Sample size and statistical power calculation in genetic association studies

GABRB2 Haplotype Association with Heroin Dependence in Chinese Population

Substance dependence is a frequently observed comorbid disorder in schizophrenia, but little is known about genetic factors possibly shared between the two psychotic disorders. GABRB2, a schizophrenia candidate gene coding for GABAA receptor β2 subunit, is examined for possible association with heroin dependence in Han Chinese population. Four single nucleotide polymorphisms (SNPs) in GABRB2, namely rs6556547 (S1), rs1816071 (S3), rs18016072 (S5), and rs187269 (S29), previously associated with schizophrenia, were examined for their association with heroin dependence. Two additional SNPs, rs10051667 (S31) and rs967771 (S32), previously associated with alcohol dependence and bipolar disorder respectively, were also analyzed. The six SNPs were genotyped by direct sequencing of PCR amplicons of target regions for 564 heroin dependent individuals and 498 controls of Han Chinese origin. Interestingly, it was found that recombination between the haplotypes of all-derived-allele (H1; OR = 1.00) and all-ancestral-allele (H2; OR = 0.74) at S5-S29 junction generated two recombinants H3 (OR = 8.51) and H4 (OR = 5.58), both conferring high susceptibility to heroin dependence. Additional recombination between H2 and H3 haplotypes at S1-S3 junction resulted in a risk-conferring haplotype H5 (OR = 1.94x109). In contrast, recombination between H1 and H2 haplotypes at S3-S5 junction rescued the risk-conferring effect of recombination at S5-S29 junction, giving rise to the protective haplotype H6 (OR = 0.68). Risk-conferring effects of S1-S3 and S5-S29 crossovers and protective effects of S3-S5 crossover were seen in both pure heroin dependent and multiple substance dependence subgroups. In conclusion, significant association was found with haplotypes of the S1-S29 segment in GABRB2 for heroin dependence in Han Chinese population. Local recombination was an important determining factor for switching haplotypes between risk-conferring and protective statuses. The present study provide evidence for the schizophrenia candidate gene GABRB2 to play a role in heroin dependence, but replication of these findings is required.

Genetics of leprosy: Expected-and unexpected-developments and perspectives

A solid body of evidence produced over decades of intense research supports the hypothesis that leprosy phenotypes are largely dependent on the genetic characteristics of the host. The early evidence of a major gene effect controlling susceptibility to leprosy came from studies of familial aggregation, twins, and complex segregation analysis. Later, linkage and association analysis, first applied to the investigation of candidate genes and chromosomal regions and more recently, to genome-wide scans, have revealed several HLA and non-HLA gene variants as risk factors for leprosy phenotypes such as disease per se, its clinical forms, and leprosy reactions. In addition, powerful, hypothesis-free strategies such as genome-wide association studies have led to an exciting, unexpected development: Leprosy susceptibility genes seem to be shared with Crohn's and Parkinson's disease. Today, a major challenge is to find the exact variants causing the biological effect underlying the genetic associations. New technologies, such as Next Generation Sequencing-that allows, for the first time, the cost- and time-effective sequencing of a complete human genome-hold the promise to reveal such variants; thus, strategies can be developed to study the functional impact of these variants in the context of infection, hopefully leading to the development of new targets for leprosy treatment and prevention.

TUBA4A may not be a significant genetic factor in Chinese ALS patients

TUBA4A gene has recently been identified as a potential candidate amyotrophic lateral sclerosis(ALS)-associated gene using exome-wide rare variant burden analysis. The identification of novel TUBA4A variants in Italian ALS patients further support the role of TUBA4A in ALS. We sequenced the coding region of exon 4 in the TUBA4A gene in a cohort consisting of 80 familial ALS probands, 500 sporadic ALS patients and 500 healthy control individuals. No TUBA4A causative variants were identified in the ALS patients. In conclusion, our current results did not find an association between TUBA4A and ALS in Chinese patients, and further studies will be required.

Polymorphisms of the Toll-Like Receptor-3 Gene in Autoimmune Adrenal Failure and Type 1 Diabetes in Polish Patients

Infectious agents are plausible environmental triggers for autoimmunity in genetically susceptible individuals. Polymorphic variants of genes implicated in innate immunity may affect immune responses and hence promote auto-aggressive reactions. Genes such as Toll-like receptor-3 (TLR3), which participate in recognizing conserved foreign molecules and mounting the first line of defence against viral infections, are promising functional candidates in autoimmune conditions. We investigated the association of the TLR3 variants, rs13126816 and rs3775291, with the autoimmune endocrine disorders, Addison's disease (AD) and type 1 diabetes (T1D) in the Polish population. The study comprised 168 AD patients, 524 individuals with T1D and 592 healthy controls. Genotyping was performed by real-time PCR. Distribution of the TLR3 genotypes and alleles did not reveal significant differences between patients and controls (p > 0.05). No effect on age at disease onset was found in affected cohorts. This analysis does not support an association between TLR3 variants and the risk for autoimmune destruction of the adrenal cortex and beta cells. However, innate immunity merits further studies in autoimmune endocrine conditions.

