Genome-wide association study with 1000 genomes imputation identifies signals for nine sex hormone-related phenotypes

Genetic factors contribute strongly to sex hormone levels, yet knowledge of the regulatory mechanisms remains incomplete. Genome-wide association studies (GWAS) have identified only a small number of loci associated with sex hormone levels, with several reproductive hormones yet to be assessed. The aim of the study was to identify novel genetic variants contributing to the regulation of sex hormones. We performed GWAS using genotypes imputed from the 1000 Genomes reference panel. The study used genotype and phenotype data from a UK twin register. We included 2913 individuals (up to 294 males) from the Twins UK study, excluding individuals receiving hormone treatment. Phenotypes were standardised for age, sex, BMI, stage of menstrual cycle and menopausal status. We tested 7 879 351 autosomal SNPs for association with levels of dehydroepiandrosterone sulphate (DHEAS), oestradiol, free androgen index (FAI), follicle-stimulating hormone (FSH), luteinizing hormone (LH), prolactin, progesterone, sex hormone-binding globulin and testosterone. Eight independent genetic variants reached genome-wide significance (P<5 × 10⁻⁸), with minor allele frequencies of 1.3–23.9%. Novel signals included variants for progesterone (P=7.68 × 10⁻¹²), oestradiol (P=1.63 × 10⁻⁸) and FAI (P=1.50 × 10⁻⁸). A genetic variant near the FSHB gene was identified which influenced both FSH (P=1.74 × 10⁻⁸) and LH (P=3.94 × 10⁻⁹) levels. A separate locus on chromosome 7 was associated with both DHEAS (P=1.82 × 10⁻¹⁴) and progesterone (P=6.09 × 10⁻¹⁴). This study highlights loci that are relevant to reproductive function and suggests overlap in the genetic basis of hormone regulation.     

Meta-analysis of telomere length in 19?713 subjects reveals high heritability,stronger maternal inheritance and a paternal age effect

Telomere length (TL) has been associated with aging and mortality, but individual differences are also influenced by genetic factors, with previous studies reporting heritability estimates ranging from 34 to 82%. Here we investigate the heritability, mode of inheritance and the influence of parental age at birth on TL in six large, independent cohort studies with a total of 19 713 participants. The meta-analysis estimate of TL heritability was 0.70 (95% CI 0.64–0.76) and is based on a pattern of results that is highly similar for twins and other family members. We observed a stronger mother–offspring (r=0.42; P-value=3.60 × 10⁻⁶¹) than father–offspring correlation (r=0.33; P-value=7.01 × 10⁻⁵), and a significant positive association with paternal age at offspring birth (β=0.005; P-value=7.01 × 10⁻⁵). Interestingly, a significant and quite substantial correlation in TL between spouses (r=0.25; P-value=2.82 × 10⁻³⁰) was seen, which appeared stronger in older spouse pairs (mean age ≥55 years; r=0.31; P-value=4.27 × 10⁻²³) than in younger pairs (mean age<55 years; r=0.20; P-value=3.24 × 10⁻¹⁰). In summary, we find a high and very consistent heritability estimate for TL, evidence for a maternal inheritance component and a positive association with paternal age.     

Comparison of genetic variation of breast cancer susceptibility genes in Chinese and German populations

Genome-wide association studies (GWAS) identified several genetic risk factors for breast cancer, however, most of them were validated among women of European ancestry. This study examined single-nucleotide polymorphisms (SNPs) contributing to breast cancer in Chinese (984 cases and 2206 controls) and German (311 cases and 960 controls) populations. Eighteen SNPs significantly associated with breast cancer, previously identified in GWAS were genotyped. Twelve SNPs passed quality control and were subjected to statistical analysis. Seven SNPs were confirmed to be significantly associated with breast cancer in the Chinese population, reflecting three independent loci (ESR1, FGFR2, TOX3) and five of these were also confirmed in the German population. The strongest association was identified for rs2046210 in the Chinese (odds ratio (OR)=1.42, 95% confidence interval (CI)=1.28–1.59, P=1.9 × 10⁻¹⁰) and rs3803662 in the German population (OR=1.43, 95% CI=1.17–1.74, P=4.01 × 10⁻⁴), located upstream of the ESR1 and TOX3 gene, respectively. For the first time, rs3757318 at 6q25.1, located next to the gene encoding estrogen receptor α (ESR1) was found to be strongly associated with breast cancer (OR=1.33, 95% CI=1.18–1.49, P=1.94 × 10⁻⁶) in the Chinese population. The frequency of this variant was markedly lower in the German population and the association was not significant. Despite the genetic differences, essentially the same risk loci were identified in the Chinese and the German populations. Our study suggested the existence of common genetic factors as well as disease susceptibility differences for breast cancer in both populations and highlighted the importance of performing comparison analyses for disease susceptibility within ethnic populations.     

