Genome-Wide Association Study of Gene by Smoking Interactions in Coronary Artery Calcification

Many GWAS have identified novel loci associated with common diseases, but have focused only on main effects of individual genetic variants rather than interactions with environmental factors (GxE). Identification of GxE interactions is particularly important for coronary heart disease (CHD), a major preventable source of morbidity and mortality with strong non-genetic risk factors. Atherosclerosis is the major cause of CHD, and coronary artery calcification (CAC) is directly correlated with quantity of coronary atherosclerotic plaque. In the current study, we tested for genetic variants influencing extent of CAC via interaction with smoking (GxS), by conducting a GxS discovery GWAS in Genetic Epidemiology Network of Arteriopathy (GENOA) sibships (N = 915 European Americans) followed by replication in Framingham Heart Study (FHS) sibships (N = 1025 European Americans). Generalized estimating equations accounted for the correlation within sibships in strata-specific groups of smokers and nonsmokers, as well as GxS interaction. Primary analysis found SNPs that showed suggestive associations (p≤10⁻⁵) in GENOA GWAS, but these index SNPs did not replicate in FHS. However, secondary analysis was able to replicate candidate gene regions in FHS using other SNPs (+/−250 kb of GENOA index SNP). In smoker and nonsmoker groups, replicated genes included TCF7L2 (p = 6.0×10⁻⁵) and WWOX (p = 4.5×10⁻⁶); and TNFRSF8 (p = 7.8×10⁻⁵), respectively. For GxS interactions, replicated genes included TBC1D4 (p = 6.9×10⁻⁵) and ADAMTS9 (P = 7.1×10⁻⁵). Interestingly, these genes are involved in inflammatory pathways mediated by the NF-κB axis. Since smoking is known to induce chronic and systemic inflammation, association of these genes likely reflects roles in CAC development via inflammatory pathways. Furthermore, the NF-κB axis regulates bone remodeling, a key physiological process in CAC development. In conclusion, GxS GWAS has yielded evidence for novel loci that are associated with CAC via interaction with smoking, providing promising new targets for future population-based and functional studies of CAC development.     

Placental Genome and Maternal-Placental Genetic Interactions: A Genome-Wide and Candidate Gene Association Study of Placental Abruption

While available evidence supports the role of genetics in the pathogenesis of placental abruption (PA), PA-related placental genome variations and maternal-placental genetic interactions have not been investigated. Maternal blood and placental samples collected from participants in the Peruvian Abruptio Placentae Epidemiology study were genotyped using Illumina’s Cardio-Metabochip platform. We examined 118,782 genome-wide SNPs and 333 SNPs in 32 candidate genes from mitochondrial biogenesis and oxidative phosphorylation pathways in placental DNA from 280 PA cases and 244 controls. We assessed maternal-placental interactions in the candidate gene SNPS and two imprinted regions (IGF2/H19 and C19MC). Univariate and penalized logistic regression models were fit to estimate odds ratios. We examined the combined effect of multiple SNPs on PA risk using weighted genetic risk scores (WGRS) with repeated ten-fold cross-validations. A multinomial model was used to investigate maternal-placental genetic interactions. In placental genome-wide and candidate gene analyses, no SNP was significant after false discovery rate correction. The top genome-wide association study (GWAS) hits were rs544201, rs1484464 (CTNNA2), rs4149570 (TNFRSF1A) and rs13055470 (ZNRF3) (p-values: 1.11e-05 to 3.54e-05). The top 200 SNPs of the GWAS overrepresented genes involved in cell cycle, growth and proliferation. The top candidate gene hits were rs16949118 (COX10) and rs7609948 (THRB) (p-values: 6.00e-03 and 8.19e-03). Participants in the highest quartile of WGRS based on cross-validations using SNPs selected from the GWAS and candidate gene analyses had a 8.40-fold (95% CI: 5.8–12.56) and a 4.46-fold (95% CI: 2.94–6.72) higher odds of PA compared to participants in the lowest quartile. We found maternal-placental genetic interactions on PA risk for two SNPs in PPARG (chr3∶12313450 and chr3∶12412978) and maternal imprinting effects for multiple SNPs in the C19MC and IGF2/H19 regions. Variations in the placental genome and interactions between maternal-placental genetic variations may contribute to PA risk. Larger studies may help advance our understanding of PA pathogenesis.     

Integrated Meta-QTL and Genome-Wide Association Study Analyses Reveal Candidate Genes for Maize Yield

Journal of Plant Growth Regulation - Crop yield is of a quantitative nature. Two complementary approaches linkage mapping and genome-wide association study (GWAS) have been employed for the...     

