals from non-African studies.

A Functional Variant on 9p21.3 Related to Glioma Risk Affects Enhancer Activity and Modulates Expression of CDKN2B-AS1.

Genome‐wide association studies have identified SNPs associated with glioma risk on 9p21.3, but biological mechanisms underlying this association are unknown. We tested the hypothesis that a functional SNP on 9p21.3 affects activity of an enhancer, causing altered expression of nearby genes. We considered all SNPs in linkage disequilibrium with the 9p21.3 sentinel SNP rs634537 that mapped to putative enhancers. An enhancer containing rs1537372 exhibited allele‐specific effects on luciferase activity. Deletion of this enhancer in GBM cell lines correlated with decreased expression of CDKN2B‐AS1. Expression quantitative trait loci analysis using non‐diseased brain samples showed rs1537372 to be a consistently significant eQTL for CDKN2B‐AS1. Additionally, our analysis of Hi‐C data generated in neural progenitor cells showed that the bait region containing rs1537372 interacted with the CDKN2B‐AS1 promoter. These data suggest rs1537372, a SNP at the 9p21.3 risk locus, is a functional variant that modulates expression of CDKN2B‐AS1.

Abstract MP10: A Novel Genetic Locus Influences Microvascular Reactivity To Acute Psychological Stress

Background: Excessive peripheral microvascular constriction during acute psychological stress, measured using peripheral arterial tonometry reflects similar changes in coronary blood flow.The ratio of digital pulse wave amplitude during stress compared to rest (sPAT) is used to estimate the degree of microvascular response to stress. Hypothesis: We hypothesized that genetic factors contribute to the degree of microvascular constriction during mental stress and that excessive vasoconstriction is associated with adverse cardiovascular outcomes. Methods: A total of 580 stable CAD subjects of European and African ancestries from two prospective cohort studies underwent mental stress testing with a standardized public speaking stressor. Digital pulse wave amplitude was continuously measured using PAT and the stress/rest PAT ratio (sPAT) of pulse wave amplitude during mental stress/baseline was calculated. Genotyping was performed using Illumina’s Multi-Ethnic Genotyping Array platform and imputed to the 1000 Genome reference panel. Ethnicity-specific genome-wide association studies (GWAS) of sPAT were conducted using linear regression of additive genetic mode adjusted for age, sex and population stratification in both cohorts. A trans-ethnic meta-analysis integrated the GWAS results from four sub-cohorts. Upon 5-year follow-up, Fine and Gray’s sub-distribution hazard ratios (sHR) were used to examine the association between sPAT ratio (> vs=< median) and the composite endpoint of cardiovascular death, myocardial infarction, revascularization, and hospitalization for heart failure. Results: Mean age was 63±9; 65% male, 35% African American. We identified three SNPs in linkage disequilibrium on chr7:111,666,943 T>C (rs6466396); chr7: 111,668,622 T>G (rs876170); chr7: 111,668,623 T>G (rs876169) that were associated with greater sPAT ratio by means of 0.13, 0.12 and 0.10, ( P = 1.42E-08). The sPAT-associated locus was within DOCK4 gene which encodes Dedicator of Cytokinesis 4, an essential protein for angiogenesis and brain development, and a known locus for obesity. After adjusting for demographic and cardiovascular risk factors, medications, and rate-pressure product change during mental stress, those with low sPAT ratio were at significantly higher risk of adverse outcomes (sHR 1.8 [95% CI 1.1 - 2.8]). Conclusion: We have identified a genetic basis for stress-induced vasomotion. Presence of allele C (rs6466396) is associated with increased vasoconstriction during mental stress, and thus may predispose CAD patients to a higher risk for adverse cardiovascular outcomes with stressful exposure.

