Association study designs for complex diseases

Family Discordance in Gender Identification Is Not Associated with Increased Depression and Anxiety Among Trans Youth

Purpose: We examined the relationship between parent- and child-reported gender identity of the youth with internalizing symptoms in transgender and gender-diverse (TGD) youth. In addition, we investigated differences in sex assigned at birth ratios and pubertal development stages in TGD and cisgender youth. Methods: We analyzed longitudinal data from the Adolescent Brain Cognitive Development study (ABCD), corresponding to baseline and 1st-to-3rd-year follow-up interviews (n = 6030 to n = 9743, age range [9-13]). Sociodemographic variables, self- and parent-reported gender identity, and clinical measures were collected. Results: TGD youth showed higher levels of internalizing symptoms compared with cisgender youth. However, this was not worsened by discordance in gender identification between TGD youth and parents. Over the 3-year follow-up period, the proportion of TGD participants increased from 0.8% (95% confidence interval (CI) [0.6-1.0]) at baseline to 1.4% (95% CI [1.1-1.7]) at the 3rd-year follow-up (χ2 = 10.476, df = 1, false discovery rate (FDR)-adjusted p = 0.00256), particularly among those assigned female at birth (AFAB) in relation to people assigned male at birth (AMAB) (AMAB:AFAB at baseline: 1:1.9 vs. AMAB:AFAB at 3rd-year follow-up: 1:4.7, χ2 = 40.357, df = 1, FDR-adjusted p < 0.0001). Conclusions: TGD youth in ABCD reported higher internalizing symptoms than cisgender youth, although this was not affected by parental discordance in gender identification. A substantial increase over time in TGD children AFAB was documented. More research is needed to understand the clinical implications of these preliminary results, for which the longitudinal design of ABCD will be crucial.

Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple (Malus × domestica Borkh.)

Genetic diversity is the primary source of variability in any crop improvement program, and the diverse germplasm of any crop species represents an important genetic resource for gene or allele mining to meet future needs. Huge genetic and phenotypic diversity is present in the apple gene pool, even though, breeding programs have been mainly focused on a few traits of interests, which have resulted in the reduction of the diversity in the cultivated lines of apple. Therefore, the present study was carried out on 70 diverse apple genotypes with the objective of analyzing the genetic diversity and to identify the genetic loci associated with important fruit quality traits. A total of 140 SSR primers were used to characterize the 70 genotypes of apples, out of which only 88 SSRs were found to be polymorphic. The PIC values varied from 0.03 to 0.75. The value of MI, EMR, and RP varied from 0.03 to 3.5, 0.5 to 5.0, and 1.89 to 6.74, respectively. The dendrogram and structure analysis divided all the genotypes into two main groups. In addition to this, large phenotypic variability was observed for the fruit quality traits under study indicated the suitability of the genotypes for association studies. Altogether 71 novel MTAs were identified for 10 fruit quality traits, of which 15 for fruit length, 15 for fruit diameter, 12 for fruit weight, 2 for total sugar, 2 for TSS, 4 for reducing sugar, 5 for non-reducing sugar, 5 for fruit firmness, 5 for fruit acidity and 6 for anthocyanin, respectively. Consistent with the physicochemical evaluation of traits, there was a significant correlation coefficient among different fruit quality characters, and many common markers were found to be associated with these traits (fruit diameter, length, TSS, total sugar, acidity and anthocyanin, respectively) by using the different modeling techniques (GLM, MLM). The inferred genetic structure, diversity pattern and the identified MTAs will be serving as resourceful grounds for better predictions and understanding of apple genome towards efficient conservation and utilization of apple germplasm for facilitating genetic improvement of fruit quality traits. Furthermore, these findings also suggested that association mapping could be a viable alternative to the conventional QTL mapping approach in apple.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01382-w.

Lack of association between the VEGFA gene polymorphisms and preterm birth in Korean women

Preterm birth (PTB), a pregnancy-related disease, is defined as a birth before 37 weeks of gestation. It is a major cause of maternal mortality and morbidity worldwide, and its incidence rate is steadily increasing. Various genetic factors can contribute to the etiology of PTB. Vascular endothelial growth factor A (VEGFA) gene is an important angiogenic gene and its polymorphisms have been reported to be associated with PTB development. Therefore, we conducted a case-control study to evaluate the association between VEGFA rs699947, rs2010963, and rs3025039 polymorphisms and PTB in Korean women. A total of 271 subjects (116 patients with PTB and 155 women at ≥38 weeks of gestation) were analyzed in this study. The genotyping of VEGFA gene polymorphisms was performed using polymerase chain reaction- restriction fragment length polymorphism. No significant association between the patients with PTB and the control groups was confirmed. In the combination analysis, we found a significant association between PTB and VEGFA rs699947 CC-rs2010963 GG-rs3025039 CC combination (odds ratio, 3.77; 95% confidence interval, 1.091 to 13.032; p = 0.031). The VEGFA rs699947, rs2010963, and rs3025039 polymorphisms might have no genetic association with the pathogenesis of PTB in Korean women. However, the combination analysis indicates the possibility that VEGFA acts in PTB pathophysiology. Therefore, larger sample sets and replication studies are required to further elucidate our findings.

Genetic Markers Predisposing to Nonalcoholic Steatohepatitis

The growing prevalence of nonalcoholic fatty liver disease (NAFLD) has sparked interest in understanding genetics and epigenetics associated with the development and progression of the disease. A better understanding of the genetic factors related to progression will be beneficial in the risk stratification of patients. These genetic markers can also serve as potential therapeutic targets in the future. In this review, we focus on the genetic markers associated with the progression and severity of NAFLD.

Haplotype-dependent HLA-DRB1-DQB1 susceptibility to occult HBV infection in Xi'an Han population

BACKGROUND

Occult hepatitis B virus (HBV) infection (OBI) is primarily characterized by the persistence of HBV-DNA in the liver tissues and/or in the serum without detectable HBsAg. Human leukocyte antigen (HLA) polymorphisms have been found to be strongly associated with HBV in different ethnic backgrounds. The association of HLA-DRB1-DQB1 haplotypes with OBI has not been previously reported in China. The aim of this study was to identify the potential association of HLA-DRB1-DQB1 haplotypes that may be involved in OBI genetic susceptibility.

METHODS

A case-control study was conducted between 107 OBI subjects and 280 healthy controls from the blood donors in the Shaanxi Province Blood Center. The HLA-DRB1, DQB1 loci were genotyped using polymerase chain reaction-sequence based typing (PCR-SBT). Based on the genotype data of the two loci, haplotype estimation was performed.

RESULTS

HLA-DRB1*07:01-DQB1*02:02 (pc = 0.344 × 10^-3 , OR = 3.489, 95%CI = 2.000-6.088) and HLA-DRB1*09:01-DQB1*03:03 (pc = 0.02, OR = 2.370, 95%CI = 1.450-3.873) serve as the possible risk and susceptibility haplotypes for OBI in Xi'an Han after Bonferroni correction.

