Genetic association studies of complex traits: design and analysis issues

Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)

BACKGROUND

Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China's freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, we screened restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F1 generation of a largemouth bass population.

RESULTS

We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, SNP19140160, SNP9639603, SNP9639605, and SNP23355498 showed significant associations; three of them (SNP9639603, SNP9639605, and SNP23355498) were significantly associated with one trait, body length, in the F1 generation, and one (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F1 generation. The markers SNP19140160 and SNP23355498 were located near two growth candidate genes, fam174b and ppip5k1b, respectively, and these candidate genes were closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F1 generation population (703.86 g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36 g).

CONCLUSIONS

Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection in the breeding of high-quality largemouth bass.

Single nucleotide polymorphisms cumulating to genetic variation for fertility in crossbred (Bos taurus × Bos indicus) bull spermatozoa

Spermatozoa from high-fertile (HF) and low-fertile (LF) breeding bulls were subjected to high-throughput next-generation sequencing to identify important Single nucleotide polymorphisms (SNPs) and novel variants associated with fertility. A total of 77,038 genome-wide SNPs were identified, among which, 10,788 were novel variants. A total of 42,290 and 34,748 variants were recorded with 6115 and 4673 novel variants in in HF and LF bulls, respectively. Higher number of SNPs were identified in HF compared to LF bulls. GO analysis of filtered genes with significant variations in HF bulls indicated their involvement in oxidative phosphorylation and metabolic pathways. GO analysis of filtered genes with significant variation in LF bulls revealed their involvement in Ca2++ ion binding, structural constituent of ribosome, and biological processes like translation and ribosomal small subunit assembly. The study identified SNPs in candidate genes including TPT1, BOLA-DRA, CD74, RPS17, RPS28, RPS29, RPL14, RPL13, and RPS27A, which are linked to sperm functionality, survival, oxidative stress, and bull fertility. The identified SNPs could be used in selection of bulls for high fertility and the variation in these genes could be established as an explanation for the fertility differences in bulls upon validation in large number of bulls.

Analysis of convergence of linkage and association studies in autism spectrum disorders

Autism spectrum disorder (ASD) is a clinically and genetically heterogeneous group of pervasive neurodevelopmental disorders with a strong hereditary component. Although genome-wide linkage studies (GWLS) and [genome-wide association studies (GWAS)] have previously identified hundreds of ASD risk gene loci, the results remain inconclusive. In this study, a genomic convergence approach of GWAS and GWLS for ASD was implemented for the first time in order to identify genomic loci supported by both methods. A database with 32 GWLS and five GWAS for ASD was created. Convergence was quantified as the proportion of significant GWAS markers located within linked regions. Convergence was not found to be significantly higher than expected by chance (z-test = 1,177, P = 0,239). Although convergence is supportive of genuine effects, the lack of agreement between GWLS and GWAS is also indicative that these studies are designed to answer different questions and are not equally well suited for deciphering the genetics of complex traits.

Detection of Association Features Based on Gene Eigenvalues and MRI Imaging Using Genetic Weighted Random Forest

In the studies of Alzheimer's disease (AD), jointly analyzing imaging data and genetic data provides an effective method to explore the potential biomarkers of AD. AD can be separated into healthy controls (HC), early mild cognitive impairment (EMCI), late mild cognitive impairment (LMCI) and AD. In the meantime, identifying the important biomarkers of AD progression, and analyzing these biomarkers in AD provide valuable insights into understanding the mechanism of AD. In this paper, we present a novel data fusion method and a genetic weighted random forest method to mine important features. Specifically, we amplify the difference among AD, LMCI, EMCI and HC by introducing eigenvalues calculated from the gene p-value matrix for feature fusion. Furthermore, we construct the genetic weighted random forest using the resulting fused features. Genetic evolution is used to increase the diversity among decision trees and the decision trees generated are weighted by weights. After training, the genetic weighted random forest is analyzed further to detect the significant fused features. The validation experiments highlight the performance and generalization of our proposed model. We analyze the biological significance of the results and identify some significant genes (CSMD1, CDH13, PTPRD, MACROD2 and WWOX). Furthermore, the calcium signaling pathway, arrhythmogenic right ventricular cardiomyopathy and the glutamatergic synapse pathway were identified. The investigational findings demonstrate that our proposed model presents an accurate and efficient approach to identifying significant biomarkers in AD.

Dissecting Meta-Analysis in GWAS Era: Bayesian Framework for Gene/Subnetwork-Specific Meta-Analysis

Over the past decades, advanced high-throughput technologies have continuously contributed to genome-wide association studies (GWASs). GWAS meta-analysis has been increasingly adopted, has cross-ancestry replicability, and has power to illuminate the genetic architecture of complex traits, informing about the reliability of estimation effects and their variability across human ancestries. However, detecting genetic variants that have low disease risk still poses a challenge. Designing a meta-analysis approach that combines the effect of various SNPs within genes or genes within pathways from multiple independent population GWASs may be helpful in identifying associations with small effect sizes and increasing the association power. Here, we proposed ancMETA, a Bayesian graph-based framework, to perform the gene/pathway-specific meta-analysis by combining the effect size of multiple SNPs within genes, and genes within subnetwork/pathways across multiple independent population GWASs to deconvolute the interactions between genes underlying the pathogenesis of complex diseases across human populations. We assessed the proposed framework on simulated datasets, and the results show that the proposed model holds promise for increasing statistical power for meta-analysis of genetic variants underlying the pathogenesis of complex diseases. To illustrate the proposed meta-analysis framework, we leverage seven different European bipolar disorder (BD) cohorts, and we identify variants in the angiotensinogen (AGT) gene to be significantly associated with BD across all 7 studies. We detect a commonly significant BD-specific subnetwork with the ESR1 gene as the main hub of a subnetwork, associated with neurotrophin signaling (p = 4e⁻¹⁴) and myometrial relaxation and contraction (p = 3e⁻⁰⁸) pathways. ancMETA provides a new contribution to post-GWAS methodologies and holds promise for comprehensively examining interactions between genes underlying the pathogenesis of genetic diseases and also underlying ethnic differences.

Feature Fusion and Detection in Alzheimer's Disease Using a Novel Genetic Multi-Kernel SVM Based on MRI Imaging and Gene Data

Voxel-based morphometry provides an opportunity to study Alzheimer's disease (AD) at a subtle level. Therefore, identifying the important brain voxels that can classify AD, early mild cognitive impairment (EMCI) and healthy control (HC) and studying the role of these voxels in AD will be crucial to improve our understanding of the neurobiological mechanism of AD. Combining magnetic resonance imaging (MRI) imaging and gene information, we proposed a novel feature construction method and a novel genetic multi-kernel support vector machine (SVM) method to mine important features for AD detection. Specifically, to amplify the differences among AD, EMCI and HC groups, we used the eigenvalues of the top 24 Single Nucleotide Polymorphisms (SNPs) in a p-value matrix of 24 genes associated with AD for feature construction. Furthermore, a genetic multi-kernel SVM was established with the resulting features. The genetic algorithm was used to detect the optimal weights of 3 kernels and the multi-kernel SVM was used after training to explore the significant features. By analyzing the significance of the features, we identified some brain regions affected by AD, such as the right superior frontal gyrus, right inferior temporal gyrus and right superior temporal gyrus. The findings proved the good performance and generalization of the proposed model. Particularly, significant susceptibility genes associated with AD were identified, such as CSMD1, RBFOX1, PTPRD, CDH13 and WWOX. Some significant pathways were further explored, such as the calcium signaling pathway (corrected p-value = 1.35 × 10-6) and cell adhesion molecules (corrected p-value = 5.44 × 10-4). The findings offer new candidate abnormal brain features and demonstrate the contribution of these features to AD.