Exome-Wide Association Analysis Suggests LRP2BP as a Susceptibility Gene for Endothelial Injury in Systemic Sclerosis in the Han Chinese Population

Genetic factors play a key role in the pathogenesis of autoimmune diseases, whereas the disease-causing variants remain largely unknown. Herein, we performed an exome-wide association study of systemic sclerosis in a Han Chinese population. In the discovery stage, 527 patients with systemic sclerosis and 5,024 controls were recruited and genotyped. In the validation study, an independent sample set of 479 patients and 1,096 controls were examined. In total, we found that four independent signals reached genome-wide significance. Among them, rs7574865 (Pcombined= 3.87× 10-12) located within signal transducer and activator of transcription 4 gene was identified previously using samples of European ancestry. Additionally, another signal including three SNPs in linkage disequilibrium might be unreported susceptibility loci located in the epidermis differentiation complex region. Furthermore, two SNPs located within exon 3 of IGHM (rs45471499, Pcombined= 1.15× 10-9) and upstream of LRP2BP (rs4317244, Pcombined= 4.17× 10-8) were found. Moreover, rs4317244 was identified as an expression quantitative trait locus for LRP2BP that regulates tight junctions, cell cycle, and apoptosis in endothelial cell lines. Collectively, our results revealed three signals associated with systemic sclerosis in Han Chinese and suggested the importance of LRP2BP in systemic sclerosis pathogenesis. Given the limited sample size and discrepancies between previous results and our study, further studies in multiethnic populations are required for verification.

Genetic variant rs2494938 of LRFN2 gene is associated with non-small cell lung cancer risk in North-Indian population.

Various Genome-wide association studies (GWAS) have reported the association of variant rs2494938 with lung cancer. However, genetic association of LRFN2 genetic variation with non-small cell lung cancer (NSCLC) in North Indian population remained unexplored. We conducted a case-control association study using TaqMan-based chemistry in which a total of 619 individuals, 189 NSCLC cases and 430 controls, were genotyped to explore the association of rs2494938 genetic variant of the LRFN2 gene with NSCLC patients from North India. The allele 'G' (risk allele) of the genetic variant rs2494938 was significantly associated with the NSCLC [OR = 1.51 (1.18-1.93 at 95% CI); p value = 0.0009]. Genetic association was also explored by applying different genetic models (Dominant, Additive). These results suggest that rs2494938 polymorphism of the LRFN2 gene is a risk factor in the North Indian populations to develop NSCLC. The LD (Linkage Disequilibrium) plot demonstrates the variant and its LD SNPs (r 2 > 0.8) and the variant has direct regulatory effect, which could affect the overall physiology of the gene. These findings could be used as diagnostic and prognostic markers in clinical studies of lung cancer patients in North Indian population groups. The present study also provides an important evidence on the genetic etiology of NSCLC in North Indian populations and further expounds GWAS findings on the role of LRFN2 in lung cancer risk. This study provides the holistic view about the non-small cell lung cancer in Jammu and Kashmir, North Indian population and it can be a hallmark of cancer if verified on a very large sample size (cohort).

A sequential methodology for the rapid identification and characterization of breast cancer-associated functional SNPs

GWAS cannot identify functional SNPs (fSNP) from disease-associated SNPs in linkage disequilibrium (LD). Here, we report developing three sequential methodologies including Reel-seq (Regulatory element-sequencing) to identify fSNPs in a high-throughput fashion, SDCP-MS (SNP-specific DNA competition pulldown-mass spectrometry) to identify fSNP-bound proteins and AIDP-Wb (allele-imbalanced DNA pulldown-Western blot) to detect allele-specific protein:fSNP binding. We first apply Reel-seq to screen a library containing 4316 breast cancer-associated SNPs and identify 521 candidate fSNPs. As proof of principle, we verify candidate fSNPs on three well-characterized loci: FGFR2, MAP3K1 and BABAM1. Next, using SDCP-MS and AIDP-Wb, we rapidly identify multiple regulatory factors that specifically bind in an allele-imbalanced manner to the fSNPs on the FGFR2 locus. We finally demonstrate that the factors identified by SDCP-MS can regulate risk gene expression. These data suggest that the sequential application of Reel-seq, SDCP-MS, and AIDP-Wb can greatly help to translate large sets of GWAS data into biologically relevant information.