CONCLUSIONS

This study demonstrated that HLA II haplotypes were significantly associated with OBI in the Xi'an Han population. To the best of our knowledge, this is the first study to associate HLA-DRB1-DQB1 haplotypes with OBI, which can provide valuable insights into the relationship between the various genetic factors and immune responses in the Xi'an population. The findings can also form the basis for future studies about the role of HLA in OBI.

The genetics of non-monogenic IBD

Inflammatory bowel disease (IBD), with Crohn's disease and ulcerative colitis as main subtypes, is a prototypical multifactorial disease with both genetic and environmental factors involved. Genetically, IBD covers a wide spectrum from monogenic to polygenic forms. In polygenic disease, many genetic variants each contribute a small amount to disease risk. With the advent of genome-wide association studies (GWAS), it became possible to find these variants and corresponding genes, leading so far to the discovery of ca 240 loci associated with IBD. Together, these however explain only 20-25% of the heritability of IBD, leaving a large portion unaccounted for. This missing heritability might be hidden in common variants with even lower effect than the ones currently found through GWAS, but also in rare variants which can be found through large-scale sequencing studies or potentially in multiplex families. In this review, we will give an overview of the current knowledge about the genetics of non-monogenic IBD and how it differs from the monogenic form(s), and future perspectives. The history of IBD genetic studies from twin studies over linkage studies to GWAS, and finally large-scale sequencing studies and the revisiting of multiplex families will be discussed.

A Guide to Genome-Wide Association Study Design for Diabetic Retinopathy

Diabetic retinopathy (DR) is the most common microvascular complication related to diabetes. There is evidence that genetics play an important role in DR pathogenesis, but the complexity of the disease makes genetic studies a challenge. This chapter is a practical overview of the basic steps for genome-wide association studies with respect to DR and its associated traits. Also described are approaches that can be adopted in future DR studies. This is intended to serve as a guide for beginners and to provide a framework for further in-depth analysis.

MDM4: What do we know about the association between its polymorphisms and cancer?

MDM4 is an important p53-negative regulator, consequently, it is involved in cell proliferation, DNA repair, and apoptosis regulation. MDM4 overexpression and amplification are described to lead to cancer formation, metastasis, and poor disease prognosis. Several MDM4 SNPs are in non-coding regions, and some affect the MDM4 regulation by disrupting the micro RNA binding site in 3'UTR (untranslated region). Here, we gathered several association studies with different MDM4 SNPs and populations to understand the relationship between its SNPs and solid tumor risk. Many studies failed to replicate their results regarding different populations, cancer types, and risk genotypes, leading to conflicting conclusions. We suggested that distinct haplotype patterns in different populations might affect the association between MDM4 SNPs and cancer risk. Thus, we propose to investigate some linkage SNPs in specific haplotypes to provide informative MDM4 markers for association studies with cancer.

A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs

To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.

Human Genetics to Identify Therapeutic Targets for NAFLD: Challenges and Opportunities

Non-alcoholic fatty liver disease (NAFLD) is a continuous progression of pathophysiologic stages that is challenging to diagnose due to its inherent heterogeneity and poor standardization across a wide variety of diagnostic measures. NAFLD is heritable, and several loci have been robustly associated with various stages of disease. In the past few years, larger genetic association studies using new methodology have identified novel genes associated with NAFLD, some of which have shown therapeutic promise. This mini-review provides an overview of the heterogeneity in NAFLD phenotypes and diagnostic methods, discusses genetic associations in relation to the specific stages for which they were identified, and offers a perspective on the design of future genetic mapping studies to accelerate therapeutic target identification.

Polygenic risk scores: the future of cancer risk prediction, screening, and precision prevention

Genome-wide association studies (GWASs) have shown that the genetic architecture of cancers are highly polygenic and enabled researchers to identify genetic risk loci for cancers. The genetic variants associated with a cancer can be combined into a polygenic risk score (PRS), which captures part of an individual's genetic susceptibility to cancer. Recently, PRSs have been widely used in cancer risk prediction and are shown to be capable of identifying groups of individuals who could benefit from the knowledge of their probabilistic susceptibility to cancer, which leads to an increased interest in understanding the potential utility of PRSs that might further refine the assessment and management of cancer risk. In this context, we provide an overview of the major discoveries from cancer GWASs. We then review the methodologies used for PRS construction, and describe steps for the development and evaluation of risk prediction models that include PRS and/or conventional risk factors. Potential utility of PRSs in cancer risk prediction, screening, and precision prevention are illustrated. Challenges and practical considerations relevant to the implementation of PRSs in health care settings are discussed.

Meta-analysis of the association between mTORC1-related genes polymorphisms and cancer risk

BACKGROUND

mTOR, mLST8 and RAPTOR are the core components of mTORC1, which has been found to be closely related to tumorigenesis. Currently, multiple single nucleotide polymorphisms (SNPs) in mTOR gene (rs2295080, rs17036508 and rs1034528), mLST8 gene (rs3160 and rs26865) and RPTOR gene (rs1062935, rs3751932, rs3751834, rs12602885) have been extensively studied for their associations with cancer risk. However, the results remained inconclusive and conflicting. Therefore, we here performed a meta-analysis of all available studies to investigate the association between these SNPs and cancer risk.

METHODS

Up to April 2021, 25 related publications were retrieved and included in this meta-analysis. The odds ratios (ORs) and 95% confidence intervals (CIs) calculated by fixed or random effects models were applied to assess the strength of association. Trial Sequential Analysis (TSA) was conducted to weaken the random error and enhance the reliability of evidence.

RESULTS

After Bonferroni correction, it was revealed that rs3160, rs26865, rs1062935, rs3751932, rs3751834 and rs10602885 were not associated with cancer risk. However, rs17036508 and rs1034528 showed significant association with total cancer risk. A significant association was also found between rs2295080 and total cancer risk, and stratified analysis by cancer type suggested that rs2295080 was specifically associated with acute lymphoblastic leukemia risk, prostate cancer risk, and breast cancer risk.

CONCLUSIONS

The present meta-analysis suggested that the rs2295080, rs17036508 and rs1034528 polymorphisms in mTOR gene may be the susceptive factors for cancer development, while the target genetic polymorphisms in mLST8 gene or RPTOR gene may not be associated with cancer risk. However, these findings remain to be confirmed or further reinforced in large and well-designed studies in different ethnic populations.

Problems and promises: How to tell the story of a Genome Wide Association Study?

The promise of treatments for common complex diseases (CCDs) is understood as an important force driving large scale genetics research over the last few decades. This paper considers the phenomenon of the Genome Wide Association Study (GWAS) via one high profile example, the Wellcome Trust Case Control Consortium (WTCCC). The WTCCC despite not fulfilling promises of new health interventions is still understood as an important step towards tackling CCDs clinically. The 'sociology of expectations' has considered many examples of failure to fulfil promises and the subsequent negative consequences including disillusionment, disappointment and disinvestment. In order to explore why some domains remain resilient in the face of apparent failure, I employ the concept of the 'problematic' found in the work of Giles Deleuze. This alternative theoretical framework challenges the idea that the failure to reach promised goals results in largely negative outcomes for a given field. I will argue that collective scientific action is motivated not only by hopes for the future but also by the drive to create solutions to the actual setbacks and successes which scientists encounter in their day-to-day work. I draw on eighteen interviews.