Research on Frequent Itemset Mining of Imaging Genetics GWAS in Alzheimer’s Disease

As an efficient method, genome-wide association study (GWAS) is used to identify the association between genetic variation and pathological phenotypes, and many significant genetic variations founded by GWAS are closely associated with human diseases. However, it is not enough to mine only a single marker effect variation on complex biological phenotypes. Mining highly correlated single nucleotide polymorphisms (SNP) is more meaningful for the study of Alzheimer's disease (AD). In this paper, we used two frequent pattern mining (FPM) framework, the FP-Growth and Eclat algorithms, to analyze the GWAS results of functional magnetic resonance imaging (fMRI) phenotypes. Moreover, we applied the definition of confidence to FP-Growth and Eclat to enhance the FPM framework. By calculating the conditional probability of identified SNPs, we obtained the corresponding association rules to provide support confidence between these important SNPs. The resulting SNPs showed close correlation with hippocampus, memory, and AD. The experimental results also demonstrate that our framework is effective in identifying SNPs and provide candidate SNPs for further research.

Sex hormone-related polymorphisms in endometriosis and migraine: A narrative review

Some evidence indicates endometriosis and migraine have a common genetic predisposition in sex-hormone genes, which could have important implications for the treatment of these two heterogenous conditions. To date, the genes responsibility remains unknown. Based on the biological hypothesis that polymorphisms of genes involved in sex-hormone pathways may influence estrogen levels and phenotypes of both disorders, we did a literature search for candidate sex-hormone genes and genes involved in the metabolism of estradiol. The aim was to review the evidence for shared sex-hormone-related polymorphisms between endometriosis and migraine and provide an exhaustive overview of the current literature. We included case-control studies investigating associations between candidate sex-hormone-related genes and the disorders endometriosis and migraine, respectively. Results showed three overlapping sex-hormone-associated polymorphisms in estrogen receptor genes that are associated with both conditions. To confirm possible associations with other sex-hormone genes, larger studies are needed.

A common variant of CNTNAP2 is associated with sub-threshold autistic traits and intellectual disability

Sub-threshold autistic traits are common in the general population. Children with sub-threshold autistic traits have difficulties with social adaptation. Contactin-associated protein-like 2 (CNTNAP2) is associated with the development of Autism spectrum disorder (ASD) and the single-nucleotide polymorphism rs2710102 (G/A) of CNTNAP2 is suggested to contribute to sub-threshold social impairments and intellectual disabilities. We recruited 67 children with Autistic disorder (AD) (49 boys, 18 girls, aged 38–98 months) and 57 typically developing (TD) children (34 boys, 23 girls, aged 53–90 months). We assessed the participants’ intelligence and social reciprocity using the Kaufman Assessment Battery for Children (K-ABC) and the Social Responsiveness Scale (SRS), respectively. Genomic DNA was extracted from the buccal mucosa and genotyped for rs2710102. A chi-square test revealed a significant association between genotype and group [χ²(2) = 6.56, p = 0.038]. When a co-dominant model was assumed, the results from linear regression models demonstrated that TD children with A-carriers (AA + AG) presented higher SRS T-scores [t(55) = 2.11, p = 0.039] and lower simultaneous processing scale scores of K-ABC [t(55) = -2.19, p = 0.032] than those with GG homozygotes. These associations were not significant in children with ASD. TD children with the rs2710102 A-allele may have more sub-threshold autistic traits than those with GG homozygotes, reflected in higher SRS scores and lower simultaneous processing scale scores. These results support the use of genetic evidence to detect sub-threshold autistic traits.

The Impact of PTPRK and ROS1 Polymorphisms on the Preeclampsia Risk in Han Chinese Women

Objective

Preeclampsia (PE) is a severe complication in pregnancy and a leading cause of maternal and infant mortality. However, the exact underlying etiology of PE remains unknown. Emerging evidence indicates that the cause of PE is associated with genetic factors. Therefore, the aim of this study is to identify susceptibility genes to PE.

Materials and Methods

Human Exome BeadChip assays were conducted using 370 cases and 482 controls and 21 loci were discovered. A further independent set of 958 cases and 1007 controls were recruited for genotyping to determine whether the genes of interest ROS1 and PTPRK are associated with PE. Immunohistochemistry was used for localization. Both qPCR and Western blotting were utilized to investigate the levels of PTPRK in placentas of 20 PE and 20 normal pregnancies.

Results

The allele frequency of PTPRK rs3190930 differed significantly between PE and controls and was particularly significant in severe PE subgroup and early-onset PE subgroup. PTPRK is primarily localized in placental trophoblast cells. The mRNA and protein levels of PTPRK in PE were significantly higher than those in controls.

Conclusion

These results suggest that PTPRK appears to be a previously unrecognized susceptibility gene for PE in Han Chinese women, and its expression is also associated with PE, while ROS1 rs9489124 has no apparent correlation with PE risk.

Genomic analysis of ionome-related QTLs in Arabidopsis thaliana

Ionome contributes to maintain cell integrity and acts as cofactors for catalyzing regulatory pathways. Identifying ionome contributing genomic regions provides a practical framework to dissect the genetic architecture of ionomic traits for use in biofortification. Meta-QTL (MQTL) analysis is a robust method to discover stable genomic regions for traits regardless of the genetic background. This study used information of 483 QTLs for ionomic traits identified from 12 populations for MQTL analysis in Arabidopsis thaliana. The selected QTLs were projected onto the newly constructed genetic consensus map and 33 MQTLs distributed on A. thaliana chromosomes were identified. The average confidence interval (CI) of the drafted MQTLs was 1.30 cM, reduced eight folds from a mean CI of 10.88 cM for the original QTLs. Four MQTLs were considered as stable MQTLs over different genetic backgrounds and environments. In parallel to the gene density over the A. thaliana genome, the genomic distribution of MQTLs over the genetic and physical maps indicated the highest density at non- and sub-telomeric chromosomal regions, respectively. Several candidate genes identified in the MQTLs intervals were associated with ion transportation, tolerance, and homeostasis. The genomic context of the identified MQTLs suggested nine chromosomal regions for Zn, Mn, and Fe control. The QTLs for potassium (K) and phosphorus (P) were the most frequently co-located with Zn (78.3%), Mn (76.2%), and Fe (88.2% and 70.6%) QTLs. The current MQTL analysis demonstrates that meta-QTL analysis is cheaper than, and as informative as genome-wide association study (GWAS) in refining the known QTLs.