Study of genetic correlation between children's sleep and obesity.

Laboratory and epidemiological studies have shown that short sleep time is associated with obesity. In this study, we conducted a post-GWAS analysis to test genetic correlation between children's sleep and obesity due to linkage disequilibrium (LD) SNPs, shared genes and pathways. Our analysis showed that genetic heritability was 0.14 (p-value = 0.0005) and 0.41 (p-value = 1.18E-24) for children's sleep and obesity, respectively, but genetic correlation due to LD SNPs was insignificant. Gene associations at children's GWAS were measured based on SNP associations and ranked by their uniform score (U-score). After adjusting for gene size, measured as the number of independent SNPs, children's sleep and obesity GWAS had significant gene correlation (r = 0.23). Pathway enrichment analysis showed that "Suz12 target genes" was the significant pathway for both children's sleep and obesity; pathways were significantly shared among top enriched pathways with an OR of 8.1-59.4; and significant correlation coefficient of pathway U-score was r = 0.36. Analysis of sleep time and obesity GWAS variants for all ages in the NHGRI-EBI GWAS Catalog also presented significant pathway correlation (r = 0.30). The "PAX3-FOXO1 target genes" was the significant pathway for all-age obesity phenotype and ranked as the second top associated pathway for all-age sleep time. Our study suggested that genetic correlation of children's sleep time and obesity is attributed to genes with pleiotropy effects and common pathway regulations that may contain only weak SNP associations.

4277 Functional consequences of the juvenile idiopathic arthritis risk variant at 1q24.3

OBJECTIVES/GOALS: Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatologic disease childhood and a cause of pain and potential disability. JIA has a strong genetic component and no known cure. The goal of this study is to evaluate allele-dependent effects of a novel JIA risk variant at 1q24.3. METHODS/STUDY POPULATION: JIA patients meeting criteria for the two most common disease subtypes (oligoarticular and RF neg polyarthritis) were genotyped using the Immunochip, an Illumina array with dense coverage of the HLA region and 186 other loci previously reported in autoimmune diseases. Phase I association findings (Hinks, 2013) and Phase II analysis (unpublished) of an expanded cohort (4,271 JIA and 14,390 controls) identified new risk loci, including rs78037977 at 1q24.3. We prioritized rs78037977 and predicted possible impacted mechanisms based on Bayesian predictions of attributable risk, the surrounding chromatin landscape, and transcription factor binding data. A luciferase reporter assay was used to assess allele-dependent enhancer activity. RESULTS/ANTICIPATED RESULTS: rs78037977 is located between FASLG and TNFSF18 at chromosome 1q24.3 is associated with JIA (p = 6.3x10−09), and explains 94% of the posterior probability at this locus; no other SNPs in linkage disequilibrium (r2>0.6). The chromatin landscape around rs78037977 contains H3K4Me1 and H3K27Ac marks, which are indicative of enhancer activity. Further, >160 transcription factors have chromatin immunoprecipitation followed by sequencing (ChIP-seq) peaks overlapping rs78037977 in various cellular contexts. In luciferase reporter assays, the region around rs78037977 containing the reference A allele had ~2-fold increased enhancer activity compared to the non-reference allele. DISCUSSION/SIGNIFICANCE OF IMPACT: This work provides in vitro evidence to support allele-dependent enhancer activity of a novel JIA-risk variant at 1q24.3. Our ongoing work investigates the effect of the DNA-containing region of rs78037977 on gene expression and differential transcription factor binding at rs78037977.