Association Study and Mendelian Randomization Analysis Reveal Effects of the Genetic Interaction Between PtoMIR403b and PtoGT31B-1 on Wood Formation in Populus tomentosa

MicroRNAs (miRNAs), important posttranscriptional regulators of gene expression, play a crucial role in plant growth and development. A single miRNA can regulate numerous target genes, making the determination of its function and interaction with targets challenging. We identified PtomiR403b target to PtoGT31B-1, which encodes a galactosyltransferase responsible for the biosynthesis of cell wall polysaccharides. We performed an association study and epistasis and Mendelian randomization (MR) analyses to explore how the genetic interaction between PtoMIR403b and its target PtoGT31B-1 underlies wood formation. Single nucleotide polymorphism (SNP)-based association studies identified 25 significant associations (P < 0.01, Q < 0.05), and PtoMIR403b and PtoGT31B-1 were associated with five traits, suggesting a role for PtomiR403b and PtoGT31B-1 in wood formation. Epistasis analysis identified 93 significant pairwise epistatic associations with 10 wood formation traits, and 37.89% of the SNP-SNP pairs indicated interactions between PtoMIR403b and PtoGT31B-1. We performed an MR analysis to demonstrate the causality of the relationships between SNPs in PtoMIR403b and wood property traits and that PtoMIR403b modulates wood formation by regulating expression of PtoGT31B-1. Therefore, our findings will facilitate dissection of the functions and interactions with miRNA-targets.

Polymorphisms in the FKBP5 gene are associated with attention deficit and hyperactivity disorder in Korean children

Attention deficit hyperactivity disorder (ADHD) is a common and heritable childhood psychiatric disorder. Recently, many studies reported a down-regulated hypothalamus-pituitary-adrenal axis (HPA-axis) with low cortisol levels in children with ADHD. The FK506 binding protein 5 or FKBP5 gene regulates the negative feedback of the HPA-axis, and genetic variants in this gene showed an association with ADHD. We investigated the genetic association between FKBP5 gene polymorphisms and susceptibility to ADHD in Korean children. We conducted a case-control study with 150 ADHD children and 322 controls. Genotyping of FKBP5 rs9394309 and rs7748266 was performed by using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP). Our results showed that rs7748266 polymorphism has significant genotype (p = 0.021) and allele (p = 0.009) frequency differences between children with ADHD and the control group. CT genotype [odds ratio (OR) 1.70, 95 % confidence interval (CI) 1.134-2.540, p = 0.010] and T allele (OR 1.54, 95 % CI 1.114-2.117, p = 0.009) were associated with increased risk of ADHD. In addition, dominant (p = 0.006) and over-dominant genetic (p = 0.016) models showed significant associations with ADHD. In the stratified analysis, a significant result was obtained from the girl samples (p = 0.048). The OR of the girls with ADHD with CT genotype was 2.29 (95 % CI 1.170-4.469, p = 0.014). In contrast to rs7748266 polymorphism, rs9394309 polymorphism did not show any significant result (p > 0.05). Haplotype analysis also revealed a significant difference of the TG haplotype for rs7748266 - rs9394309 (p = 0.028, global haplotype association p-value of 0.0091). Conclusively, we confirmed that FKBP5 gene polymorphisms were associated with ADHD in Korean children. These results suggested that FKBP5 may factor in the development of ADHD.

Investigation of eNOS gene polymorphism exposes a genetic association between endothelial dysfunction and osteoporosis in postmenopausal women

OBJECTIVES

To investigate the association of genetic polymorphisms of endothelial nitric oxide synthase (eNOS) gene with endothelial dysfunction associated osteoporosis in postmenopausal women of Punjab, India.

METHODS

The study involved 456 postmenopausal women having endothelial dysfunction categorized according to women with (n = 236) and without osteoporosis (n = 220). Bone mineral density (BMD) and reactive hyperemia index (RHI) were evaluated together with six single-nucleotide polymorphisms (SNPs) within the eNOS gene (rs2070744, rs1799983, rs1800780, rs3918181, rs891512, and rs1808593).

RESULTS

A moderate association between RHI and BMD at femoral neck (r = 0.213, P = 0.002) and lumbar spine (r = 0.267, P < 0.001) was observed. Minor alleles C and T of SNPs rs2070744 and rs1799983 were associated with chances of osteoporosis in both co-dominant (odds ratio [OR] 2.13, P = 0.017; OR 2.77, P = 0.009) and dominant (OR 2.10, P = 0.011; OR 2.45, P = 0.007) modes, whereas minor allele A of SNP rs891512 showed marginal probability in dominant model (OR 1.68, P = 0.047). A susceptibility haplotype (CTAAAT) was observed within the eNOS gene which conferred 2.32 times higher chances of osteoporosis (OR 2.32, 95% confidence interval 1.18-4.54, P = 0.021) after adjusting for the effect of confounders. Genetic model analysis revealed that each copy of susceptibility haplotype increased the possibility of osteoporosis by a factor of 2.11 ± 0.63 (P < 0.001). RHI was significantly associated with susceptibility haplotype CTAAAT in a dose-dependent manner, whereby the severity of endothelial dysfunction increased significantly in women having two copies over women having one copy or no copy (β = 2.13, P < 0.001) of susceptibility haplotype.

CONCLUSION

A susceptibility haplotype CTAAAT within the eNOS gene is associated with double the possibility of endothelial dysfunction affiliated osteoporosis in postmenopausal women of Punjab, India.

Network-based modeling of herb combinations in traditional Chinese medicine

Traditional Chinese medicine (TCM) has been practiced for thousands of years for treating human diseases. In comparison to modern medicine, one of the advantages of TCM is the principle of herb compatibility, known as TCM formulae. A TCM formula usually consists of multiple herbs to achieve the maximum treatment effects, where their interactions are believed to elicit the therapeutic effects. Despite being a fundamental component of TCM, the rationale of combining specific herb combinations remains unclear. In this study, we proposed a network-based method to quantify the interactions in herb pairs. We constructed a protein–protein interaction network for a given herb pair by retrieving the associated ingredients and protein targets, and determined multiple network-based distances including the closest, shortest, center, kernel, and separation, both at the ingredient and at the target levels. We found that the frequently used herb pairs tend to have shorter distances compared to random herb pairs, suggesting that a therapeutic herb pair is more likely to affect neighboring proteins in the human interactome. Furthermore, we found that the center distance determined at the ingredient level improves the discrimination of top-frequent herb pairs from random herb pairs, suggesting the rationale of considering the topologically important ingredients for inferring the mechanisms of action of TCM. Taken together, we have provided a network pharmacology framework to quantify the degree of herb interactions, which shall help explore the space of herb combinations more effectively to identify the synergistic compound interactions based on network topology.