Hippocampal Subregion and Gene Detection in Alzheimer's Disease Based on Genetic Clustering Random Forest

The distinguishable subregions that compose the hippocampus are differently involved in functions associated with Alzheimer's disease (AD). Thus, the identification of hippocampal subregions and genes that classify AD and healthy control (HC) groups with high accuracy is meaningful. In this study, by jointly analyzing the multimodal data, we propose a novel method to construct fusion features and a classification method based on the random forest for identifying the important features. Specifically, we construct the fusion features using the gene sequence and subregions correlation to reduce the diversity in same group. Moreover, samples and features are selected randomly to construct a random forest, and genetic algorithm and clustering evolutionary are used to amplify the difference in initial decision trees and evolve the trees. The features in resulting decision trees that reach the peak classification are the important "subregion gene pairs". The findings verify that our method outperforms well in classification performance and generalization. Particularly, we identified some significant subregions and genes, such as hippocampus amygdala transition area (HATA), fimbria, parasubiculum and genes included RYR3 and PRKCE. These discoveries provide some new candidate genes for AD and demonstrate the contribution of hippocampal subregions and genes to AD.

Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage

BACKGROUND

Brain image genetics provides enormous opportunities for examining the effects of genetic variations on the brain. Many studies have shown that the structure, function, and abnormality (e.g., those related to Alzheimer's disease) of the brain are heritable. However, which genetic variations contribute to these phenotypic changes is not completely clear. Advances in neuroimaging and genetics have led us to obtain detailed brain anatomy and genome-wide information. These data offer us new opportunities to identify genetic variations such as single nucleotide polymorphisms (SNPs) that affect brain structure. In this paper, we perform a genome-wide variant-based study, and aim to identify top SNPs or SNP sets which have genetic effects with the largest neuroanotomic coverage at both voxel and region-of-interest (ROI) levels. Based on the voxelwise genome-wide association study (GWAS) results, we used the exhaustive search to find the top SNPs or SNP sets that have the largest voxel-based or ROI-based neuroanatomic coverage. For SNP sets with >2 SNPs, we proposed an efficient genetic algorithm to identify top SNP sets that can cover all ROIs or a specific ROI.

RESULTS

We identified an ensemble of top SNPs, SNP-pairs and SNP-sets, whose effects have the largest neuroanatomic coverage. Experimental results on real imaging genetics data show that the proposed genetic algorithm is superior to the exhaustive search in terms of computational time for identifying top SNP-sets.

CONCLUSIONS

We proposed and applied an informatics strategy to identify top SNPs, SNP-pairs and SNP-sets that have genetic effects with the largest neuroanatomic coverage. The proposed genetic algorithm offers an efficient solution to accomplish the task, especially for identifying top SNP-sets.

Targeted Gene Candidates for Treatment and Early Diagnosis of Age-Related Macular Degeneration

Age-related macular degeneration (AMD) is an eye disease that impairs the sharp and central vision need for daily activities. Recent advances in molecular biology research not only lead to a better understanding of the genetics and pathophysiology of AMD but also to the development of applications based on targeted gene expressions to treat the disease. Clarification of molecular pathways that causing to development and progression in dry and wet types of AMD needs comprehensive and comparative investigations in particular precious biopsies involving peripheral blood samples from the patients. Therefore, in this investigation, dry and wet types of AMD patients and healthy individuals were aimed at investigating in regard to targeted gene candidates by using gene expression analysis for the first time. 13 most potent candidate genes involved in neurodegeneration were selected via in silico approach and investigated through gene expression analysis to suggest new targets for disease therapy. For the analyses, 30 individuals (10 dry and 10 wet types AMD patients and 10 healthy people) were involved in the study. SYBR-Green based Real-Time PCR analysis was performed on isolated peripheral blood mononuclear cells (PBMCs) to analyze differentially expressed genes related to these cases. According to the investigations, only the CRP gene was found to be upregulated for both dry and wet disease types. When the downregulated genes were analyzed, it was found that 11 genes were commonly decreased for both dry and wet types in the aspect of expression pattern. From these genes, CFH, CX3CR1, FLT1, and TIMP3 were found to have the most downregulated gene expression properties for both diseases. From these results, it might be concluded that these common upregulated and downregulated genes could be used as targets for early diagnosis and treatment for AMD.

Screening of Microbes Associated With Swine Growth and Fat Deposition Traits Across the Intestinal Tract

Pigs, as one of the most common livestock species worldwide, are expected to have a fast growth rate and lower subcutaneous fatness but higher intramuscular fat ("marbling meat"). Nowadays, it is believed that not only host genetics but also its gut microbiomes can modulate farm animal phenotypes, however, many of the mechanisms remain elusive. We measured the body weight (BW), average daily gain (ADG), backfat thickness (BFT), and intramuscular fatness (IMF) of 91 Enshi pigs at 260 days of age, then genotyped each one individually using a 50K single nucleotide polymorphism array and performed 16S ribosomal RNA gene sequencing on 455 microbial samples from the jejunum, ileum, cecum, colon, and rectum. The microbial diversity showed notable spatial variation across the entire intestinal tract, with the cecum and colon having the highest α-diversity. The cecal and colonic microbiotas made greater contributions to BW and ADG and accounted for 22-37% of the phenotypic variance. The jejunal and cecal microbiotas contributed more (13-31%) to the BFT and IMF than the other segments. Finally, from cecum, colon, and jejunum, we identified eight microbial taxa that were significantly correlated with the target traits. The genera Alloprevotella and Ruminococcaceae UCG-005 were highly positively correlated with BW and ADG. The genera Prevotellaceae UCG-001 and Alistipes in the cecum and Clostridium sensu stricto 1 in the jejunum were highly positively correlated with BFT and IMF. The genera Stenotrophomonas, Sphaerochaeta, and Desulfovibrio were negatively associated with the mentioned traits. These findings could aid in developing strategies for manipulating the gut microbiota to alter production performance in pigs.

Genotypes and Phenotypes: A Search for Influential Genes in Diabetic Retinopathy

Although gene–environment interactions are known to play an important role in the inheritance of complex traits, it is still unknown how a genotype and the environmental factors result in an observable phenotype. Understanding this complex interaction in the pathogenesis of diabetic retinopathy (DR) remains a big challenge as DR appears to be a disease with heterogenous phenotypes with multifactorial influence. In this review, we examine the natural history and risk factors related to DR, emphasizing distinct clinical phenotypes and their natural course in retinopathy. Although there is strong evidence that duration of diabetes and metabolic factors play a key role in the pathogenesis of DR, accumulating new clinical studies reveal that this disease can develop independently of duration of diabetes and metabolic dysfunction. More recently, studies have emphasized the role of genetic factors in DR. However, linkage analyses, candidate gene studies, and genome-wide association studies (GWAS) have not produced any statistically significant results. Our recently initiated genomics study, the Diabetic Retinopathy Genomics (DRGen) Study, aims to examine the contribution of rare and common variants in the development DR, and how they can contribute to clinical phenotype, rate of progression, and response to available therapies. Our preliminary findings reveal a novel set of genetic variants associated with proangiogenic and inflammatory pathways that may contribute to DR pathogenesis. Further investigation of these variants is necessary and may lead to development of novel biomarkers and new therapeutic targets in DR.