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

Genome-wide association studies have been successful in identifying genes involved in polygenic traits and are valuable for crop improvement. Tomato (Solanum lycopersicum) is a major crop and is highly appreciated worldwide for its health value. We used a core collection of 163 tomato accessions composed of S. lycopersicum, S. lycopersicum var cerasiforme, and Solanum pimpinellifolium to map loci controlling variation in fruit metabolites. Fruits were phenotyped for a broad range of metabolites, including amino acids, sugars, and ascorbate. In parallel, the accessions were genotyped with 5,995 single-nucleotide polymorphism markers spread over the whole genome. Genome-wide association analysis was conducted on a large set of metabolic traits that were stable over 2 years using a multilocus mixed model as a general method for mapping complex traits in structured populations and applied to tomato. We detected a total of 44 loci that were significantly associated with a total of 19 traits, including sucrose, ascorbate, malate, and citrate levels. These results not only provide a list of candidate loci to be functionally validated but also a powerful analytical approach for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex traits.In crops, linkage mapping has proved invaluable for detecting quantitative trait loci (QTLs) for traits of interest and to unravel their underlying genetic architecture. This approach is based on the analysis of the segregation of polymorphism between the parental lines and their progeny. However, one of the limitations of this approach is the reduced number of recombination events that occur per generation (for review, see Korte and Farlow, 2013). This leads to extended linkage blocks that reduce the accuracy of the linkage mapping. An alternative to linkage-based mapping studies is to perform linkage disequilibrium (LD) mapping in a population of theoretically unrelated individuals. The ancestral polymorphism segregating through this population (or panel) is far more informative compared with the polymorphism of the parental lines of the linkage mapping population (Mauricio, 2001). LD mapping, also known as genome-wide association (GWA), relies on the natural patterns of LD in the population investigated. The aim of GWA is to reveal trait-associated loci by taking advantage of the level of LD. Depending on the decay of LD, the mapping resolution can be narrowed from a large genomic portion where the level of LD is relatively high to a single marker when the LD level is very low.Following domestication, crops are prone to (1) increased levels of LD, (2) population structure (remote common ancestry of large groups of individuals), and (3) cryptic relatedness (the presence of close relatives in a sample of unrelated individuals; Riedelsheimer et al., 2012). Population structure and cryptic relatedness may lead to false-positive association in GWA studies (Astle and Balding, 2009), but their effect is now relatively well accounted for in mixed linear models (for review, see Sillanpää, 2011; Listgarten et al., 2012). The problem of high LD in GWA scans also must be taken into account: Segura et al. (2012) investigated this difficulty by proposing a multilocus mixed model (MLMM) that handles the confounding effect of background loci that may be present throughout the genome due to LD. This approach revealed multiple loci in LD and associated with sodium concentration in leaves in Arabidopsis (Arabidopsis thaliana), while previous methods failed to identify this complex pattern (Segura et al., 2012).In parallel, the development of cost-effective high-throughput sequencing technologies has identified increasingly dense variant loci necessary to conduct GWA scans, especially in model species such as rice (Oryza sativa) for agronomic traits (Huang et al., 2010) or maize (Zea mays) for drought tolerance (Lu et al., 2010; for review, see Soto-Cerda and Cloutier, 2012). However, GWA is not restricted to model species and is becoming increasingly widespread in nonmodel ones such as sunflower (Helianthus annuus; Mandel et al., 2013) and tomato (Solanum lycopersicum; Xu et al., 2013), where numerous associations have been successfully identified for traits related to plant architecture (branching in the case of sunflower) and fruit quality (e.g. fresh weight in tomato).Tomato is a crop of particular interest, as the fruit are an important source of fiber and nutrients in the human diet and a model for the study of fruit development (Giovannoni, 2001). Over the last two decades, numerous QTLs have been identified for traits such as fresh weight using linkage approaches (Frary et al., 2000; Zhang et al., 2012; Chakrabarti et al., 2013) but also for other fruit-related traits such as fruit ascorbic acid levels (Stevens et al., 2007), sensory and instrumental quality traits (Causse et al., 2002), sugar and organic acids (Fulton et al., 2002), and metabolic components (Schauer et al., 2008). Large tomato germplasm collections have been characterized at the molecular level using simple sequence repeat (Ranc et al., 2008) and single-nucleotide polymorphism (SNP) markers (Blanca et al., 2012; Shirasawa et al., 2013), giving insights into population structure, tomato evolutionary history, and the genetic architecture of traits of agronomic interest. These screens of nucleotide diversity were made possible (for review, see Bauchet and Causse, 2012) in the last couple of years due to the release of the tomato genome sequence (Tomato Genome Consortium, 2012) and derived genomic tools such as a high-density SNP genotyping array (Sim et al., 2012). The combination of large germplasm collections, high-throughput genomic tools, and traits of economic interest provide a framework to apply genome-wide association study (GWAS) in this species. In tomato, previous association studies have been limited to a targeted region (e.g. chromosome 2; Ranc et al., 2012), used low-density genome-wide-distributed SNP markers (Xu et al., 2013), or investigated a limited number of agronomic traits with low precision on the association panel (Shirasawa et al., 2013).Using tomato as a model, we aimed to investigate the genetic architecture of traits related to fruit metabolic composition at high resolution. To reach this objective, we carried out an investigation into LD patterns at the genome-wide scale and a GWA scan using the MLMM approach. We present results on the genetic architecture of fruit metabolic composition for metabolites such as organic acids, amino acids, sugars, and ascorbate in tomato.     