Genome-Wide Association Study Reveals Marker-Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker-trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.

MiRNA Polymorphisms and Hepatocellular Carcinoma Susceptibility: A Systematic Review and Network Meta-Analysis

Background

Hepatocellular carcinoma (HCC) is an intractable public health threat worldwide, representing the second leading cause of cancer-related mortality, with limited early detection and therapeutic options. Recent findings have revealed that the susceptibility of HCC is closely related to microRNA (miRNA). We performed this systematic review with a network meta-analysis to investigated four single nucleotide polymorphisms (SNPs) that most regularly reported in miRNAs, exploring their involvement in HCC susceptibility and interaction with hepatitis B virus (HBV).

Methods

Databases were reviewed for related studies published up to May 2019 to identify all studies that compared genotypes of miR-146a rs2910164, miR-149 rs2292832, miR-196a2 rs11614913, and miR-499 rs3746444 with no language and date restrictions. A pairwise meta-analysis was performed to estimate pooled odds ratios and 95% confidence intervals incorporating heterogeneity to assess the relationship between four miRNA polymorphisms and HCC. To further clarify the effect of polymorphisms on HCC, a Bayesian network meta-analysis was conducted to combine the effective sizes of direct and indirect comparisons. Calculations were performed by R version 3.6.1 and STATA 14.0. All steps were performed according to PRISMA guidelines.

Results

A total of 20 studies were enrolled in this network meta-analysis, providing 5,337 hepatocellular carcinoma cases and 6,585 controls. All included studies had an acceptable quality. Pairwise meta-analysis demonstrated that miR-196a2 rs11614913 was significantly associated with the susceptibility of HCC, while the other three SNPs were not found to have a significant association. In the analysis of HCC patients under different HBV infection status, only miR-196a2 revealed correlation of threefold risk. The network results showed no significant difference in the distribution of genotype frequencies except for miR-196a2, which appeared to have the highest superiority index when comparing and ranking four SNPs.

Conclusion

MiR-196a2 rs11614913 was significantly associated with the susceptibility of HCC, especially for HBV- related HCC, and that individuals with TC/CC were more susceptible. No significant association was found in the other three miRNA genes. MiR-196a2 could serve as the best predictor of susceptibility in HCC.

Mendelian Randomization in Cardiovascular Research: Establishing Causality When There Are Unmeasured Confounders

Mendelian randomization is an epidemiological approach to making causal inferences using observational data. It makes use of the natural randomization that occurs in the generation of an individual's genetic makeup in a way that is analogous to the study design of a randomized controlled trial and uses instrumental variable analysis where the genetic variant(s) are the instrument (analogous to random allocation to treatment group in an randomized controlled trial). As with any instrumental variable, there are 3 assumptions that must be made about the genetic instrument: (1) it is associated (not necessarily causally) with the exposure (relevance condition); (2) it is associated with the outcome only through the exposure (exclusion restriction condition); and (3) it does not share a common cause with the outcome (ie, no confounders of the genetic instrument and outcome, independence condition). Using the example of type II diabetes and coronary artery disease, we demonstrate how the method may be used to investigate causality and discuss potential benefits and pitfalls. We conclude that although Mendelian randomization studies can usually not establish causality on their own, they may usefully contribute to the evidence base and increase our certainty about the effectiveness (or otherwise) of interventions to reduce cardiovascular disease.

Association of Vitamin D Metabolism Gene Polymorphisms with Autoimmunity: Evidence in Population Genetic Studies

A high prevalence of vitamin D (calcidiol) serum deficiency has been described in several autoimmune diseases, including multiple sclerosis (MS), rheumatoid arthritis (AR), and systemic lupus erythematosus (SLE). Vitamin D is a potent immunonutrient that through its main metabolite calcitriol, regulates the immunomodulation of macrophages, dendritic cells, T and B lymphocytes, which express the vitamin D receptor (VDR), and they produce and respond to calcitriol. Genetic association studies have shown that up to 65% of vitamin D serum variance may be explained due to genetic background. The 90% of genetic variability takes place in the form of single nucleotide polymorphisms (SNPs), and SNPs in genes related to vitamin D metabolism have been linked to influence the calcidiol serum levels, such as in the vitamin D binding protein (VDBP; rs2282679 GC), 25-hydroxylase (rs10751657 CYP2R1), 1α-hydroxylase (rs10877012, CYP27B1) and the vitamin D receptor (FokI (rs2228570), BsmI (rs1544410), ApaI (rs7975232), and TaqI (rs731236) VDR). Therefore, the aim of this comprehensive literature review was to discuss the current findings of functional SNPs in GC, CYP2R1, CYP27B1, and VDR associated to genetic risk, and the most common clinical features of MS, RA, and SLE.

Genetic control of tracheid properties in Norway spruce wood

Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 (PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.

Lipid levels linked to symptomatic aortic valve stenosis: evidence from Mendelian randomization?

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The association study between CYP24A1 gene polymorphisms and risk of liver, lung and gastric cancer in a Chinese population

Recently, four single nucleotide polymorphisms (rs2585428, rs4809960, rs6022999 and rs6068816) in CYP24A1 gene were extensively studied for their associations with cancer risk. However, these studies included only a few types of cancer, which calls for further investigations. In view of this, we here conducted a case-control study to explore the associations between these four CYP24A1 gene polymorphisms and risk of liver, lung and gastric cancer in a Chinese population. A total of 480 liver cancer patients, 550 lung cancer patients, 460 gastric cancer patients and 800 normal controls were recruited in this study. The genotyping of CYP24A1 gene polymorphisms was applied with Sanger sequencing assay. Single-locus analysis demonstrated that rs6022999 was significantly associated with risk of liver and lung cancer, while rs6068816 was significantly associated with the risk of gastric cancer. Haplotype analysis revealed that haplotype GTAT was associated with an increased risk of liver cancer and a decreased risk of lung cancer, and haplotype ATGC was associated with a decreased risk of lung cancer. The further meta-analysis of rs6068816 and lung cancer risk showed that rs6068816 was not associated with lung cancer risk in Chinese population, which confirmed our present finding. Conclusively, rs6022999 may be a genetic biomarker for liver and lung cancer susceptibility in Chinese population, and rs6068816 may be used to predict gastric cancer risk in Chinese population.

Lack of association between interleukin-22 gene polymorphisms and cancer risk: a case-control study and a meta-analysis

BACKGROUND

Interleukin-22 (IL22) has been implicated in inflammation and tumorigenesis. The association between IL22 gene polymorphisms and cancer risk has been widely explored. However, the limited sample sizes of previous studies may produce inadequate statistical power and conflicting results, which calls for further investigations. In this study, we recruited a total of 1490 cancer patients (480 liver cancer patients, 550 lung cancer patients, and 460 gastric cancer patients) and 800 normal controls to explore the associations between IL22 gene polymorphisms (rs1179251, rs2227485, rs2227511, and rs2227473) and cancer risk.