Do Genomic Factors Play a Role in Diabetic Retinopathy?

Although there is strong clinical evidence that the control of blood glucose, blood pressure, and lipid level can prevent and slow down the progression of diabetic retinopathy (DR) as shown by landmark clinical trials, it has been shown that these factors only account for 10% of the risk for developing this disease. This suggests that other factors, such as genetics, may play a role in the development and progression of DR. Clinical evidence shows that some diabetics, despite the long duration of their diabetes (25 years or more) do not show any sign of DR or show minimal non-proliferative diabetic retinopathy (NPDR). Similarly, not all diabetics develop proliferative diabetic retinopathy (PDR). So far, linkage analysis, candidate gene studies, and genome-wide association studies (GWAS) have not produced any statistically significant results. We recently initiated a genomics study, the Diabetic Retinopathy Genetics (DRGen) Study, to examine the contribution of rare and common variants in the development of different phenotypes of DR, as well as their responsiveness to anti-VEGF treatment in diabetic macular edema (DME). Our preliminary findings reveal a novel set of genetic variants involved in the angiogenesis and inflammatory pathways that contribute to DR progression or protection. Further investigation of variants can help to develop novel biomarkers and lead to new therapeutic targets in DR.

Matrix metalloproteinases 3 polymorphism increases the risk of developing advanced endometriosis and infertility: A case-control study

Objective

Endometriosis has a complex and multifactorial pathology, and it is considered one of the main causes of infertility nowadays. The angiogenic process, which involves remodeling of extracellular matrix, is crucial for the development of this disease, mainly by the action of the matrix metalloproteinase 3 (MMP-3). It is known that genetic factors can influence endometriosis, thus; we investigated the role of MMP3 276G>A polymorphism as a risk factor for the development of the disease and its symptoms.

Study Design

This case-control study included 283 women with endometriosis (cases) and 217 women without the disease (controls) who were submitted to laparoscopic or laparotomy surgery. Real-time polymerase chain reaction performed by TaqMan system was applied for all polymorphisms. A multivariate logistic regression was performed to evaluate the association between polymorphism and endometriosis or clinical and gynecological characteristics of the disease, using their respective odds ratios (OR) and 95% confidence intervals (CI).

Results

The allelic frequency of the MMP3 276 G > A polymorphism was 33.6% in controls and 40.3% in endometriosis cases. The allelic distribution was significantly different between the two (P = 0.03). The variant genotype of MMP3 276AA was associated with increased endometriosis risk in the advanced endometriosis cases (OR: 2.08, 95% CI: 1.05 – 4.07 and OR: 1.87, 95% CI: 1.01 – 3.45). Regarding the symptoms, endometriosis-related infertile women had a positive association with the presence of MMP3 276 G > A polymorphism (OR: 3.13, 95% CI: 1.08–9.08 and OR: 3.30, 95% CI: 1.31 – 8.33).

Conclusions

These findings suggest that the MMP3 276A polymorphism is involved with advanced endometriosis cases and infertility, and these associations may implicate in the behavior of disease.

Tendon and Ligament Injuries in Elite Rugby: The Potential Genetic Influence

This article reviews tendon and ligament injury incidence and severity within elite rugby union and rugby league. Furthermore, it discusses the biological makeup of tendons and ligaments and how genetic variation may influence this and predisposition to injury. Elite rugby has one of the highest reported injury incidences of any professional sport. This is likely due to a combination of well-established injury surveillance systems and the characteristics of the game, whereby high-impact body contact frequently occurs, in addition to the high intensity, multispeed and multidirectional nature of play. Some of the most severe of all these injuries are tendon and ligament/joint (non-bone), and therefore, potentially the most debilitating to a player and playing squad across a season or World Cup competition. The aetiology of these injuries is highly multi-factorial, with a growing body of evidence suggesting that some of the inter-individual variability in injury susceptibility may be due to genetic variation. However, little effort has been devoted to the study of genetic injury traits within rugby athletes. Due to a growing understanding of the molecular characteristics underpinning the aetiology of injury, investigating genetic variation within elite rugby is a viable and worthy proposition. Therefore, we propose several single nucleotide polymorphisms within candidate genes of interest; COL1A1, COL3A1, COL5A1, MIR608, MMP3, TIMP2, VEGFA, NID1 and COLGALT1 warrant further study within elite rugby and other invasion sports.

Single Nucleotide Polymorphisms and Post-operative Complications Following Major Gastrointestinal Surgery: a Systematic Review and Meta-analysis

BACKGROUND

The human genome is an under-researched area of pre-operative risk stratification. Studies of genetic polymorphisms and their associations with acute post-operative complications in gastrointestinal surgery have reported statistically significant results, but have varied in methodology, genetic variations studied, and conclusions reached. To provide clarity, we conducted a systematic review and meta-analysis of single nucleotide polymorphisms and their association with post-operative complications after major gastrointestinal surgery.

METHODS

We performed a literature search using Ovid MEDLINE and Web of Science databases. Studies were included if they investigated genetic polymorphisms and their associations with post-operative complications after major gastrointestinal surgery. We extracted clinical and genetic data from each paper and assessed for quality against the STrengthening the REporting of Genetic Association Studies (STREGA) guidelines. Odds ratios were presented, with 95% confidence intervals, to assess strengths of association. We conducted a meta-analysis on TNF-α-308, which had been assessed in three papers.

RESULTS

Our search returned 68 papers, of which 5 were included after screening and full-text review. Twenty-two different single nucleotide polymorphisms (SNPs) were investigated in these studies. We found that all papers were genetic association studies, and had selected SNPs related to inflammation. The outcome investigated was most commonly post-operative infection, but also anastomotic leak and other non-infectious complications. Statistically significant associations were found for TNF-α-308, IL-10-819, PTGS2-765 and IFN-γ-874. There was significant variability in study quality and methodology. We conducted a meta-analysis on associations between the TNF-α-308 polymorphism and post-operative infection and report an OR of 1.18 (CI 0.27-5.21).

CONCLUSIONS

We found biologically plausible associations between SNPs involved in inflammation and post-operative infection, but the available data were too limited and of insufficient quality to reach definitive conclusions. Further work is needed, including genome-wide association studies (GWAS).

The Genetic Diagnosis of Neurodegenerative Diseases and Therapeutic Perspectives

Genetics has led to a new focus regarding approaches to the most prevalent diseases today. Ascertaining the molecular secrets of neurodegenerative diseases will lead to developing drugs that will change natural history, thereby affecting the quality of life and mortality of patients. The sequencing of candidate genes in patients suffering neurodegenerative pathologies is faster, more accurate, and has a lower cost, thereby enabling algorithms to be proposed regarding the risk of neurodegeneration onset in healthy persons including the year of onset and neurodegeneration severity. Next generation sequencing has resulted in an explosion of articles regarding the diagnosis of neurodegenerative diseases involving exome sequencing or sequencing a whole gene for correlating phenotypical expression with genetic mutations in proteins having key functions. Many of them occur in neuronal glia, which can trigger a proinflammatory effect leading to defective proteins causing sporadic or familial mutations. This article reviews the genetic diagnosis techniques and the importance of bioinformatics in interpreting results from neurodegenerative diseases. Risk scores must be established in the near future regarding diseases with a high incidence in healthy people for defining prevention strategies or an early start for giving drugs in the absence of symptoms.