Genome-Wide Association Study Identifies Loci and Candidate Genes for Body Composition and Meat Quality Traits in Beijing-You Chickens

Body composition and meat quality traits are important economic traits of chickens. The development of high-throughput genotyping platforms and relevant statistical methods have enabled genome-wide association studies in chickens. In order to identify molecular markers and candidate genes associated with body composition and meat quality traits, genome-wide association studies were conducted using the Illumina 60 K SNP Beadchip to genotype 724 Beijing-You chickens. For each bird, a total of 16 traits were measured, including carcass weight (CW), eviscerated weight (EW), dressing percentage, breast muscle weight (BrW) and percentage (BrP), thigh muscle weight and percentage, abdominal fat weight and percentage, dry matter and intramuscular fat contents of breast and thigh muscle, ultimate pH, and shear force of the pectoralis major muscle at 100 d of age. The SNPs that were significantly associated with the phenotypic traits were identified using both simple (GLM) and compressed mixed linear (MLM) models. For nine of ten body composition traits studied, SNPs showing genome wide significance (P<2.59E−6) have been identified. A consistent region on chicken (Gallus gallus) chromosome 4 (GGA4), including seven significant SNPs and four candidate genes (LCORL, LAP3, LDB2, TAPT1), were found to be associated with CW and EW. Another 0.65 Mb region on GGA3 for BrW and BrP was identified. After measuring the mRNA content in beast muscle for five genes located in this region, the changes in GJA1 expression were found to be consistent with that of breast muscle weight across development. It is highly possible that GJA1 is a functional gene for breast muscle development in chickens. For meat quality traits, several SNPs reaching suggestive association were identified and possible candidate genes with their functions were discussed.     

Genome-Wide Association Implicates Candidate Genes Conferring Resistance to Maize Rough Dwarf Disease in Maize

Maize rough dwarf disease (MRDD) is a destructive viral disease in China, which results in 20–30% of the maize yield losses in affected areas and even as high as 100% in severely infected fields. Understanding the genetic basis of resistance will provide important insights for maize breeding program. In this study, a diverse maize population comprising of 527 inbred lines was evaluated in four environments and a genome-wide association study (GWAS) was undertaken with over 556000 SNP markers. Fifteen candidate genes associated with MRDD resistance were identified, including ten genes with annotated protein encoding functions. The homologous of nine candidate genes were predicted to relate to plant defense in different species based on published results. Significant correlation (R² = 0.79) between the MRDD severity and the number of resistance alleles was observed. Consequently, we have broadened the resistant germplasm to MRDD and identified a number of resistance alleles by GWAS. The results in present study also imply the candidate genes in defense pathway play an important role in resistance to MRDD in maize.     

Genome-Wide Association Analyses Point to Candidate Genes for Electric Shock Avoidance in Drosophila melanogaster

Electric shock is a common stimulus for nociception-research and the most widely used reinforcement in aversive associative learning experiments. Yet, nothing is known about the mechanisms it recruits at the periphery. To help fill this gap, we undertook a genome-wide association analysis using 38 inbred Drosophila melanogaster strains, which avoided shock to varying extents. We identified 514 genes whose expression levels and/ or sequences co-varied with shock avoidance scores. We independently scrutinized 14 of these genes using mutants, validating the effect of 7 of them on shock avoidance. This emphasizes the value of our candidate gene list as a guide for follow-up research. In addition, by integrating our association results with external protein-protein interaction data we obtained a shock avoidance-associated network of 38 genes. Both this network and the original candidate list contained a substantial number of genes that affect mechanosensory bristles, which are hair-like organs distributed across the fly’s body. These results may point to a potential role for mechanosensory bristles in shock sensation. Thus, we not only provide a first list of candidate genes for shock avoidance, but also point to an interesting new hypothesis on nociceptive mechanisms.     