METHOD

The genotyping was performed with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and Sanger sequencing.

RESULTS

Our results showed that none of the four IL22 gene polymorphisms was associated with the risk of liver, lung or gastric cancer in Hubei Han Chinese population. To improve the statistical strength, a meta-analysis was further conducted. The results further confirmed our present findings and showed that rs1179251, rs2227485, and rs2227473 were not associated with cancer risk in total or stratified analysis.

CONCLUSION

Consequently, the rs1179251, rs2227485, rs2227511, and rs2227473 polymorphisms may not be associated with cancer risk. However, further investigations using larger samples in different ethnic populations are required.

Genetic association of FKBP5 with PTSD in US service members deployed to Iraq and Afghanistan

Post-traumatic stress disorder (PTSD) is a debilitating mental disorder with a prevalence of more than 7% in the US population and 12% in the military. An interaction of childhood trauma with FKBP5 (a glucocorticoid-regulated immunophilin) has been reported to be associated with PTSD in the general population. However, there are few reports on the association of FKBP5 with PTSD, particularly in important high-risk population such as the military. Here, we examined the association between four single-nucleotide polymorphisms (SNPs; rs3800373, rs9296158, rs1360780, rs9470080) covering the FKBP5 gene and probable PTSD in US service members deployed to Iraq and Afghanistan, a high-risk military population (n = 3890) (Hines et al., 2014). We found that probable PTSD subjects were significantly more likely to carry the A-allele of rs3800373, G-allele of rs9296158, C-allele of rs1360780, and C-allele of rs9470080. Furthermore, the four SNPs were in one block of strong pairwise linkage disequilibrium (r = 0.91-0.96). Within the block there were two major haplotypes of CATT and AGCC (rs3800373-rs9296158-rs1360780-rs9470080) that account for 99% of haplotype diversity. The distribution of the AGCC haplotype was significantly higher in probable PTSD subjects compared to non-PTSD (p<.05). The diplotype-based analysis indicated that the AGCC carriers tended to be probable PTSD. In this study, we demonstrated the association between FKBP5 and probable PTSD in US service members deployed to Iraq and Afghanistan, indicating that FKBP5 might be a risk factor for PTSD.

Interleukin 1 alpha (IL1A) polymorphisms and risk of endometriosis in Iranian population: a case-control study

Endometriosis is one of the most common gynecological diseases and a major cause of pain and infertility. It is influenced by genetic, epigenetic, and environmental factors. Recently, genome-wide association studies have revealed a strong association between IL1A single nucleotide polymorphisms (SNPs) and increased risk of endometriosis in Japanese women. The aim of the present study was to evaluate the association of three IL1A SNPs, rs17561, rs1304037, and rs2856836 with the risk of endometriosis in Iranian population. Totally, 105 women with diagnosis of endometriosis and 102 healthy women as control group were included. Three SNPs of the IL1A, rs17561 G/T, rs1304037 A/G, and rs2856836 T/C, were genotyped by PCR and RFLP. The rs2856836 TC genotype was significantly higher (p = .002; OR = 3.1, 95% CI: 1.5-6.5) in the patients (28.1%) than the control group (12.7%). The rs2856836 CC genotype was significantly higher (p = .047; OR = 2.3, 95% CI: 1.0-5.3) in the patients (17.5%) than the control group (10.8%). The rs2856836 C allele was significantly higher (p = .001; OR = 2.2, 95% CI: 1.4-3.6) in the patients (31.6%) than the control group (17.2%). The IL1A rs2856836 T/C SNP was associated with susceptibility to endometriosis and the rs2856836 C allele may increase the risk of endometriosis in Iranian women.

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.

The genetic etiology of eosinophilic esophagitis

Eosinophilic esophagitis (EoE) is a chronic allergic disease associated with marked mucosal eosinophil accumulation. Multiple studies have reported a strong familial component to EoE, with the presence of EoE increasing the risk for other family members with EoE. Epidemiologic studies support an important role for environmental risk factors as modulators of genetic risk. In a small percentage of cases, including patients who have Mendelian diseases with co-occurrent EoE, rare genetic variation with large effect sizes could mediate EoE and explain multigenerational incidence in families. Common genetic risk variants mediate genetic risk for the majority of patients with EoE. Across the 31 reported independent EoE risk loci (P < 10-5), most of the EoE risk variants are located in between genes (36.7%) or within the introns of genes (42.4%). Although some variants do change the amino acid sequence of genes (2.2%), only 3 of the 31 EoE risk loci harbor an amino acid-changing variant. Thus most EoE risk loci are outside of the coding regions of genes, suggesting a key role for gene regulation in patients with EoE, which is consistent with most other complex diseases.

The Role of TNF-α as a Proinflammatory Cytokine in Pathological Processes

TNF-α is a member of the vast cytokine family being considered a proinflammatory substance produced many by macrophages and other cells belonging to the innate immunity, many of them classified as indeed Antigen Presenting Cells (APCs) involved in the complex chemotactic process of activation of the adaptive immunity. The aim of this work was to accomplish a literature review concerning the main pathologies that have TNF-α as a modulating agent in other to bring light to the main interactions present in the inflammation installed.

Genetic association of interleukin 18 (-607C/A, rs1946518) single nucleotide polymorphism with asthmatic children, disease severity and total IgE serum level

Introduction

Bronchial asthma is a chronic inflammatory disease. Interleukin 18 (IL-18) single nucleotide polymorphisms (SNPs) can influence IL-18 production and activity. IL-18-607C/A and -137 C/G are two of the commonly studied SNPs of IL-18 due to their role in the etiopathogenesis of allergic diseases.

Aim of the study

The case control study was conducted to investigate the genetic association between IL-18-607C/A polymorphism and pediatric asthma. Also attempts were made to evaluate the prognostic effect of -607C/A SNP with disease severity and total serum IgE.

Material and methods

The case control study was conducted on 60 asthmatic children and 40 healthy subjects; aged 2 to 12 years. PCR-RFLP was used to detect IL-18-607C/A SNP and total serum IgE level was detected using ELISA technique.

Results

Regarding IL-18-607C/A SNP, the frequency of the A allele and CA genotype was significantly higher in asthmatic children compared to healthy control subjects (p < 0.001). Further on, asthmatic children carrying the AA/AC genotype of -607C/A SNP were associated with an increased risk of occurrence of asthma (OR = 6.417; CI = 2.432-17.289). IgE was higher in asthmatic patients carrying the heterozygous CA genotype compared to patients carrying the AA and CC genotypes (p = 0.054).

Conclusion

The frequency of the heterozygous CA genotype and A allele in IL-18-607C/A SNP was higher in asthmatic children. There is no association between the severity of asthma and -607C/A SNP. Total IgE was higher in patients carrying the CA genotypes compared to patients carrying the AA and CC genotypes, respectively.