Association between single nucleotide polymorphisms in MiR219-1 and MiR137 and susceptibility to schizophrenia in a Chinese population

•

A case-control study investigated rs107822, rs1625579 and risk of schizophrenia.

•

rs107822 was negatively associated with susceptibility to schizophrenia.

•

No association was found between rs1625579 and the disorder.

Schizophrenia is one of the most common mental disorders to severely affect human health worldwide. Single nucleotide polymorphisms (SNPs) within related genes are candidate susceptible factors for the disorder. Rs107822 within MiR219-1 and rs1625579 within MiR137 were genotyped in 589 cases and 622 controls to investigate the possible association between the loci and schizophrenia in a Chinese population. Our results showed significant association between rs107822 and the disorder in allele (C vs. T: adjusted OR = 0.773, 95%CI = 0.655–0.912), co-dominant (TC vs. TT: adjusted OR = 0.734, 95%CI = 0.571–0.943; CC vs. TT: adjusted OR = 0.655, 95%CI = 0.459–0.936), dominant (TC + CC vs. TT: adjusted OR = 0.707, 95%CI = 0.559–0.895), and recessive (CC vs. TC + TT: adjusted OR = 0.724, 95%CI = 0.524–0.999) models, respectively. Meanwhile, negative associations were also observed between rs107822 and the disorder in male and female subgroups, and genotype CC of the locus was significantly associated with a lower positive symptom score of PANSS compared to genotype TT carrier in the cases group. However, we didn’t observe a significant association between rs1625579 and the disorder. These findings indicate that rs107822 within MiR219-1 might be involved in pathogenesis of schizophrenia and that genotypes TC, CC and allele C of the locus are protective factors for schizophrenia in a Chinese population.

Gender-specific associations between ADIPOQ gene polymorphisms and adiponectin levels and obesity in the Jackson Heart Study cohort

BACKGROUND

Despite the important role of adiponectin in regulating general metabolic homeostasis, analysis of genetic determinants of adiponectin and the related cardio-metabolic traits in African American population has been limited and inconsistent. Considering the high genetic admixture of African Americans and thus the important population stratification that may confound the genetic-trait associations, the objective of this work was to perform a comprehensive analysis of the associations between ADIPOQ variants and adiponectin levels and obesity phenotypes in a large African American population from the Jackson Heart Study (JHS) cohort.

METHODS

Genotype data was available for 2968 JHS participants (1131men; 1837women). Single Nucleotide Polymorphisms (SNPs) were selected by a Tag-SNP Approach and literature review. The genotype imputation was performed using IMPUTE2 software and reference phased data from the 1000G project. PLINK software was used for the genetic analysis. Plasma specimens were analyzed by ELISA for adiponectin levels. All analyses were controlled for population stratification assessed by Individual Proportions of European Ancestry (PEA) estimates calculated in HAPMIX using ancestry informative markers (AIMs).

RESULTS

We found a gender-dependent association of some ADIPOQ variants and adiponectin levels. In women four of the studied polymorphisms (rs6444174, rs16861205, rs1403697, rs7641507) were associated with adiponectin levels after Bonferroni correction and controlling for the percentage of PEA, age, annual household income and smoking. These results were consistent with the haplotype analysis. The association between the rs12495941 variant and obesity is modulated by the PEA, so that the relationship between the G allele and a higher incidence of obesity was present in those individuals within the lower PEA group. In addition we found an effect modification of obesity on the association between the ADIPOQ rs6444174 SNP and BMI so that the presence of the T allele was negatively and significantly associated with BMI only in participants with a normal weight.

CONCLUSIONS

In this large African American cohort, ADIPOQ variants were associated with adiponectin levels in a gender-dependent manner and the relationship of some of these variants with obesity and BMI was modulated by the PEA and obesity status respectively. This suggests that the effects of these polymorphisms on adiponectin and obesity phenotypes are subject to a strong interaction with genetic and environmental factors in African American population.

Genetics of leprosy: expected and unexpected developments and perspectives

A solid body of evidence produced over decades of intense research supports the hypothesis that leprosy phenotypes are largely dependent on the genetic characteristics of the host. The early evidence of a major gene effect controlling susceptibility to leprosy came from studies of familial aggregation, twins, and Complex Segregation Analysis. Later, linkage and association analysis, first applied to the investigation of candidate genes and chromosomal regions and more recently, to genome-wide scans, have revealed several leukocyte antigen complex and nonleukocyte antigen complex gene variants as risk factors for leprosy phenotypes such as disease per se, its clinical forms and leprosy reactions. In addition, powerful, hypothesis-free strategies such as Genome-Wide Association Studies have led to an exciting, unexpected development: Leprosy susceptibility genes seem to be shared with Crohn's and Parkinson's diseases. Today, a major challenge is to find the exact variants causing the biological effect underlying the genetic associations. New technologies, such as Next Generation Sequencing that allows, for the first time, the cost and time-effective sequencing of a complete human genome, hold the promise to reveal such variants. Strategies can be developed to study the functional effect of these variants in the context of infection, hopefully leading to the development of new targets for leprosy treatment and prevention.