Cigarette Smoking and Platelet Aggregation

The influence of cigarette smoking on platelet aggregation was studied in habitual and non-habitual smokers. The results indicate that habitual smokers have a greater tendency to platelet aggregation than do non-habitual smokers. Acute effects of cigarette smoking were, however, not significant. The nucleotide content and the serotonin content of the platelets were analyzed. The adenosine nucleotide and serotonin contents were similar in smokers and non-smokers in the control state and neither showed significant changes on cigarette smoking. There were significant correlations between the control concentrations of the various nucleotides in both groups and there were even higher correlations after smoking. Platelet aggregation bore no demonstrable relationship to the nucleotide or serotonin contents of the platelet. We conclude that the long-term effect of smoking is probably more important than the acute effect.     

Genome-Wide Association Study of Proneness to Anger

Background

Community samples suggest that approximately 1 in 20 children and adults exhibit clinically significant anger, hostility, and aggression. Individuals with dysregulated emotional control have a greater lifetime burden of psychiatric morbidity, severe impairment in role functioning, and premature mortality due to cardiovascular disease.

Methods

With publically available data secured from dbGaP, we conducted a genome-wide association study of proneness to anger using the Spielberger State-Trait Anger Scale in the Atherosclerosis Risk in Communities (ARIC) study (n = 8,747).

Results

Subjects were, on average, 54 (range 45–64) years old at baseline enrollment, 47% (n = 4,117) were male, and all were of European descent by self-report. The mean Angry Temperament and Angry Reaction scores were 5.8±1.8 and 7.6±2.2. We observed a nominally significant finding (p = 2.9E-08, λ = 1.027 - corrected p_gc = 2.2E-07, λ = 1.0015) on chromosome 6q21 in the gene coding for the non-receptor protein-tyrosine kinase, Fyn.

Conclusions

Fyn interacts with NDMA receptors and inositol-1,4,5-trisphosphate (IP3)-gated channels to regulate calcium influx and intracellular release in the post-synaptic density. These results suggest that signaling pathways regulating intracellular calcium homeostasis, which are relevant to memory, learning, and neuronal survival, may in part underlie the expression of Angry Temperament.     

Practice and Attitude of Cigarette Smoking: A Community-Based Study

Background

In Saudi Arabia many studies have addressed cigarette smoking from various perspectives. Most of these studies, however, were conducted among males and confined to Riyadh, the capital city. Such limitations have enhanced the need for community-based epidemiological studies that include both genders and various age groups and socio-demographic features, as well as different regions.

Objective

This cross-sectional study aims to assess the prevalence of cigarette smoking and to discuss the association between cigarette smoking habits and socio-demographic factors among community members of the Jazan area in southwest Saudi Arabia.

Methods

A pre-coded questionnaire was designed and tested for data consistency. A well-trained health team was assigned to gather the data from the 30 primary healthcare centers distributed across eight provinces. The response rate was 92.8% (4,326 respondents ≥13 years old). The associations among the subjects'' socio-demographic characteristics were examined by the chi-square test. A multiple logistic regression and odds ratios were calculated as well.

Results

A total of 1,017 (23.5%), 1,042 (24.1%), and 3,284 (75.9%) respondents were, respectively, current smokers (TCS), ever-smokers (TES), and non-smokers (TNS). Though current smokers seem to be more prevalent in urban populations (13.8%) than in rural populations (9.7%), the association of urbanization with a current smoking habit is insignificant.

Conclusion

Having fun, relieving stress, and the influence of parents, particularly of mothers, were the main motives that encouraged participants'' cigarette-smoking habits. This situation was worsened by the fact that accessing cigarettes was either very easy or easy for over 90% of the respondents.     

Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches

To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1–7 seasons and 1–3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r²; when r²<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance.     