Gene by stress genome-wide interaction analysis and path analysis identify EBF1 as a cardiovascular and metabolic risk gene

We performed gene–environment interaction genome-wide association analysis (G × E GWAS) to identify SNPs whose effects on metabolic traits are modified by chronic psychosocial stress in the Multi-Ethnic Study of Atherosclerosis (MESA). In Whites, the G × E GWAS for hip circumference identified five SNPs within the Early B-cell Factor 1 (EBF1) gene, all of which were in strong linkage disequilibrium. The gene-by-stress interaction (SNP × STRESS) term P-values were genome-wide significant (Ps=7.14E−09 to 2.33E−08, uncorrected; Ps=1.99E−07 to 5.18E−07, corrected for genomic control). The SNP-only (without interaction) model P-values (Ps=0.011–0.022) were not significant at the conventional genome-wide significance level. Further analysis of related phenotypes identified gene-by-stress interaction effects for waist circumference, body mass index (BMI), fasting glucose, type II diabetes status, and common carotid intimal–medial thickness (CCIMT), supporting a proposed model of gene-by-stress interaction that connects cardiovascular disease (CVD) risk factor endophenotypes such as central obesity and increased blood glucose or diabetes to CVD itself. Structural equation path analysis suggested that the path from chronic psychosocial stress to CCIMT via hip circumference and fasting glucose was larger (estimate=0.26, P=0.033, 95% CI=0.02–0.49) in the EBF1 rs4704963 CT/CC genotypes group than the same path in the TT group (estimate=0.004, P=0.34, 95% CI=−0.004–0.012). We replicated the association of the EBF1 SNPs and hip circumference in the Framingham Offspring Cohort (gene-by-stress term P-values=0.007–0.012) as well as identified similar path relationships. This observed and replicated interaction between psychosocial stress and variation in the EBF1 gene may provide a biological hypothesis for the complex relationship between psychosocial stress, central obesity, diabetes, and cardiovascular disease.     

Lipids,obesity and gallbladder disease in women: insights from genetic studies using the cardiovascular gene-centric 50K SNP array

Gallbladder disease (GBD) has an overall prevalence of 10–40% depending on factors such as age, gender, population, obesity and diabetes, and represents a major economic burden. Although gallstones are composed of cholesterol by-products and are associated with obesity, presumed causal pathways remain unproven, although BMI reduction is typically recommended. We performed genetic studies to discover candidate genes and define pathways involved in GBD. We genotyped 15 241 women of European ancestry from three cohorts, including 3216 with GBD, using the Human cardiovascular disease (HumanCVD) BeadChip containing up to ~53 000 single-nucleotide polymorphisms (SNPs). Effect sizes with P-values for development of GBD were generated. We identify two new loci associated with GBD, GCKR rs1260326:T>C (P=5.88 × 10⁻⁷, ß=−0.146) and TTC39B rs686030:C>A (P=6.95x10⁻⁷, ß=0.271) and detect four independent SNP effects in ABCG8 rs4953023:G>A (P=7.41 × 10⁻⁴⁷, ß=0.734), ABCG8 rs4299376:G^>T (P=2.40 × 10⁻¹⁸, ß=0.278), ABCG5 rs6544718:T>C (P=2.08 × 10⁻¹⁴, ß=0.044) and ABCG5 rs6720173:G>C (P=3.81 × 10⁻¹², ß⁼0.262) in conditional analyses taking genotypes of rs4953023:G>A as a covariate. We also delineate the risk effects among many genotypes known to influence lipids. These data, from the largest GBD genetic study to date, show that specific, mainly hepatocyte-centred, components of lipid metabolism are important to GBD risk in women. We discuss the potential pharmaceutical implications of our findings.     