Association between bone marrow stromal cell antigen 1 gene polymorphisms and the susceptibility to Parkinson's disease: a meta-analysis

A number of studies have investigated the association between Parkinson's disease (PD) and genetic polymorphisms of bone marrow stromal cell antigen 1 (BST-1). However, the results to date have been conflicting. In this study a meta-analysis was performed to assess the association between BST-1 polymorphisms and PD. Previous relevant studies were identified from Medline, Embase and Cochrane databases, among which the studies evaluating the association of BST-1 polymorphisms with risk of PD were used in the meta-analysis. Summary odds ratios (ORs) and 95% confidence intervals (CIs) were determined for different genetic models using meta-analytic methods. Subgroup analysis was performed based on study designs and participant ethnicity, and sensitivity analysis was also performed. Eleven studies comprising 11,070 cases and 19,169 controls were included in this meta-analysis. ORs and 95% CIs were used to assess the strength of association. The rs4698412 variant (G→A) showed a significant summary OR of 1.12 (95% CI: 1.05-1.20; P=0.001) in an allelic model. This significant association was also observed in the subgroup analysis based on participants' ethnicity and study designs. The pooled OR of the rs11724635 variant (C→A) indicated a non-significant association with PD in a recessive model (OR, 1.16, 95% CI: 0.97-1.40; P=0.112), dominant model (OR, 1.10, 95% CI: 0.86-1.41; P=0.458) and allelic model (OR, 1.10, 95% CI: 0.95-1.27; P=0.224). Although the rs11931532 variant (T→C) did not show association with PD (OR, 0.99, 95% CI: 0.85-1.15; P=0.9), the pooled estimation of genome-wide association studies (GWAS) showed a significant connection with PD (OR, 1.19, 95% CI: 1.08-1.31; P=0.001). Sensitivity analysis supported these findings, and no evidence of publication bias was observed in the meta-analysis. Our studies suggested that the rs4698412 variant of BST-1 may increase the PD susceptibility.

The heritable path of human physical performance: from single polymorphisms to the "next generation"

Human physical performance is a complex multifactorial trait. Historically, environmental factors (e.g., diet, training) alone have been unable to explain the basis of all prominent phenotypes for physical performance. Therefore, there has been an interest in the study of the contribution of genetic factors to the development of these phenotypes. Support for a genetic component is found with studies that shown that monozygotic twins were more similar than were dizygotic twins for many physiological traits. The evolution of molecular techniques and the ability to scan the entire human genome enabled association of several genetic polymorphisms with performance. However, some biases related to the selection of cohorts and inadequate definition of the study variables have complicated the already difficult task of studying such a large and polymorphic genome, often resulting in inconsistent results about the influence of candidate genes. This review aims to provide a critical overview of heritable genetic aspects. Novel molecular technologies, such as next-generation sequencing, are discussed and how they can contribute to improving understanding of the molecular basis for athletic performance. It is important to ensure that the large amount of data that can be generated using these tools will be used effectively by ensuring well-designed studies.

Replication of NTNG1 association in schizophrenia

This is a case-control study of the association of NTNG1 subtypes with schizophrenia among a group of individuals from a Caucasian population. Netrins including NTNG1 are known to be axon guidance factors in the developing brain. They could be very important contributors to the genetic risk for psychosis. We examined the hypothesis that NTNG1 allelic variation contributes to the risk for schizophrenia. Our group was able to replicate the findings of Zhu and colleagues among Han Chinese individuals. This is the first finding of this association in a North American population.

Pathway-focused genetic evaluation of immune and inflammation related genes with chronic fatigue syndrome