Genome-Wide Association Study Identifies ALDH7A1 as a Novel Susceptibility Gene for Osteoporosis

Osteoporosis is a major public health problem. It is mainly characterized by low bone mineral density (BMD) and/or low-trauma osteoporotic fractures (OF), both of which have strong genetic determination. The specific genes influencing these phenotypic traits, however, are largely unknown. Using the Affymetrix 500K array set, we performed a case-control genome-wide association study (GWAS) in 700 elderly Chinese Han subjects (350 with hip OF and 350 healthy matched controls). A follow-up replication study was conducted to validate our major GWAS findings in an independent Chinese sample containing 390 cases with hip OF and 516 controls. We found that a SNP, rs13182402 within the ALDH7A1 gene on chromosome 5q31, was strongly associated with OF with evidence combined GWAS and replication studies (P = 2.08×10⁻⁹, odds ratio = 2.25). In order to explore the target risk factors and potential mechanism underlying hip OF risk, we further examined this candidate SNP''s relevance to hip BMD both in Chinese and Caucasian populations involving 9,962 additional subjects. This SNP was confirmed as consistently associated with hip BMD even across ethnic boundaries, in both Chinese and Caucasians (combined P = 6.39×10⁻⁶), further attesting to its potential effect on osteoporosis. ALDH7A1 degrades and detoxifies acetaldehyde, which inhibits osteoblast proliferation and results in decreased bone formation. Our findings may provide new insights into the pathogenesis of osteoporosis.     

Genome-Wide Association Study of Parity in Bangladeshi Women

Human fertility is a complex trait determined by gene-environment interactions in which genetic factors represent a significant component. To better understand inter-individual variability in fertility, we performed one of the first genome-wide association studies (GWAS) of common fertility phenotypes, lifetime number of pregnancies and number of children in a developing country population. The fertility phenotype data and DNA samples were obtained at baseline recruitment from individuals participating in a large prospective cohort study in Bangladesh. GWAS analyses of fertility phenotypes were conducted among 1,686 married women. One SNP on chromosome 4 was non-significantly associated with number of children at P <10^-7 and number of pregnancies at P <10^-6. This SNP is located in a region without a gene within 1 Mb. One SNP on chromosome 6 was non-significantly associated with extreme number of children at P <10^-6. The closest gene to this SNP is HDGFL1, a hepatoma-derived growth factor. When we excluded hormonal contraceptive users, a SNP on chromosome 5 was non-significantly associated at P <10^-5 for number of children and number of pregnancies. This SNP is located near C5orf64, an open reading frame, and ZSWIM6, a zinc ion binding gene. We also estimated the heritability of these phenotypes from our genotype data using GCTA (Genome-wide Complex Trait Analysis) for number of children (h_g ² = 0.149, SE = 0.24, p-value = 0.265) and number of pregnancies (h_g ² = 0.007, SE = 0.22, p-value = 0.487). Our genome-wide association study and heritability estimates of number of pregnancies and number of children in Bangladesh did not confer strong evidence of common variants for parity variation. However, our results suggest that future studies may want to consider the role of 3 notable SNPs in their analysis.     

A Genome-Wide Association Study of Optic Disc Parameters

The optic nerve head is involved in many ophthalmic disorders, including common diseases such as myopia and open-angle glaucoma. Two of the most important parameters are the size of the optic disc area and the vertical cup-disc ratio (VCDR). Both are highly heritable but genetically largely undetermined. We performed a meta-analysis of genome-wide association (GWA) data to identify genetic variants associated with optic disc area and VCDR. The gene discovery included 7,360 unrelated individuals from the population-based Rotterdam Study I and Rotterdam Study II cohorts. These cohorts revealed two genome-wide significant loci for optic disc area, rs1192415 on chromosome 1p22 (p = 6.72×10⁻¹⁹) within 117 kb of the CDC7 gene and rs1900004 on chromosome 10q21.3-q22.1 (p = 2.67×10⁻³³) within 10 kb of the ATOH7 gene. They revealed two genome-wide significant loci for VCDR, rs1063192 on chromosome 9p21 (p = 6.15×10⁻¹¹) in the CDKN2B gene and rs10483727 on chromosome 14q22.3-q23 (p = 2.93×10⁻¹⁰) within 40 kbp of the SIX1 gene. Findings were replicated in two independent Dutch cohorts (Rotterdam Study III and Erasmus Rucphen Family study; N = 3,612), and the TwinsUK cohort (N = 843). Meta-analysis with the replication cohorts confirmed the four loci and revealed a third locus at 16q12.1 associated with optic disc area, and four other loci at 11q13, 13q13, 17q23 (borderline significant), and 22q12.1 for VCDR. ATOH7 was also associated with VCDR independent of optic disc area. Three of the loci were marginally associated with open-angle glaucoma. The protein pathways in which the loci of optic disc area are involved overlap with those identified for VCDR, suggesting a common genetic origin.