Design Considerations for Genetic Linkage and Association Studies

This chapter describes the main issues that genetic epidemiologists usually consider in the design of linkage and association studies. For linkage, we briefly consider the situation of rare highly penetrant alleles showing a disease pattern consistent with Mendelian inheritance investigated through parametric methods in large pedigrees, or with autozygosity mapping in inbred families, and we then turn our focus to the most common design, the affected sibling pair design that is of more relevance for common, complex diseases. Power and sample size calculations are provided as a function of the strength of the genetic effect being investigated. We also discuss the impact of other determinants of statistical power such as disease heterogeneity, pedigree and genotyping errors and the effect of the type and density of genetic markers. For association studies, we consider the popular case-control design for dichotomous phenotypes and we provide power and sample size calculations for one-stage and multistage designs. For candidate genes, guidelines are given on the prioritization of genetic variants, and for genome-wide association studies (GWAS) the issue of choosing an appropriate SNP array is discussed. A warning is issued regarding the danger of designing an underpowered replication study following an initial GWAS. The risk of finding spurious association due to population stratification, cryptic relatedness, and differential bias is underlined.

Haplotype association and synergistic effect of human aldosterone synthase (CYP11B2) gene polymorphisms causing susceptibility to essential hypertension in Indian patients

BACKGROUND

Aldosterone synthase (CYP11B2) is a key enzyme involved in the terminal steps of aldosterone biosynthesis. Genetic variability in CYP11B2 gene has been associated with heterogeneous aldosterone production, which can affect sodium homeostasis and thereby regulation of blood pressure. Hence, the present study was aimed to explore the single-locus variations, haplotype and epistasis patterns of CYP11B2 (C-344T, intron-2 gene conversion and Lys173Arg) gene polymorphisms, and the risk contributed by them to the development of essential hypertension (EHT).

METHODS

A total of 279 hypertensive patients and 200 normotensive controls were enrolled in this study. C-344T and Lys173Arg polymorphisms of CYP11B2 gene were genotyped by PCR-RFLP method and intron-2 gene conversion (IC) polymorphism by allele-specific PCR analysis.

RESULTS

Single-locus analysis revealed significant association of CYP11B2 C-344T and Lys173Arg polymorphisms with EHT (p < 0.05). Considering the sexes, Lys173 allele was found to be at risk for hypertension in males (OR 1.40; 95% CI = 1.01-1.96). Unphased haplotype analysis revealed H1 (T-Conv-Lys; p = 0.0017) to have significant risk for EHT, while haplotype H4 (T-Wt-Arg) had a significant protective effect. Multifactor dimensionality reduction (MDR) interaction analysis found the overall best model with C-344T and IC polymorphisms exhibiting strong synergistic effect.

CONCLUSION

The present study revealed a strong synergistic effect of CYP11B2 C-344T and IC polymorphisms causing susceptibility to EHT and haplotype H1 (-344T-Conv-Lys173) as the risk-conferring factor for hypertension predisposition.

Positive association of genetic variations in the phospholipase C-like 1 gene with dermatomyositis in Chinese Han

Idiopathic inflammatory myopathies (IIMs) are autoimmune diseases with an underlying yet undefined genetic component. Recently, phospholipase C-like 1 (PLCL1) has been identified as a potential genetic susceptibility locus for dermatomyositis (DM) in patients of European ancestry. Here, association between PLCL1 polymorphisms and IIMs was investigated in Chinese Han. Genomic DNA was isolated from blood samples (2 mL) collected from Chinese Han (≥18 years) with polymyositis (PM, n = 286) or dermatomyositis (DM, n = 535) and ethnically matched controls (n = 968). Patients and controls were genotyped for five SNPs (rs938929, rs1518364, rs6738825, rs2117339, and rs7572733) previously associated with DM, with the Sequenom MassARRAY system. SNPs rs6738825 and rs7572733 were found to be associated with the development of DM in Chinese Han (P c = 0.015; P c = 0.025, respectively) as well as the risk A allele of rs938929 and T allele of rs1518364 (P c = 0.030; P c = 0.029). None of the five SNPs were associated with PM (all P c > 0.05). The frequency of the two haplotypes of these five SNPs was also significantly different between DM patients and healthy controls. In addition, conditional analysis with rs6738825 revealed that these SNPs were not independent factors contributing to DM. Finally, a novel association between rs6738825 and rs7572733 and DM with complicating interstitial lung disease was observed (ILD; P c = 0.040; P c = 0.030, respectively). A positive association between PLCL1 polymorphisms and DM patients and DM patients with ILD was observed, indicating that PLCL1 might be the susceptibility gene for DM patients in Chinese Han.

Electrophysiological Endophenotypes for Schizophrenia

Endophenotypes are quantitative, heritable traits that may help to elucidate the pathophysiologic mechanisms underlying complex disease syndromes, such as schizophrenia. They can be assessed at numerous levels of analysis; here, we review electrophysiological endophenotypes that have shown promise in helping us understand schizophrenia from a more mechanistic point of view. For each endophenotype, we describe typical experimental procedures, reliability, heritability, and reported gene and neurobiological associations. We discuss recent findings regarding the genetic architecture of specific electrophysiological endophenotypes, as well as converging evidence from EEG studies implicating disrupted balance of glutamatergic signaling and GABAergic inhibition in the pathophysiology of schizophrenia. We conclude that refining the measurement of electrophysiological endophenotypes, expanding genetic association studies, and integrating data sets are important next steps for understanding the mechanisms that connect identified genetic risk loci for schizophrenia to the disease phenotype.

Genetic variants of the class A scavenger receptor gene are associated with essential hypertension in Chinese

BACKGROUND

The class A scavenger receptor, which is encoded by the macrophage scavenger receptor 1 (MSR1) gene, is a pattern recognition receptor (PPR) primarily expressed in macrophages. It has been reported that genetic polymorphisms of MSR1 are significantly associated with many cardiovascular events. However, whether it links genetically to essential hypertension (EH) in Chinese is not defined.

METHODS

We performed an independent case-control study in a Chinese population consisting of 617 EH cases and 620 controls by genotyping three single nucleotide polymorphisms (SNPs) of MSR1.

RESULTS

We found that rs13306541 and rs3747531 were significantly associated with an increased risk of EH with per allele odds ratio (OR) of 1.63 [95% confidence interval (CI): 1.27-2.09; P<0.001] and 1.29 (95% CI: 1.09-1.52; P=0.003), respectively. Individuals with 2-4 risk alleles had a 2.03-fold (95% CI: 1.48-2.78) increased risk of EH compared with those having none of the risk alleles (P for trend <0.001).