Recent evidence suggests immune and inflammatory alterations are important in chronic fatigue syndrome (CFS). This study was done to explore the association of functionally important genetic variants in inflammation and immune pathways with CFS. Peripheral blood DNA was isolated from 50 CFS and 121 non-fatigued (NF) control participants in a population-based study. Genotyping was performed with the Affymetrix Immune and Inflammation Chip that covers 11K single nucleotide polymorphisms (SNPs) following the manufacturer's protocol. Genotyping accuracy for specific genes was validated by pyrosequencing. Golden Helix SVS software was used for genetic analysis. SNP functional annotation was done using SPOT and GenomePipe programs. CFS was associated with 32 functionally important SNPs: 11 missense variants, 4 synonymous variants, 11 untranslated regulatory region (UTR) variants and 6 intronic variants. Some of these SNPs were in genes within pathways related to complement cascade (SERPINA5, CFB, CFH, MASP1 and C6), chemokines (CXCL16, CCR4, CCL27), cytokine signaling (IL18, IL17B, IL2RB), and toll-like receptor signaling (TIRAP, IRAK4). Of particular interest is association of CFS with two missense variants in genes of complement activation, rs4151667 (L9H) in CFB and rs1061170 (Y402H) in CFH. A 5' UTR polymorphism (rs11214105) in IL18 also associated with physical fatigue, body pain and score for CFS case defining symptoms. This study identified new associations of CFS with genetic variants in pathways including complement activation providing additional support for altered innate immune response in CFS. Additional studies are needed to validate the findings of this exploratory study.

Association between a polymorphism of the vasopressin 1B receptor gene and aggression in children

OBJECTIVES

The involvement of arginine-vasopressin (AVP) in animal and human aggression has been well established in the literature. Recent research has shown an association between the minor allele (C) of single-nucleotide polymorphism rs35369693 located on the AVP 1B receptor gene and childhood aggression.

MATERIALS AND METHODS

The present study sought to replicate the association between rs35369693 and aggression using a sample of clinically referred children (N=141) with behavioural problems.

RESULTS

Analyses confirmed a significant relationship between the minor C allele on rs35369693 and teacher-rated reactive aggression. Although males had significantly greater aggression than females on three of the four measures, sex was not shown to moderate the effect of the C allele on any of the aggression measures.

CONCLUSION

These findings reinforce the results from previous research and also suggest that the associations of the AVP 1B receptor may be specific to reactive, emotional rather than proactive or callous types of aggression.

Big data challenges in bone research: genome-wide association studies and next-generation sequencing

Genome-wide association studies (GWAS) have been developed as a practical method to identify genetic loci associated with disease by scanning multiple markers across the genome. Significant advances in the genetics of complex diseases have been made owing to advances in genotyping technologies, the progress of projects such as HapMap and 1000G and the emergence of genetics as a collaborative discipline. Because of its great potential to be used in parallel by multiple collaborators, it is important to adhere to strict protocols assuring data quality and analyses. Quality control analyses must be applied to each sample and each single-nucleotide polymorphism (SNP). The software package PLINK is capable of performing the whole range of necessary quality control tests. Genotype imputation has also been developed to substantially increase the power of GWAS methodology. Imputation permits the investigation of associations at genetic markers that are not directly genotyped. Results of individual GWAS reports can be combined through meta-analysis. Finally, next-generation sequencing (NGS) has gained popularity in recent years through its capacity to analyse a much greater number of markers across the genome. Although NGS platforms are capable of examining a higher number of SNPs compared with GWA studies, the results obtained by NGS require careful interpretation, as their biological correlation is incompletely understood. In this article, we will discuss the basic features of such protocols.

Association of the apolipoprotein E 2 allele with concurrent occurrence of endometrial hyperplasia and endometrial carcinoma

Genes encoding proteins with antioxidant properties may influence susceptibility to endometrial hyperplasia (EH) and endometrial carcinoma (ECa). Patients with EH (n = 89), EH concurrent with ECa (n = 76), ECa (n = 186), and healthy controls (n = 1110) were genotyped for five polymorphic variants in the genes involved in metabolism of lipoproteins (APOE Cys112Arg and Arg158Cys), iron (HFE Cys282Tyr and His63Asp), and catecholamines (COMT Val158Met). Patients and controls were matched by ethnicity (all Caucasians), age, body mass index (BMI), and incidence of hypertension and diabetes. The frequency of the APOE E 2 allele (158Cys) was higher in patients with EH + ECa than in controls (P = 0.0012, P(Bonferroni) = 0.018, OR = 2.58, 95% CI 1.49-4.45). The APOE E 4 allele (112Arg) was more frequently found in patients with EH than in controls and HFE minor allele G (63Asp) had a protective effect in the ECa group, though these results appeared to be nonsignificant after correction for multiple comparisons. The results of the study indicate that E 2 allele might be associated with concurrent occurrence of EH and ECa.

Cytotoxic T lymphocyte associated antigen-4 (CTLA-4) +49 A>G gene polymorphism in Egyptian cases with rheumatoid arthritis

BACKGROUND

The gene encoding cytotoxic T lymphocyte associated antigen-4 (CTLA-4) has been reported to be associated with rheumatoid arthritis (RA) in several ethnic populations. The aim of this work is to assess the association of this polymorphism with the susceptibility, activity and functional disability of RA in Egyptian subjects.