Brain MRI Phenotypes Associated with Polymorphisms at or near the MAPT (Microtubule Associated Protein Tau) and COASY (Coenzyme A Synthase) Genes

Abstract Objectives Impaired metal homeostasis in the brain has been reported in neurodegenerative diseases such as Alzheimer's Disease and Parkinson's Disease and can be detected using magnetic resonance imaging (MRI). Many factors, including genetics, affect brain metal accumulation and the risk of neurodegeneration or premature brain aging. Our objective is to uncover independent association signals at chromosome 17 associated with susceptibility-weighted MRI (swMRI) intensities in the caudate and putamen. Methods Conditional and joint association analysis by GCTA-COJO was performed on the summary statistics dataset from a genome-wide association study (GWAS) on brain swMRI phenotypes from 7778 healthy adults of European descent aged 40–69 years from the UK BioBank. Independent association signals (single nucleotide polymorphisms or SNPs) found by GCTA-COJO were grouped further by SNPclip to identify additional candidate SNPs in high linkage disequilibrium (LD) (R2 > 0.8, P < 5.0 × 10–8) with the independent lead/index SNP at each signal. Correlations were performed to show the similarity of impacts (beta) of SNPs significantly associated with MRI differences in both caudate and putamen at one locus. Results There are 2 independent and distinct loci at chromosome 17 associated with MRI differences in the putamen, whereas there is only 1 locus for the caudate. One locus for the putamen is associated with the MAPT H2 haplotype, which has been linked to different neurological diseases. Another locus for both putamen and caudate is located near the genes COASY, NAGLU, and MLX, which are all plausible candidate genes for brain metal accumulation. For one locus identified by GCTA-COJO, there are 19 SNPs in LD (R2 > 0.8) and overlapping in both the caudate and the putamen. The effects (beta) of the SNPs in the putamen and caudate are highly correlated across both brain regions (R2 = 0.907, P-value = 0.000921). Conclusions There is likely 1 signal from the COASY/NAGLU locus on chromosome 17 affecting both brain regions. The signal from the MAPT locus only affects the MRI pattern seen in the putamen. These results connect genetics with brain MRI patterns and an individual's risk for neurodegenerative diseases. Funding Sources This work was funded by grants from the Oklahoma Center for the Advancement of Science & Technology and the Oklahoma Agricultural Experiment Station.

Abstract P141: A Novel GWAS Locus Influences Microvascular Response to Acute Psychological Stress

Background: Excessive peripheral microvascular constriction during acute psychological stress, measured using peripheral arterial tonometry reflects similar changes in coronary blood flow and is a predictor of adverse cardiovascular outcomes. The ratio of digital pulse wave amplitude during stress compared to rest (sPAT) is used to estimate the degree of microvascular response to stress. We sought to determine if genetic factors contribute to the degree of microvascular constriction during mental stress. Methods: A total of 642 post-MI and stable CAD subjects from two prospective cohort studies underwent mental stress testing with a standardized public speaking stressor. Digital pulse wave amplitude was continuously measured using PAT and the stress/rest PAT ratio (sPAT) of pulse wave amplitude during mental stress/baseline was calculated. Genotyping was performed using Illumina’s Multi-Ethnic Genotyping Array (MEGA) platform and imputed to the 1000 Genome reference panel. Race stratified genome-wide association studies (GWAS) of sPAT were conducted using linear regression of additive genetic mode adjusted for age, sex and population stratification in the two cohorts. A trans-ethnic meta-analysis integrated the four sets GWAS results. Results: Mean age was 63±9; 65% male, 35% Black. We identified two SNPs in linkage disequilibrium on chr4:185503564 and chr4:185491706 rs13353812 (with 35% and 28% allele frequency, respectively) that were associated with greater sPAT ratio ( P = 1.42E-08). The mean sPAT ratio during mental stress for subjects with none, one and two AT insertion alleles of SNP chr4:185503564 were 0.67, 0.76 and 0.93, respectively, an average of 12% (P < 0.001), per allele. Results were similar for G insertion alleles of SNP rs13353812. The nearest gene of the sPAT-associated locus is CASP3 which encodes caspase, an essential protein for apoptosis signaling and brain and hematopoietic stem cell development. Conclusion: We have identified a genetic basis for stress-induced vasomotion. Presence of the chr4:185503564 allele is associated with less vasoconstriction during mental stress, and thus may be protective against long term cardiovascular risk. These findings need further exploration.