CONCLUSIONS

Our results indicate that genetic variants of MSR1 may serve as predictive markers for the risk of EH in combination with traditional risk factors of EH in Chinese population.

Family-based analysis of eight susceptibility loci in polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is a complex endocrine disorder that is proposed to have a genetic basis. A recent genome-wide association study (GWAS) identified eight new risk loci that are independently associated with PCOS. To further validate the findings, a total of 321 case-parent trios (963 participants) who had a proband affected with PCOS were recruited for the family-based study. The transmission disequilibrium test (TDT) was used to analyze associations between PCOS and ten single nucleotide polymorphisms (SNPs) mapped to eight new susceptibility loci. Significant differences in transmission were observed for the SNPs rs2349415 (located in the FSHR gene, P = 0.0001) and rs3802457 (located in the C9orf3 gene, P = 0.0001), even after correction for multiple testing bias. The present data provides further evidence for an association between two susceptibility loci, 2p16.3 and 9q22.32, and PCOS. Follow-up functional studies on the FSHR and C9orf3 genes are required to understand their roles in PCOS development.

An association study between USP34 and polycystic ovary syndrome

Background

Polycystic ovary syndrome (PCOS) is a complex multifactor disorder and genetic factors have been implicated in its pathogenesis. Our previous genome-wide association study (GWAS) had identified allele frequencies in several single nucleotide polymorphisms (SNPs) in gene USP34 (Ubiquitin-Specific Protease 34) were significantly different between PCOS cases and controls. This study was aimed to replicate the previous results in another independent cohort.

Methods

One thousand two hundred eighteen PCOS cases and 1057 controls were recruited. Genotyping of two SNPs (rs17008097 and rs17008940) in USP34 gene were performed by TaqMan-MGB probe assay and genotype-phenotype analysis was conducted subsequently.

Results

The differences of allele or genotype frequencies were not significant statistically between PCOS and controls, even after age and BMI adjustment. For clinical and metabolic features (LH, T and HOMA-IR) analysis in PCOS cases, no statistical differences among three genotypes of rs17008097 and rs17008940 were found. However, rs17008940 was shown to be slightly associated with BMI in PCOS cases rather than in controls, even after age adjustment (TC vs CC P = 0.006, OR = 1.042, 95% CI 1.012–1.073; TT vs CC P = 0.037, OR = 1.050, 95% CI 1.003–1.100).

Conclusions

USP34 gene polymorphisms (rs17008097 and rs17008940) may not be associated with PCOS in the Han Chinese women.

Electronic supplementary material

The online version of this article (doi:10.1186/s13048-015-0158-y) contains supplementary material, which is available to authorized users.

Clinical genetic research 2: Genetic epidemiology of complex phenotypes

Genetic factors play a substantive role in the susceptibility to common diseases. Due to recent and rapid advancements in characterization of genetic variants and large-scale genotyping platforms, multiple genes and genetic variants have now been identified for common, complex diseases. The most efficient method for gene identification at present appears to be large-scale association-based studies, which integrate genetic and epidemiological principles. As the strategy for gene identification studies has shifted towards genetic association-based methods rather than traditional linkage analysis, epidemiological methods are increasingly being integrated into genetic investigations. Consequently, the disciplines of genetics and epidemiology, which historically have functioned separately, have been integrated into a discipline referred to as genetic epidemiology. In this chapter, we review methods for establishing the genetic burden of complex genetic disease, followed by methods for gene and/or genetic variant identification and when appropriate we highlight the epidemiological issues that guide these methods.

Combined effects of genetic variants of the PTEN, AKT1, MDM2 and p53 genes on the risk of nasopharyngeal carcinoma

Phosphatase and tensin homolog (PTEN), v-akt murine thymoma viral oncogene homolog 1 (AKT1), mouse double minute 2 (MDM2) and p53 play important roles in the development of cancer. We examined whether the single nucleotide polymorphisms (SNPs) in the PTEN, AKT1, MDM2 and p53 genes were related to the risk and severity of nasopharyngeal carcinoma (NPC) in the Chinese population. Seven SNPs [p53 rs1042522, PTEN rs11202592, AKT1 SNP1-5 (rs3803300, rs1130214, rs3730358, rs1130233 and rs2494732)] were genotyped in 593 NPC cases and 480 controls by PCR direct sequencing or PCR-RFLP analysis. Multivariate logistic regression analysis was used to calculate adjusted odds ratios (ORs) and 95% confidence intervals (CIs). None of the polymorphisms alone was associated with the risk or severity of NPC. However, haplotype analyses indicated that a two-SNP core haplotype (SNP4-5, AA) in AKT1 was associated with a significantly increased susceptibility to NPC risk (adjusted OR  =  3.87, 95% CI  =  1.96-7.65; P<0.001). Furthermore, there was a significantly increased risk of NPC associated with the combined risk genotypes (i.e., p53 rs1042522 Arg/Pro + Pro/Pro, MDM2 rs2279244 G/T + G/G, PTEN rs11202592 C/C, AKT1 rs1130233 A/A). Compared with the low-risk group (0-2 combined risk genotypes), the high-risk group (3-4 combined risk genotypes) was associated with a significantly increased susceptibility to NPC risk (adjusted OR  =  1.67, 95% CI  =  1.12-2.50; P = 0.012). Our results suggest that genetic variants in the PTEN, AKT1, MDM2 and p53 tumor suppressor-oncoprotein network may play roles in mediating the susceptibility to NPC in Chinese populations.

Genome-wide association mapping of acute lung injury in neonatal inbred mice

Reactive oxygen species (ROS) contribute to the pathogenesis of many acute and chronic pulmonary disorders, including bronchopulmonary dysplasia (BPD), a respiratory condition that affects preterm infants. However, the mechanisms of susceptibility to oxidant stress in neonatal lungs are not completely understood. We evaluated the role of genetic background in response to oxidant stress in the neonatal lung by exposing mice from 36 inbred strains to hyperoxia (95% O2) for 72 h after birth. Hyperoxia-induced lung injury was evaluated by using bronchoalveolar lavage fluid (BALF) analysis and pathology. Statistically significant interstrain variation was found for BALF inflammatory cells and protein (heritability estimates range: 33.6-55.7%). Genome-wide association mapping using injury phenotypes identified quantitative trait loci (QTLs) on chromosomes 1, 2, 4, 6, and 7. Comparative mapping of the chromosome 6 QTLs identified Chrm2 (cholinergic receptor, muscarinic 2, cardiac) as a candidate susceptibility gene, and mouse strains with a nonsynonymous coding single-nucleotide polymorphism (SNP) in Chrm2 that causes an amino acid substitution (P265L) had significantly reduced hyperoxia-induced inflammation compared to strains without the SNP. Further, hyperoxia-induced lung injury was significantly reduced in neonatal mice with targeted deletion of Chrm2, relative to wild-type controls. This study has important implications for understanding the mechanisms of oxidative lung injury in neonates.