SUBJECTS AND METHODS

This study included 112 unrelated RA Egyptian patients who were compared to 122 healthy controls from the same locality. For all subjects, DNA was genotyped for CTLA-4 +49 A>G (rs231775) polymorphism using the PCR-RFLP technique. Antibodies to cyclic citrullinated peptides (anti-CCP) were measured by enzyme-linked immunosorbent assay (ELISA).

RESULTS

The frequency of the CTLA-4 G allele was significantly higher among cases compared to controls (37.1% vs. 23.4%, OR=1.93; 95% CI=1.29-2.89, p=0.002). Also, the frequency of CTLA-4 +49 G allele carriage (AG+GG genotypes) was significantly higher among cases with RA compared to controls (61.6% vs. 41.8%, OR=2.23, 95% CI=1.32-3.77, p=0.003). Logistic regression analysis showed that cases positive to the G allele (GA+GG genotypes) had less frequency of rheumatoid deformities and also a lower DAS28-CRP score, yet with a higher visual analogue scale (VAS) i.e. more functional disability than other cases.

CONCLUSIONS

CTLA-4 +49 G allele carriage was associated with increased susceptibility and functional disability of RA in Egyptian patients.

Analysis of association of MEF2C, SOST and JAG1 genes with bone mineral density in Mexican-Mestizo postmenopausal women

Background

Osteoporosis, a disease characterized by low bone mineral density (BMD), is an important health problem in Mexico. BMD is a highly heritable trait, with heritability estimates of 50-85%. Several candidate genes have been evaluated to identify those involved in BMD variation and the etiology of osteoporosis. This study investigated the possible association of single-nucleotide polymorphisms (SNPs) in the MEF2C, SOST and JAG1 genes with bone mineral density (BMD) variation in postmenopausal Mexican-Mestizo women.

Methods

Four hundred unrelated postmenopausal women were included in the study. Risk factors were recorded and BMD was measured in total hip, femoral neck and lumbar spine using dual-energy X-ray absorptiometry. In an initial stage, a total of twenty-five SNPs within or near SOST gene and seven SNPs in the JAG1 gene were genotyped using a GoldenGate assay. In a second stage, three MEF2C gene SNPs were also genotyped and SOST and JAG1 gene variants were validated. Real time PCR and TaqMan probes were used for genotyping.

Results

Linear regression analyses adjusted by age, body mass index and ancestry estimates, showed that five SNPs in the SOST gene were significantly associated with BMD in total hip and femoral neck but not lumbar spine. The lowest p value was 0.0012, well below the multiple–test significance threshold (p = 0.009), with mean effect size of -0.027 SD per risk allele. We did not find significant associations between BMD and MEF2C/JAG1 gene variants [rs1366594 “A” allele: β = 0.001 (95% CI -0.016; 0.017), P = 0.938; rs2273061 “G” allele: β = 0.007 (95% CI -0.007; 0.023), p = 0.409].

Conclusions

SOST polymorphisms may contribute to total hip and femoral neck BMD variation in Mexican postmenopausal women. Together, these and prior findings suggest that this gene may contribute to BMD variation across populations of diverse ancestry.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2474-15-400) contains supplementary material, which is available to authorized users.

Resequencing and association analysis of PTPRA, a possible susceptibility gene for schizophrenia and autism spectrum disorders

Background

The PTPRA gene, which encodes the protein RPTP-α, is critical to neurodevelopment. Previous linkage studies, genome-wide association studies, controlled expression analyses and animal models support an association with both schizophrenia and autism spectrum disorders, both of which share a substantial portion of genetic risks.

Methods

We sequenced the protein-encoding areas of the PTPRA gene for single nucleotide polymorphisms or small insertions/deletions (InDel) in 382 schizophrenia patients. To validate their association with the disorders, rare (minor allele frequency <1%), missense mutations as well as one InDel in the 3′UTR region were then genotyped in another independent sample set comprising 944 schizophrenia patients, 336 autism spectrum disorders patients, and 912 healthy controls.

Results

Eight rare mutations, including 3 novel variants, were identified during the mutation-screening phase. In the following association analysis, L59P, one of the two missense mutations, was only observed among patients of schizophrenia. Additionally, a novel duplication in the 3′UTR region, 174620_174623dupTGAT, was predicted to be located within a Musashi Binding Element.

Major Conclusions

No evidence was seen for the association of rare, missense mutations in the PTPRA gene with schizophrenia or autism spectrum disorders; however, we did find some rare variants with possibly damaging effects that may increase the susceptibility of carriers to the disorders.

Genome wide association scan for chronic periodontitis implicates novel locus

BACKGROUND

There is evidence for a genetic contribution to chronic periodontitis. In this study, we conducted a genome wide association study among 866 participants of the University of Pittsburgh Dental Registry and DNA Repository, whose periodontal diagnosis ranged from healthy (N = 767) to severe chronic periodontitis (N = 99).