Fine mapping of eight psoriasis susceptibility loci

Previous studies have identified 41 independent genome-wide significant psoriasis susceptibility loci. After our first psoriasis genome-wide association study, we designed a custom genotyping array to fine-map eight genome-wide significant susceptibility loci known at that time (IL23R, IL13, IL12B, TNIP1, MHC, TNFAIP3, IL23A and RNF114) enabling genotyping of 2269 single-nucleotide polymorphisms (SNPs) in the eight loci for 2699 psoriasis cases and 2107 unaffected controls of European ancestry. We imputed these data using the latest 1000 Genome reference haplotypes, which included both indels and SNPs, to increase the marker density of the eight loci to 49 239 genetic variants. Using stepwise conditional association analysis, we identified nine independent signals distributed across six of the eight loci. In the major histocompatibility complex (MHC) region, we detected three independent signals at rs114255771 (P=2.94 × 10⁻⁷⁴), rs6924962 (P=3.21 × 10⁻¹⁹) and rs892666 (P=1.11 × 10⁻¹⁰). Near IL12B we detected two independent signals at rs62377586 (P=7.42 × 10⁻¹⁶) and rs918518 (P=3.22 × 10⁻¹¹). Only one signal was observed in each of the TNIP1 (rs17728338; P=4.15 × 10⁻¹³), IL13 (rs1295685; P=1.65 × 10⁻⁷), IL23A (rs61937678; P=1.82 × 10⁻⁷) and TNFAIP3 (rs642627; P=5.90 × 10⁻⁷) regions. We also imputed variants for eight HLA genes and found that SNP rs114255771 yielded a more significant association than any HLA allele or amino-acid residue. Further analysis revealed that the HLA-C*06-B*57 haplotype tagged by this SNP had a significantly higher odds ratio than other HLA-C*06-bearing haplotypes. The results demonstrate allelic heterogeneity at IL12B and identify a high-risk MHC class I haplotype, consistent with the existence of multiple psoriasis effectors in the MHC.     

Interleukin 10 gene promoter polymorphisms in women with early-onset pre-eclampsia

Pre-eclampsia is one of the most serious disorders of human pregnancy and T helper type 1 (Th1)/Th2 imbalance plays a major role in its aetiology. The Th2 cytokine, interleukin (IL)-10, plays a significant role in the maintenance of pregnancy. The present study is aimed at understanding the role of IL-10 promoter polymorphisms (−1082 G/A; −592 A/C and −819 C/T) and their haplotypes in early-onset pre-eclampsia. A total of 120 patients and an equal number of women with normal pregnancy, from Government Maternity Hospital, Petlaburz, Hyderabad, India, were considered for the present study. A standard amplification refractory mutation system–polymerase chain reaction (ARMS–PCR) was carried out for genotyping followed by agarose gel electrophoresis. Appropriate statistical methods were applied to test for the significance of the results. It was found that the IL-10 −819 C allele (P = 0·003) and −592 A (P = 0·005) allele frequencies increased significantly in patients compared to controls. No significant difference was found with regard to −1082 promoter polymorphism. Haplotype analysis of the IL-10 single nucleotide polymorphisms (SNPs) revealed a significant association with ACC haplotype with a twofold increased risk in patients compared to controls. The frequencies of two common IL-10 haplotypes (GCC and ATA) did not show any significant difference. Further, the diplotype analysis revealed five genotypes: −1082A with −819C (P = 0·0016); −1082G with −819C (P = 0·0018); −819C with −592C (P = 0·001); −1082A with −592C (P = 0·032); and −1082G with −592C (P = 0·005) associated with the disease. These findings support the concept of contribution of IL-10 gene polymorphisms in the pathogenesis of early-onset pre-eclampsia.     

Genetics of eye colours in different rural populations on the Silk Road

Eye colour is a highly transmissible and discernible trait in humans. A genome-wide association scan for variants associated to eye pigmentation was carried out on a large group of individuals coming from the Silk Road. Significant associations were detected not only with HERC2 (P-value=4.99 × 10⁻³⁷) and OCA2 (P-value=4.51 × 10⁻⁹) genes but also with CTNNA2 gene (P-value=4.06 × 10⁻⁸). Moreover, the multifactor dimensionality reduction analysis clearly showed the effect of HERC2 haplotype over OCA2 mostly associated with SNP, thus enabling a highly accurate eye-colour prediction. Finally, the regression tree analysis showed that individuals carrying a given combination of haplotypes have a significant probability to show a blue or green/grey iris colour as compared with brown, with a gradient from west to east.     