Epigenetics in posttraumatic stress disorder

Reported exposure to traumatic event is relatively common within the general population (40-90%), but only a fraction of individuals will develop posttraumatic stress disorder (PTSD). Indeed, the lifetime prevalence of PTSD is estimated to range between 7% and 12%. The factors influencing risk or resilience to PTSD after exposure to traumatic events are likely both environmental, such as type, timing, and extent of trauma, and genetic. Recently, epigenetic mechanisms have been implicated in mediating altered risk for PTSD as they can reflect both genetic and environmental influences. In this chapter, we describe the accumulating evidences for epigenetic factors in PTSD highlighting the importance of sensitive periods as well as methodological aspects such as tissue availabilities for such studies. We describe studies using a candidate gene approach focusing mainly on key players in the stress hormone regulation that show epigenetic alterations both in humans and in animal models for PTSD. We also summarize the results of epigenome-wide studies reporting associations with PTSD. For the above, we focus on one epigenetic mechanism, DNA methylation, as it is so far the best studied for this disorder. Finally, we describe how epigenetic mechanisms could be responsible for the long-lasting effects of gene-environment interactions observed in PTSD.

Association study of germline variants in CCNB1 and CDK1 with breast cancer susceptibility, progression, and survival among Chinese Han women

The CCNB1 and CDK1 genes encode the proteins of CyclinB1 and CDK1 respectively, which interact with each other and are involved in cell cycle regulation, centrosome duplication and chromosome segregation. This study aimed to investigate whether the genetic variants in these two genes may affect breast cancer (BC) susceptibility, progression, and survival in Chinese Han population using haplotype-based analysis. A total of ten tSNPs spanning from 2kb upstream to 2kb downstream of these genes were genotyped in 1204 cases and 1204 age-matched cancer-free controls. The haplotype blocks were determined according to our genotyping data and linkage disequilibrium (LD) status of these SNPs. For CCNB1, rs2069429 was significantly associated with increased BC susceptibility under recessive model (OR=2.352, 95%CI=1.480-3.737), so was the diplotype TAGT/TAGT (OR=1.947 95%CI=1.154-3.284, P=0.013). In addition, rs164390 was associated with Her2-negative BC. For CDK1, rs2448343 and rs1871446 were significantly associated with decreased BC risk under dominant models, so was the haplotype ATATT. These two SNPs also showed a dose-dependent effect on BC susceptibility. Using stratified association analysis, we found that women with the heterozygotes or minor allele homozygotes of rs2448343 had much less BC susceptibility among women with BMI<23. In CDK1, three closely located SNPs, rs2448343, rs3213048 and rs3213067, were significantly associated with tumor’s PR status: the heterozygotes of rs2448343 were associated with PR-positive tumors, while the minor allele homozygotes of rs3213048 and heterozygotes of rs3213067 were associated with PR-negative BC tumors. In survival analysis, rs1871446 was associated with unfavorable event-free survival under recessive model, so was the CDK1 diplotype ATATG/ATATG, which carried the minor allele homozygote of rs1871446. Our study indicates that genetic polymorphisms of CCNB1 and CDK1 are related to BC susceptibility, progression, and survival in Chinese Han women. Further studies need to be performed in other populations as an independent replication to verify these results.

Demonstration of genome-wide association studies for identifying markers for wood property and male strobili traits in Cryptomeria japonica

Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. In the present study, we examined the potential of GWAS in conifers using 367 unrelated plus trees of Cryptomeria japonica D. Don, which is the most widely planted and commercially important tree species in Japan, and tried to detect significant associations between wood property traits and quantity of male strobili on the one hand, and 1,032 single nucleotide polymorphisms (SNPs) assigned to 1,032 genes on the other. Association analysis was performed with the mixed linear model taking into account kinship relationships and subpopulation structure. In total, 6 SNPs were found to have significant associations with the variations in phenotype. These SNPs were not associated with the positions of known genes and QTLs that have been reported to date, thus they may identify novel QTLs. These 6 SNPs were all found in sequences showing similarities with known genes, although further analysis is required to dissect the ways in which they affect wood property traits and abundance of male strobili. These presumptive QTL loci provide opportunities for improvement of C. japonica, based on a marker approach. The results suggest that GWAS has potential for use in future breeding programs in C. japonica.

Genome-wide association analysis for nine agronomic traits in maize under well-watered and water-stressed conditions

Drought can cause severe reduction in maize production, and strongly threatens crop yields. To dissect this complex trait and identify superior alleles, 350 tropical and subtropical maize inbred lines were genotyped using a 1536-SNP array developed from drought-related genes and an array of 56,110 random SNPs. The inbred lines were crossed with a common tester, CML312, and the testcrosses were phenotyped for nine traits under well-watered and water-stressed conditions in seven environments. Using genome-wide association mapping with correction for population structure, 42 associated SNPs (P ≤ 2.25 × 10(-6) 0.1/N) were identified, located in 33 genes for 126 trait × environment × treatment combinations. Of these genes, three were co-localized to drought-related QTL regions. Gene GRMZM2G125777 was strongly associated with ear relative position, hundred kernel weight and timing of male and female flowering, and encodes NAC domain-containing protein 2, a transcription factor expressed in different tissues. These results provide some good information for understanding the genetic basis for drought tolerance and further studies on identified candidate genes should illuminate mechanisms of drought tolerance and provide tools for designing drought-tolerant maize cultivars tailored to different environmental scenarios.

Interactions between the FTO and GNB3 genes contribute to varied clinical phenotypes in hypertension

BACKGROUND

The genes FTO and GNB3 are implicated in essential hypertension but their interaction remains to be explored. This study investigates the role of interaction between the two genes in the pathophysiology of essential hypertension.

METHODS/PRINCIPAL FINDINGS

In a case-control study comprising 750 controls and 550 patients, interaction between the polymorphisms of FTO and GNB3 was examined using multifactor dimensionality reduction (MDR). The influence of interaction on clinical phenotypes like systolic and diastolic blood pressure, mean arterial pressure and body mass index was also investigated. The 3-locus MDR model comprising FTO rs8050136C/A and GNB3 rs1129649T/C and rs5443C/T emerged as the best disease conferring model. Moreover, the interacted-genotypes having either 1, 2, 3, 4 or 5 risk alleles correlated with linearly increasing odds ratios of 1.91 (P = 0.027); 3.93 (P = 2.08E-06); 4.51 (P = 7.63E-07); 7.44 (P = 3.66E-08) and 11.57 (P = 1.18E-05), respectively, when compared with interacted-genotypes devoid of risk alleles. Furthermore, interactions among haplotypes of FTO (H1-9) and GNB3 (Ha-d) differed by >1.5-fold for protective-haplotypes, CTGGC+TC [H2+Ha] and CTGAC+TC [H4+Ha] (OR = 0.39, P = 0.003; OR = 0.22, P = 6.86E-05, respectively) and risk-haplotypes, AAAGC+CT [H3+Hc] and AAAGC+TT [H3+Hd] (OR = 2.91, P = 9.98E-06; OR = 2.50, P = 0.004, respectively) compared to individual haplotypes. Moreover, the effectiveness of gene-gene interaction was further corroborated with a 1.29-, 1.25- and 1.38-fold higher SBP, MAP and BMI, respectively, in patients having risk interacted-haplotype H3+Hc and 2.48-fold higher SBP having risk interacted-haplotype H3+Hd compared to individual haplotypes.