An investigation of polymorphisms in innate and adaptive immune response genes in canine leishmaniosis

The outcome of infection with Leishmania infantum in dogs is variable, which is thought to be due to the nature of the immune response mounted by the host. As a consequence, the clinical signs and severity of canine leishmaniosis vary between individual dogs. Host immunogenetic factors might play an important role in determining the outcome of infection. The aim of this study was to examine polymorphisms in innate and adaptive immune response genes, to determine whether any of these were associated with susceptibility or resistance to L. infantum infection. Genomic DNA was obtained from two groups: pet dogs in endemic regions of Europe and a group of Beagles exposed to sand fly infection as part of a vaccine study. Genotyping was performed using a SNP (single nucleotide polymorphism) array for selected immune response genes. The first part of the study compared 62 clinical cases with 101 clinically unaffected dogs that were seronegative for Leishmania antibodies. One SNP in the CIITA gene demonstrated a significantly higher minor allele frequency in the case group, compared with the control group at the individual SNP level after permutation, but was not significant after correction for multiple testing. The second part of the study examined 48 Beagle dogs exposed to L. infantum over two transmission seasons. Twenty-seven dogs with a resistant phenotype (no evidence of clinical disease, seronegative at the end of the study period, negative on lymph node culture and only transiently PCR positive in bone marrow) were compared with 21 dogs demonstrating a susceptible phenotype (clinical disease, seropositive, positive lymph node culture and consistently PCR positive in bone marrow). Three SNPs in TLR3, two SNPs in PTPN22 and one SNP in TLR4 and IL1A were associated with the susceptible phenotype in the Beagle group at the individual SNP level after permutation analysis, but were not significant after correction for multiple testing. Further validation of these SNPs is required in a larger cohort of dogs, ideally with extreme phenotypes to confirm an association with the outcome of L. infantum infection.

Favorable alleles mining for gelatinization temperature, gel consistency and amylose content in Oryza sativa by association mapping

Background

Improving the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) for parental grain eating and cooking qualities (ECQs) are key factors for enhancing average grain ECQs for hybrid japonica rice.

Results

In this study, a genome-wide association mapping (GWAS) for ECQs was performed on a selected sample of 462 rice accessions in 5 environments using 262 simple sequence repeat markers. We identified 10 loci and 27 favorable alleles for GT, GC and AC, and some of these loci were overlapped with starch synthesis-related genes. Four SSR loci for the GT trait were distributed on chromosomes 3, 5, 8, and 9, of which two SSR loci were novel. Two SSR loci associated with the GC trait were distributed on chromosomes 3 and 6, although only one SSR locus was novel. Four SSR loci associated with the AC trait were distributed on chromosomes 3, 6, 10, and 11, of which three SSR loci were novel. The novel loci RM6712 and RM6327 were simultaneously identified in more than 2 environments and were potentially reliable QTLs for ECQs, with 15 parental combinations being predicted. These QTLs and parental combinations should be used in molecular breeding to improve japonica rice average ECQs.

Conclusions

Among the 10 SSR loci associated with GT, GC and AC for grain ECQs detected in 27 favorable alleles, the favorable allele RM3600-90bp on chromosome 9 could significantly reduce GT, RM5753-115bp on chromosome 6 could significantly increase GC, and RM6327-230bp on chromosome 11 could significantly reduce AC in hybrid japonica rice mixed rice samples.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0735-y) contains supplementary material, which is available to authorized users.

The interaction between the ZNF804A gene and cannabis use on the risk of psychosis in a non-clinical sample

The ZNF804A gene and cannabis use are risk factors for psychosis and both have also been associated with schizotypal traits. This study aimed to investigate: i) the association of lifetime cannabis use (and its dose effect) with schizotypal personality traits, and ii) whether the genetic variability at ZNF804A gene modulates that association. Our sample consisted of 385 Spanish non-clinical subjects (43.1% males, mean age = 21.11(2.19)). Schizotypy was evaluated using the three factors of the Schizotypal Personality Questionnaire-Brief (SPQ-B): Cognitive-Perceptual (SPQ-CP), Interpersonal (SPQ-I) and Disorganized (SPQ-D). Subjects were classified according to their frequency of cannabis consumption, and dichotomized as users or non-users. The effects of a genetic variant of ZNF804A (rs1344706) and cannabis use, as well as their interaction, on each of the three SPQ-B factors were assessed using linear models and permutation tests. Sex, SCL anxiety scores and use of other drugs were included as covariates. Our analysis showed a significant relationship between ZNF804A and SPQ-I: AA genotype was associated with higher scores (β = 0.885 p_FDR = .018). An interaction between the AA genotype and lifetime cannabis use was found in SPQ-CP (β = 1.297 p_FDR = 0.018). This interaction showed a dose-effect pattern among AA subjects: schizotypy scores increased with increasing frequency of cannabis use (sporadic users: β = 0.746 p_FDR = 0.208; monthly users: β = 1.688 p_FDR = 0.091; intense users: β = 1.623 p_FDR = 0.038). These results add evidence on that the ZNF804A gene is associated with schizotypy and suggest that the interaction between cannabis use and ZNF804A genotype could modulate psychosis proneness.

A Genetic Variant in GPR126 Causing a Decreased Inclusion of Exon 6 Is Associated with Cartilage Development in Adolescent Idiopathic Scoliosis Population

Adolescent idiopathic scoliosis (AIS) is the most common spinal deformity disease in adolescents but its etiology and pathogenesis are still unclear. The current study aims to identify the relationship between single nucleotide polymorphisms (SNPs) of G protein-coupled receptor 126 (GPR126) gene and AIS predisposition. GPR126 contains 26 exons and alternative splicing of exon 6 and exon 25 produces 4 protein-coding transcripts. We genotyped SNPs of GPR126 gene around exon 6 and exon 25 in 131 Chinese AIS patients and 132 healthy controls and provided evidence that SNP rs41289839 G>A is strongly associated with AIS susceptibility. Linkage disequilibrium analysis suggests that rs41289839 and other AIS-related SNPs were in strong LD. Next, we demonstrated that rs41289839 G>A inhibits the inclusion of exon 6 during alternative splicing, resulting in a decreased expression level of exon 6-included transcript (GPR126-exon6ⁱⁿ) relative to the exon 6 excluded transcript (GPR126-exon6^ex) by minigene assay. Chondrogenic differentiation experiment showed that GPR126-exon6ⁱⁿ has a high expression level relative to GPR126-exon6^ex during chondrogenic differentiation of hMSCs. Our findings indicate that newly discovered SNP is related to cartilage development and may provide valuable insights into the etiology and pathogenesis of adolescent idiopathic scoliosis.