METHODS

Genotypingi of over half-million single nucleotide polymorphisms was determined. Analyses were done twice, first in the complete dataset of all ethnicities, and second including only samples defined as self-reported Whites. From the top 100 results, twenty single nucleotide polymorphisms had consistent results in both analyses (borderline p-values ranging from 1E-05 to 1E-6) and were selected to be tested in two independent datasets derived from 1,460 individuals from Porto Alegre, and 359 from Rio de Janeiro, Brazil. Meta-analyses of the Single nucleotide polymorphisms showing a trend for association in the independent dataset were performed.

RESULTS

The rs1477403 marker located on 16q22.3 showed suggestive association in the discovery phase and in the Porto Alegre dataset (p = 0.05). The meta-analysis suggested the less common allele decreases the risk of chronic periodontitis.

CONCLUSIONS

Our data offer a clear hypothesis to be independently tested regarding the contribution of the 16q22.3 locus to chronic periodontitis.

SOD2 gene polymorphism and muscle damage markers in elite athletes

Exercise-induced oxidative stress is a state that primarily occurs in athletes involved in high-intensity sports when pro-oxidants overwhelm the antioxidant defense system to oxidize proteins, lipids, and nucleic acids. During exercise, oxidative stress is linked to muscle metabolism and muscle damage, because exercise increases free radical production. The T allele of the Ala16Val (rs4880 C/T) polymorphism in the mitochondrial superoxide dismutase 2 (SOD2) gene has been reported to reduce SOD2 efficiency against oxidative stress. In the present study we tested the hypothesis that the SOD2 TT genotype would be underrepresented in elite athletes involved in high-intensity sports and associated with increased values of muscle and liver damage biomarkers. The study involved 2664 Caucasian (2262 Russian and 402 Polish) athletes. SOD2 genotype and allele frequencies were compared to 917 controls. Muscle and liver damage markers [creatine kinase (CK), creatinine, alanine transaminase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP)] were examined in serum from 1444 Russian athletes. The frequency of the SOD2 TT genotype (18.6%) was significantly lower in power/strength athletes (n = 524) compared to controls (25.0%, p = 0.0076) or athletes involved in low-intensity sports (n = 180; 33.9%, p < 0.0001). Furthermore, the SOD2 T allele was significantly associated with increased activity of CK (females: p = 0.0144) and creatinine level (females: p = 0.0276; males: p = 0.0135) in athletes. Our data show that the SOD2 TT genotype might be unfavorable for high-intensity athletic events.

Application of routine electronic health record databases for pharmacogenetic research

Inter-individual variability in drug responses is a common problem in pharmacotherapy. Several factors (non-genetic and genetic) influence drug responses in patients. When aiming to obtain an optimal benefit-risk ratio of medicines and with the emergence of genotyping technology, pharmacogenetic studies are important for providing recommendations on drug treatments. Advances in electronic healthcare information systems can contribute to increasing the quality and efficiency of such studies. This review describes the definition of pharmacogenetics, gene selection and study design for pharmacogenetic research. It also summarizes the potential of linking pharmacoepidemiology and pharmacogenetics (along with its strengths and limitations) and provides examples of pharmacogenetic studies utilizing electronic health record databases.

Association between polymorphisms in the flanking region of the TAFI gene and atherosclerotic cerebral infarction in a Chinese population

Background

Atherosclerosis is the leading etiologic factor of Atherosclerotic Cerebral Infarction (ACI). Previous studies have shown that thrombin activatable fibrinolysis inhibitor (TAFI) may play an important role in the occurrence of acute cerebral infarction, and the levels of TAFI are affected by several single nucleotide polymorphisms (SNPs) located in the regulatory and coding regions of the gene encoding TAFI. The present study aimed to determine whether polymorphisms (TAFI –2345 2G/1G, –1690 A/G, –438 A/G, +1583 A/T) of the TAFI gene were associated with ACI in a Han Chinese population.

Methods

The variant genotypes were identified by restriction fragment length polymorphism (RFLP) and allele-specific polymerase chain reactions (AS-PCR) in 225 patients with ACI and 184 age-matched healthy individuals.

Results

There was a significant difference in the genotype and allele frequencies of TAFI –2345 2G/1G and −1690 A/G polymorphisms between the ACI and control subjects. Further stratification analysis by gender revealed that the presence of the –438 AA genotype and the A allele conferred a higher risk of developing ACI in male patients (p < 0.05). Haplotype analysis demonstrated that four haplotypes of TAFI are significantly associated with ACI.

Conclusions

Our study provides preliminary evidence that the TAFI –2345 2G/1G and –1690 A/G polymorphisms are associated with ACI susceptibility in a Han Chinese population.

Natural selection and infectious disease in human populations

Infectious pathogens are among the strongest selective forces that shape the human genome. Migrations and cultural changes in the past 100,000 years exposed populations to dangerous new pathogens.

Host genetics influences susceptibility to infectious disease. Evolutionary adaptations for resistance and symbiosis may underlie common immune-mediated diseases.