CONCLUSION

Interactions between genetic variants of FTO and GNB3 influence clinical parameters to augment hypertension.

Population-based case-control association studies

This unit provides an overview of the design and analysis of population-based case-control studies of genetic risk factors for complex disease. Considerations specific to genetic studies are emphasized. The unit reviews basic study designs differentiating case-control studies from others, presents different genetic association strategies (candidate gene, genome-wide association, and high-throughput sequencing), introduces basic methods of statistical analysis for case-control data and approaches to combining case-control studies, and discusses measures of association and impact. Admixed populations, controlling for confounding (including population stratification), consideration of multiple loci and environmental risk factors, and complementary analyses of haplotypes, genes, and pathways are briefly discussed. Readers are referred to basic texts on epidemiology for more details on general conduct of case-control studies.

SNP in the genome-wide association study hotspot on chromosome 9p21 confers susceptibility to diabetic nephropathy in type 1 diabetes

AIMS/HYPOTHESIS

Parental type 2 diabetes mellitus increases the risk of diabetic nephropathy in offspring with type 1 diabetes mellitus. Several single nucleotide polymorphisms (SNPs) that predispose to type 2 diabetes mellitus have recently been identified. It is, however, not known whether such SNPs also confer susceptibility to diabetic nephropathy in patients with type 1 diabetes mellitus.

METHODS

We genotyped nine SNPs associated with type 2 diabetes mellitus in genome-wide association studies in the Finnish population, and tested for their association with diabetic nephropathy as well as with severe retinopathy and cardiovascular disease in 2,963 patients with type 1 diabetes mellitus. Replication of significant SNPs was sought in 2,980 patients from three other cohorts.

RESULTS

In the discovery cohort, rs10811661 near gene CDKN2A/B was associated with diabetic nephropathy. The association remained after robust Bonferroni correction for the total number of tests performed in this study (OR 1.33 [95% CI 1.14, 1.56], p = 0.00045, p (36tests) = 0.016). In the meta-analysis, the combined result for diabetic nephropathy was significant, with a fixed effects p value of 0.011 (OR 1.15 [95% CI 1.02, 1.29]). The association was particularly strong when patients with end-stage renal disease were compared with controls (OR 1.35 [95% CI 1.13, 1.60], p = 0.00038). The same SNP was also associated with severe retinopathy (OR 1.37 [95% CI 1.10, 1.69] p = 0.0040), but the association did not remain after Bonferroni correction (p (36tests) = 0.14). None of the other selected SNPs was associated with nephropathy, severe retinopathy or cardiovascular disease.

CONCLUSIONS/INTERPRETATION

A SNP predisposing to type 2 diabetes mellitus, rs10811661 near CDKN2A/B, is associated with diabetic nephropathy in patients with type 1 diabetes mellitus.

A comparison of approaches for association studies of polymorphisms and colorectal cancer risk

AIM

Meta-analyses have been used to evaluate associations between polymorphisms and colorectal cancer risk, but the quality of individual studies used to inform them may vary substantially. Our aim was to apply well-established quality-control criteria to individual association studies and then compare the results of meta-analyses that included or excluded studies that did not meet these criteria.

METHOD

We used meta-analyses of studies reporting a relationship between polymorphisms and colorectal cancer published between 1996 and 2008. Polymorphism-cancer associations were derived in separate meta-analyses including only those meeting the quality-control criteria.

RESULTS

Relative ORs varied substantially between the open and restricted group meta-analyses for all variants except MTHFR 677 CT. However, the associations were modest and the direction of relative risk did not change after applying criteria. Publication bias was detected for all associations, except the restricted set of studies for GSTP1 GG.

CONCLUSION

We observed variation in calculated relative risk and changes in tests for publication bias that were dependent on the inclusion criteria used for association studies of polymorphisms and colorectal cancer. Standardizing study inclusion criteria may reduce the variation in findings for meta-analyses of gene-association studies of common diseases such as colorectal cancer.

ADRB2 G-G haplotype associated with breast cancer risk among Hispanic and non-Hispanic white women: interaction with type 2 diabetes and obesity

INTRODUCTION

Polymorphisms in the beta-2-adrenergic receptor (ADRB2) gene have been studied in relation to risk of type 2 diabetes and obesity, risk factors that have received increased attention in relation to breast cancer. We evaluated the hypothesis that ADRB2 variants (rs1042713, rs1042714) are associated with breast cancer risk in non-Hispanic white (NHW) and Hispanic (H) women using data from a population-based case-control study conducted in the southwestern United States.

METHODS

Data on lifestyle and medical history, and blood samples, were collected during in-person interviews for incident primary breast cancer cases (1,244 NHW, 606 H) and controls (1,330 NHW, 728 H). ADRB2 genotypes for rs1042713(G/A) and rs1042714(G/C) were determined using TaqMan assays. The associations of each variant and corresponding haplotypes with breast cancer were estimated using multivariable logistic regression.

RESULTS

Two copies compared to one or zero copies of the ADRB2 G-G haplotype were associated with increased breast cancer risk for NHW women [odds ratio (OR), 1.95; 95 % confidence interval (95 % CI), 1.26-3.01], but with reduced risk for H women [OR, 0.74; 95 % CI, 0.50-1.09]. Effect estimates were strengthened for women with a body mass index (BMI) ≥25 kg/m(2) [H: OR, 0.50; 95 % CI, 0.31-0.82; NHW: OR, 3.85; 95 % CI, 1.88-7.88] and for H women with a history of diabetes [H: OR, 0.32; 95 % CI, 0.12-0.89].

CONCLUSIONS

These data suggest that ethnicity modifies the association between the ADRB2 G-G haplotype and breast cancer risk, and being overweight or obese enhances the divergence of risk between H and NHW women.

Genetic variability in glutamic acid decarboxylase genes: associations with post-traumatic seizures after severe TBI

Post traumatic seizures (PTS) occur frequently after traumatic brain injury (TBI). Since gamma-amino butyric acid (GABA) neurotransmission is central to excitotoxicity and seizure development across multiple models, we investigated how genetic variability for glutamic acid decarboxylase (GAD) influences risk for PTS. Using both a tagging and functional single nucleotide polymorphism (SNP) approach, we genotyped the GAD1 and GAD2 genes and linked them with PTS data, regarding time to first seizure, obtained for 257 adult subjects with severe TBI. No significant associations were found for GAD2. In the GAD1 gene, the tagging SNP (tSNP) rs3828275 was associated with an increased risk for PTS occurring <1 wk. The tSNP rs769391 and the functional SNP rs3791878 in the GAD1 gene were associated with increased PTS risk occurring 1 wk-6 mo post-injury. Both risk variants conferred an increased susceptibility to PTS compared to subjects with 0-1 risk variant. Also, those with haplotypes having both risk variants had a higher PTS risk 1 wk-6 mo post-injury than those without these haplotypes. Similarly, diplotype analysis showed those with 2 copies of the haplotype containing both risk alleles were at the highest PTS risk. These results implicate genetic variability within the GABA system in modulating the development of PTS.