Mitochondrial haplogroups are not associated with diabetic retinopathy in a large Australian and British Caucasian sample

Mitochondrial haplogroups H1, H2 and UK have previously been reported to be associated with proliferative diabetic retinopathy (PDR) in Caucasian patients with diabetes. We aimed to replicate this finding with a larger sample and expand the analysis to include different severities of DR, and diabetic macular edema (DME). Caucasian participants (n = 2935) with either type 1 or type 2 diabetes from the Australian Registry of Advanced Diabetic Retinopathy were enrolled in this study. Twenty-two mitochondrial single nucleotide polymorphisms were genotyped by MassArray and haplogroups reconstructed using Haplogrep. Chi square tests and logistic regressions were used to test associations between haplogroup and DR phenotypes including any DR, non-proliferative DR (NPDR), proliferative DR (PDR) and DME. After stratifying the samples in type 1 and type 2 diabetes groups, and adjusting for sex, age, diabetes duration, concurrent HbA1c and hypertension, neither haplogroups H1, H2, UK, K or JT were associated with any DR, NPDR, PDR or DME.

Risk Factor Genes in Patients with Dystonia: A Comprehensive Review

Background

Dystonia is a movement disorder with high heterogeneity regarding phenotypic appearance and etiology that occurs in both sporadic and familial forms. The etiology of the disease remains unknown. However, there is increasing evidence suggesting that a small number of gene alterations may lead to dystonia. Although pathogenic variants to the familial type of dystonia have been extensively reviewed and discussed, relatively little is known about the contribution of single-nucleotide polymorphisms (SNPs) to dystonia. This review focuses on the potential role of SNPs and other variants in dystonia susceptibility.

Methods

We searched the PubMed database for peer-reviewed articles published in English, from its inception through January 2018, that concerned human studies of dystonia and genetic variants. The following search terms were included: “dystonia” in combination with the following terms: 1) “polymorphisms” and 2) “SNPs” as free words.

Results

A total of 43 published studies regarding TOR1A, BDNF, DRD5, APOE, ARSG, NALC, OR4X2, COL4A1, TH, DDC, DBH, MAO, COMT, DAT, GCH1, PRKRA, MR-1, SGCE, ATP1A3, TAF1, THAP1, GNAL, DRD2, HLA-DRB, CBS, MTHFR, and MS genes, were included in the current review.

Discussion

To date, a few variants, which are possibly involved in several molecular pathways, have been related to dystonia. Large cohort studies are needed to determine robust associations between variants and dystonia with adjustment for other potential cofounders, in order to elucidate the pathogenic mechanisms of dystonia and the net effect of the genes.

The Interaction of TPH2 and 5-HT2A Polymorphisms on Major Depressive Disorder Susceptibility in a Chinese Han Population: A Case-Control Study

Purpose: TPH2 and 5-HT2A appear to play vital roles in the homeostatic regulation of serotonin levels in the brain, their genetic variations may lead to impaired homeostatic regulation of serotonin resulting in abnormal levels of serotonin in the brain, thus predisposing individuals to MDD. However, research studies have yet to confirm which gene-gene interaction effect between TPH2 and 5-HT2A polymorphisms results in increased susceptibility to MDD. Methods: A total of 565 participants, consisting of 278 MDD patients and 287 healthy controls from the Chinese Han population, were recruited for the present study. Six single nucleotide polymorphisms (SNPs) of TPH2/5-HT2A were selected to assess their interaction by use of a generalized multifactor dimensionality reduction method. Results: A-allele carriers of rs11178997 and rs120074175 were more likely to suffer from MDD than T-allele carriers of rs11178997, or G-allele carriers of rs120074175. The interaction between TPH2 (rs120074175, rs11178997) and 5-HT2A (rs7997012) was considered as the best multi-locus model upon the MDD susceptibility. Conclusions: Our data identified an important effect of TPH2 genetic variants (rs11178997 and rs120074175) upon the risk of MDD, and suggested that the interaction of TPH2/5-HT2A polymorphism variants confer a greater susceptibility to MDD in Chinese Han population.

Genetic associations in community context: a mixed model approach identifies a functional variant in the RBP4 gene associated with HDL-C dyslipidemia

Background

The objective of this study was to examine individual and community factors that influence high-density lipoprotein cholesterol (HDL-C) dyslipidemia in Newfoundland and Labrador (NL), a genetically isolated population in Canada with a high prevalence of HDL-C dyslipidemia.

Methods

First, a group of single nucleotide polymorphisms from 10 metabolic trait candidate genes was tested using a multivariate logistic regression model. The significant SNPs were entered into the second phase, where a mixed logistic model incorporated the community disease risk factors together with the individual factors as the fixed part of the model and the geographic region as a random effect.

Results

Analysis of 1489 subjects (26.9% HDL-C dyslipidemia) identified rs3758539, a non-coding variant in the 5’UTR of RBP4, to be associated with HDL-C dyslipidemia (odds ratio = 1.45, 95% confidence interval = 1.08–1.97, p = 0.01). The association remained significant, and the effect size did not change after the incorporation of individual and community risk factors from 17 geographic regions (odds ratio: 1.41, 95% confidence interval = 1.03–1.93, p = 0.03) in NL. Besides this variant, sex, BMI, and smoking also showed significant associations with HDL-C dyslipidemia, whereas no role was identified for the community factors.

Conclusions

This study demonstrates the use of community-level data in a genetic association testing. It reports a functional variant in the promoter of RBP4, a gene directly involved in lipoprotein metabolism, to be associated with HDL-C dyslipidemia. These findings indicate that individual factors are the main reason for a higher prevalence of HDL-C dyslipidemia in the NL population.

Aggregation of experts: an application in the field of "interactomics" (detection of interactions on the basis of genomic data)

Background

Despite the successful mapping of genes involved in the determinism of numerous traits, a large part of the genetic variation remains unexplained. A possible explanation is that the simple models used in many studies might not properly fit the actual underlying situations. Consequently, various methods have attempted to deal with the simultaneous mapping of genomic regions, assuming that these regions might interact, leading to a complex determinism for various traits. Despite some successes, no gold standard methodology has emerged. Actually, combining several interaction mapping methods might be a better strategy, leading to positive results over a larger set of situations. Our work is a step in that direction.

Results

We first have demonstrated why aggregating results from several distinct methods might increase the statistical power while controlling the type I error. We have illustrated the approach using 6 existing methods (namely: MDR, Boost, BHIT, KNN-MDR, MegaSNPHunter and AntEpiSeeker) on simulated and real data sets. We have used a very simple aggregation strategy: a majority vote across the best loci combinations identified by the individual methods. In order to assess the performances of our aggregation approach in problems where most individual methods tend to fail, we have simulated difficult situations where no marginal effects of individual genes exist and where genetic heterogeneity is present. we have also demonstrated the use of the strategy on real data, using a WTCCC dataset on rheumatoid arthritis.

Since we have been using simplistic assumptions to infer the expected power of the aggregation method, the actual power we estimated from our simulations has turned out to be a bit smaller than theoretically expected. Results nevertheless have shown that grouping the results of several methods is advantageous in terms of power, accuracy and type I error control. Furthermore, as more methods should become available in the future, using a grouping strategy will become more advantageous since adding more methods seems to improve the performances of the aggregated method.