Signatures of selection and methods to detect them vary with the age, geographical spread and virulence of the pathogen.

A history of selection on a trait adds power to association studies by driving the emergence of common alleles of strong effect. Combining selection and association metrics can further increase power.

Genome-wide association studies (GWASs) of susceptibility to pathogens that are moderately old (1,000–50,000 years ago), geographically limited in history and exerted strong positive selective pressure will have the most power if GWASs can be done in the historically affected population.

An understanding of host–pathogen interactions can inform the development of new therapies for both infectious diseases and common immune-mediated diseases.

The impact of various infectious agents on human survival and reproduction over thousands of years has exerted selective pressure on numerous regions of the human genome. This Review describes how such signatures of selection can be detected and integrated with data from complementary approaches, such as genome-wide association studies, to provide biological insights into host–pathogen interactions.

The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important implications for the growing field of medical genomics. As humans migrated throughout the world, populations encountered distinct pathogens, and natural selection increased the prevalence of alleles that are advantageous in the new ecosystems in both host and pathogens. This ancient history now influences human infectious disease susceptibility and microbiome homeostasis, and contributes to common diseases that show geographical disparities, such as autoimmune and metabolic disorders. Using new high-throughput technologies, analytical methods and expanding public data resources, the investigation of natural selection is leading to new insights into the function and dysfunction of human biology.

ACTN3 R577X Polymorphism and Explosive Leg-Muscle Power in Elite Basketball Players

Purpose:

To determine the association of the ACTN3 R577X polymorphism with leg-muscle explosive power in Spanish (white) elite basketball players and controls.

Participants:

100 (60 men) elite basketball players (cases) and 283 nonathletic controls.

Methods:

The authors assessed power performance by means of the vertical-squat and countermovement-jump tests.

Results:

Genotype distributions did not differ between groups (cases: 37.0% [RR], 42.0% [RX], and 21.0% [XX]; controls: 31.8% [RR], 49.8% [RX], and 18.4% [XX]; P = .353). The authors did not observe any effect of the ACTN3 R577X polymorphism on study phenotypes in either group, including when they performed the analyses separately in men and women. They found no association between the ACTN3 R577X polymorphism and the likelihood of being an elite basketball player using the dominant or the recessive model, and the results remained unaltered when the analyses were adjusted for sex, weight, height, and age or when performed for men and women separately.

Conclusions:

Although the ACTN3 R577X is associated with explosive muscle performance and this phenotype is important in the sport of basketball (ie, during jumps), the authors found no association with leg explosive power in elite basket players or with the status of being this type of athlete.

Association of polymorphisms of the receptor for advanced glycation end products gene with COPD in the Chinese population

The receptor for advanced glycation end products (RAGE) is a cell surface molecule of the immunoglobulin superfamily that binds diverse endogenous ligands involved in the development of chronic diseases and inflammatory damage. A growing body of evidence has suggested that RAGE is involved in the development and progression of chronic obstructive pulmonary disease (COPD). The present study investigated the existence of an association among three polymorphisms (-374T/A, -429T/C, and G82S) of the RAGE gene with the risk of COPD in the Chinese population. The RAGE genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism in 216 patients with COPD and 239 age-matched healthy individuals. Our study demonstrated that the frequencies of the GS genotype and the S allele in the G82S mutation were significantly higher in COPD patients than in controls (odds ratios [OR]=1.70, 95% confidence interval [CI]: 1.15-2.50, p=0.0098 and OR=1.42, 95% CI: 1.06-1.91, p=0.023, respectively). Further stratification analysis by smoking status revealed that the presence of the GS genotype conferred a higher risk of developing COPD in current smokers (p=0.044). In contrast, mutations at -374T/A and -429T/C did not demonstrate any association with COPD, even after taking into account the patients' smoking history. Our study provides preliminary evidence that the G82S polymorphism in the RAGE gene is associated with an increased risk of COPD and that the GS genotype of the G82S variant is a risk factor for COPD in the Chinese population.

CYP1A1, GCLC, AGT, AGTR1 gene-gene interactions in community-acquired pneumonia pulmonary complications