Conclusions

The aggregation of methods as a tool to detect genetic interactions is a potentially useful addition to the arsenal used in complex traits analyses.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2447-0) contains supplementary material, which is available to authorized users.

ClusterMI: Detecting High-Order SNP Interactions Based on Clustering and Mutual Information

Identifying single nucleotide polymorphism (SNP) interactions is considered as a popular and crucial way for explaining the missing heritability of complex diseases in genome-wide association studies (GWAS). Many approaches have been proposed to detect SNP interactions. However, existing approaches generally suffer from the high computational complexity resulting from the explosion of candidate high-order interactions. In this paper, we propose a two-stage approach (called ClusterMI) to detect high-order genome-wide SNP interactions based on significant pairwise SNP combinations. In the screening stage, to alleviate the huge computational burden, ClusterMI firstly applies a clustering algorithm combined with mutual information to divide SNPs into different clusters. Then, ClusterMI utilizes conditional mutual information to screen significant pairwise SNP combinations in each cluster. In this way, there is a higher probability of identifying significant two-locus combinations in each group, and the computational load for the follow-up search can be greatly reduced. In the search stage, two different search strategies (exhaustive search and improved ant colony optimization search) are provided to detect high-order SNP interactions based on the cardinality of significant two-locus combinations. Extensive simulation experiments show that ClusterMI has better performance than other related and competitive approaches. Experiments on two real case-control datasets from Wellcome Trust Case Control Consortium (WTCCC) also demonstrate that ClusterMI is more capable of identifying high-order SNP interactions from genome-wide data.

Association of DNMT3B -283T>C polymorphism with risk of lung and gastric cancer: a case-control study and a meta-analysis

PURPOSE

To investigate the association of DNMT3B -283T>C polymorphism with the risk of lung or gastric cancer, which was followed by a meta-analysis.

METHODS

The genotyping of -283T>C was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and was confirmed by sequencing.

RESULTS

The results of this case-control study showed that -283T>C was not associated with the risk of lung or gastric cancer, and further stratified analysis according to age, gender, smoking status, and alcohol status confirmed the present finding. However, data from a meta-analysis in the Asian population revealed a significant association between -283T>C and lung cancer risk in the allelic model (C vs. T: odds ratio [OR] = 1.28, 95% confidence interval [CI], 1.06-1.55, p = 0.01) and two genetic models (CC vs. TC: OR = 1.29, 95% CI, 1.04-1.59, p = 0.02; CC vs. TC + TT: OR = 1.30, 95% CI, 1.06-1.60, p = 0.01).

CONCLUSIONS

These results provided evidence that the DNMT3B -283T>C polymorphism might significantly contribute to the lung cancer risk in the Asian population, but not the gastric cancer risk in the Chinese population.

Yeast-based assays for characterization of the functional effects of single nucleotide polymorphisms in human DNA repair genes

DNA repair mechanisms maintain genomic integrity upon exposure to various types of DNA damage, which cause either single- or double-strand breaks in the DNA. Here, we propose a strategy for the functional study of single nucleotide polymorphisms (SNPs) in the human DNA repair genes XPD/ERCC2, RAD18, and KU70/XRCC6 and the checkpoint activation gene ATR that are essentially involved in the cell cycle and DNA damage repair. We analyzed the mutational effects of the DNA repair genes under DNA-damaging conditions, including ultraviolet irradiation and treatment with genotoxic reagents, using a Saccharomyces cerevisiae system to overcome the limitations of the human cell-based assay. We identified causal variants from selected SNPs in the present analyses. (i) R594C SNP in RAD3 (human XPD/ERCC2) caused severe reductions in the growth rate of mutant cells upon short-wavelength UV irradiation or chemical reagent treatment. (ii) The growth rates of the selected variants in RAD18, YKU70, and MEC1 were similar to those of wild-type cells on methyl methanesulfonate and hydroxyurea treated media. (iii) We also assessed the structural impact of the SNPs by analyzing differences in the structural conformation and calculating the root mean square deviation, which is a measure of the discordance of the Cα atoms between protein structures. Based on the above results, we propose that these analytical approaches serve as efficient methods for the identification of causal variants of human disease-causing genes and elucidation of yeast-cell based molecular mechanisms.

Using Y-Chromosomal Haplogroups in Genetic Association Studies and Suggested Implications

Y-chromosomal (Y-DNA) haplogroups are more widely used in population genetics than in genetic epidemiology, although associations between Y-DNA haplogroups and several traits, including cardiometabolic traits, have been reported. In apparently homogeneous populations defined by principal component analyses, there is still Y-DNA haplogroup variation which will result from population history. Therefore, hidden stratification and/or differential phenotypic effects by Y-DNA haplogroups could exist. To test this, we hypothesised that stratifying individuals according to their Y-DNA haplogroups before testing for associations between autosomal single nucleotide polymorphisms (SNPs) and phenotypes will yield difference in association. For proof of concept, we derived Y-DNA haplogroups from 6537 males from two epidemiological cohorts, Avon Longitudinal Study of Parents and Children (ALSPAC) (n = 5080; 816 Y-DNA SNPs) and the 1958 Birth Cohort (n = 1457; 1849 Y-DNA SNPs), and studied the robust associations between 32 SNPs and body mass index (BMI), including SNPs in or near Fat Mass and Obesity-associated protein (FTO) which yield the strongest effects. Overall, no association was replicated in both cohorts when Y-DNA haplogroups were considered and this suggests that, for BMI at least, there is little evidence of differences in phenotype or SNP association by Y-DNA structure. Further studies using other traits, phenome-wide association studies (PheWAS), other haplogroups and/or autosomal SNPs are required to test the generalisability and utility of this approach.

Association mapping of drought tolerance-related traits in barley to complement a traditional biparental QTL mapping study

Association mapping of drought-related traits in barley was used to increase the density of existing QTL maps without recreating mapping populations. We used 109 spring barley genotypes exhibiting high or low drought tolerance to elucidate the associations between diversity array technology sequencing (DArTseq) and single nucleotide polymorphism (SNP) markers and various physiological parameters related to plant responses to drought conditions. The study was performed in controlled conditions (growth chambers), drought tolerance was phenotyped in the four-leaf seedlings. We identified 58 associations including 34 new markers (i.e., 16 DArTseq and 18 SNP markers). The results for three markers were consistent with the data obtained in an earlier traditional biparental QTL mapping study. The regions neighboring markers on linkage group 2H contained the highest number of significant marker-trait associations. Five markers related to the photosynthetic activity of photosystem II were detected on chromosome 4H. The lowest number of associations were observed for the sequences neighboring DArT markers on linkage group 6H. A chromosome 3H region related to water use efficiency and net photosynthesis rate in both biparental QTL, and association study, may be particularly valuable, as these parameters correspond to the ability of plants to remain highly productive under water deficit stress. Our findings confirm that association mapping can increase the density of existing QTL maps without recreating mapping populations.