This study was conducted to establish the possible contribution of functional gene polymorphisms in detoxification/oxidative stress and vascular remodeling pathways to community-acquired pneumonia (CAP) susceptibility in the case-control study (350 CAP patients, 432 control subjects) and to predisposition to the development of CAP complications in the prospective study. All subjects were genotyped for 16 polymorphic variants in the 14 genes of xenobiotics detoxification CYP1A1, AhR, GSTM1, GSTT1, ABCB1, redox-status SOD2, CAT, GCLC, and vascular homeostasis ACE, AGT, AGTR1, NOS3, MTHFR, VEGFα. Risk of pulmonary complications (PC) in the single locus analysis was associated with CYP1A1, GCLC and AGTR1 genes. Extra PC (toxic shock syndrome and myocarditis) were not associated with these genes. We evaluated gene-gene interactions using multi-factor dimensionality reduction, and cumulative gene risk score approaches. The final model which included >5 risk alleles in the CYP1A1 (rs2606345, rs4646903, rs1048943), GCLC, AGT, and AGTR1 genes was associated with pleuritis, empyema, acute respiratory distress syndrome, all PC and acute respiratory failure (ARF). We considered CYP1A1, GCLC, AGT, AGTR1 gene set using Set Distiller mode implemented in GeneDecks for discovering gene-set relations via the degree of sharing descriptors within a given gene set. N-acetylcysteine and oxygen were defined by Set Distiller as the best descriptors for the gene set associated in the present study with PC and ARF. Results of the study are in line with literature data and suggest that genetically determined oxidative stress exacerbation may contribute to the progression of lung inflammation.

Association of Leukotriene Gene Variants and Plasma LTB4 Levels with Coronary Artery Disease in Asian Indians

Leukotrienes are potent inflammatory and lipid mediators that participate in atherosclerosis. We analyzed the association of Leukotriene gene (ALOX5, ALOX5AP, LTA4H, and LTC4S) polymorphisms and plasma Leukotriene B4 (LTB4) levels with coronary artery disease (CAD) in a representative cohort of Asian Indians. In all, 136 functional single nucleotide polymorphisms (SNPs) were selected using in silico tools. Forty-five polymorphic SNPs were ranked for predicted functional effect using FastSNP. Finally, 14 functional SNPs along with 10 SNPs identified from the literature were genotyped in 340 CAD patients and 340 controls. Plasma LTB4 levels were measured in 150 cases and 150 controls. None of the 24 SNPs showed significant association with CAD. Plasma LTB4 levels were higher in cases than in controls (76.42 ± 4.46 pg/mL versus 60.89 ± 2.61 pg/mL) (P=0.003), with greater risk being associated with the top quartile as compared to the bottom quartile after adjusting for potential confounders (OR 8.94, 95% CI 2.56–31.95; P=0.001). Four SNPs in the LTA4H gene showed significant association with LTB4 levels (P<0.05) of which rs1978331 (P=0.035) remained significant after correction for multiple testing. LTB4 showed strong correlation with lipids (r=0.24–34) only in cases. Our pilot study suggests that the association between Leukotrienes gene polymorphisms and CAD risk may be modulated through plasma LTB4 levels.

The FTO A/T polymorphism and elite athletic performance: a study involving three groups of European athletes

Objective

The FTO A/T polymorphism (rs9939609) is a strong candidate to influence obesity-related traits. Elite athletes from many different sporting disciplines are characterized by low body fat. Therefore, the aim of this study was to assess whether athletic status is associated with the FTO A/T polymorphism.

Subjects and Methods

A large cohort of European Caucasians from Poland, Russia and Spain were tested to examine the association between FTO A/T polymorphism (rs9939609) and athletic status. A total of 551 athletes were divided by type of sport (endurance athletes, n = 266 vs. sprint/power athletes, n = 285) as well as by level of competition (elite-level vs. national-level). The control group consisted of 1,416 ethnically-matched, non-athletic participants, all Europeans. Multinomial logistic regression analyses were conducted to assess the association between FTO A/T genotypes and athletic status/competition level.

Results

There were no significantly greater/lesser odds of harbouring any type of genotype when comparing across athletic status (endurance athletes, sprint/power athletes or control participants). These effects were observed after controlling for sex and nationality. Furthermore, no significantly greater/lesser odds ratios were observed for any of the genotypes in respect to the level of competition (elite-level vs. national-level).

Conclusion

The FTO A/T polymorphism is not associated with elite athletic status in the largest group of elite athletes studied to date. Large collaborations and data sharing between researchers, as presented here, are strongly recommended to enhance the research in the field of exercise genomics.

Genes, physical fitness and ageing

Persons aged 80 years and older are the fastest growing segment of the population. As more individuals live longer, we should try to understand the mechanisms involved in healthy ageing and preserving functional independence in later life. In elderly people, functional independence is directly dependent on physical fitness, and ageing is inevitably associated with the declining functions of systems and organs (heart, lungs, blood vessels, skeletal muscles) that determine physical fitness. Thus, age-related diminished physical fitness contributes to the development of sarcopenia, frailty or disability, all of which severely deteriorate independent living and thus quality of life. Ageing is a complex process involving many variables that interact with one another, including - besides lifestyle factors or chronic diseases - genetics. Thus, several studies have examined the contribution of genetic endowment to a decline in physical fitness and subsequent loss of independence in later life. In this review, we compile information, including data from heritability, candidate-gene association, linkage and genome-wide association studies, on genetic factors that could influence physical fitness in the elderly.