Genome-wide association study of coronary artery disease in the Japanese

A new understanding of the genetic basis of coronary artery disease (CAD) has recently emerged from genome-wide association (GWA) studies of common single-nucleotide polymorphisms (SNPs), thus far performed mostly in European-descent populations. To identify novel susceptibility gene variants for CAD and confirm those previously identified mostly in populations of European descent, a multistage GWA study was performed in the Japanese. In the discovery phase, we first genotyped 806 cases and 1337 controls with 451 382 SNP markers and subsequently assessed 34 selected SNPs with direct genotyping (541 additional cases) and in silico comparison (964 healthy controls). In the replication phase, involving 3052 cases and 6335 controls, 12 SNPs were tested; CAD association was replicated and/or verified for 4 (of 12) SNPs from 3 loci: near BRAP and ALDH2 on 12q24 (P=1.6 × 10⁻³⁴), HLA-DQB1 on 6p21 (P=4.7 × 10⁻⁷), and CDKN2A/B on 9p21 (P=6.1 × 10⁻¹⁶). On 12q24, we identified the strongest association signal with the strength of association substantially pronounced for a subgroup of myocardial infarction cases (P=1.4 × 10⁻⁴⁰). On 6p21, an HLA allele, DQB1^*0604, could show one of the most prominent association signals in an ∼8-Mb interval that encompasses the LTA gene, where an association with myocardial infarction had been reported in another Japanese study. CAD association was also identified at CDKN2A/B, as previously reported in different populations of European descent and Asians. Thus, three loci confirmed in the Japanese GWA study highlight the likely presence of risk alleles with two types of genetic effects – population specific and common – on susceptibility to CAD.     

Search for new loci and low-frequency variants influencing glioma risk by exome-array analysis

To identify protein-altering variants (PAVs) for glioma, we analysed Illumina HumanExome BeadChip exome-array data on 1882 glioma cases and 8079 controls from three independent European populations. In addition to single-variant tests we incorporated information on the predicted functional consequences of PAVs and analysed sets of genes with a higher likelihood of having a role in glioma on the basis of the profile of somatic mutations documented by large-scale sequencing initiatives. Globally there was a strong relationship between effect size and PAVs predicted to be damaging (P=2.29 × 10⁻⁴⁹); however, these variants which are most likely to impact on risk, are rare (MAF<5%). Although no single variant showed an association which was statistically significant at the genome-wide threshold a number represented promising associations – BRCA2:c.9976A>T, p.(Lys3326Ter), which has been shown to influence breast and lung cancer risk (odds ratio (OR)=2.3, P=4.00 × 10⁻⁴ for glioblastoma (GBM)) and IDH2:c.782G>A, p.(Arg261His) (OR=3.21, P=7.67 × 10⁻³, for non-GBM). Additionally, gene burden tests revealed a statistically significant association for HARS2 and risk of GBM (P=2.20 × 10⁻⁶). Genome scans of low-frequency PAVs represent a complementary strategy to identify disease-causing variants compared with scans based on tagSNPs. Strategies to lessen the multiple testing burden by restricting analysis to PAVs with higher priors affords an opportunity to maximise study power.     

Differences in potential for selection of clindamycin-resistant mutants between inducible erm(A) and erm(C) Staphylococcus aureus genes

In staphylococci, inducible macrolide-lincosamide-streptogramin B (MLS_B) resistance is conferred by the erm(C) or erm(A) gene. This phenotype is characterized by the erythromycin-clindamycin “D-zone” test. Although clindamycin appears active in vitro, exposure of MLS_B-inducible Staphylococcus aureus to this antibiotic may result in the selection of clindamycin-resistant mutants, either in vitro or in vivo. We have compared the frequencies of mutation to clindamycin resistance for 28 isolates of S. aureus inducibly resistant to erythromycin and bearing the erm(C) (n = 18) or erm(A) (n = 10) gene. Seven isolates susceptible to erythromycin or bearing the msr(A) gene (efflux) were used as controls. The frequencies of mutation to clindamycin resistance for the erm(A) isolates (mean ± standard deviation, 3.4 × 10⁻⁸ ± 2.4 × 10⁻⁸) were only slightly higher than those for the controls (1.1 × 10⁻⁸ ± 6.4 × 10⁻⁹). By contrast, erm(C) isolates displayed a mean frequency of mutation to clindamycin resistance (4.7 × 10⁻⁷ ± 5.5 × 10⁻⁷) 14-fold higher than that of the S. aureus isolates with erm(A). The difference was also observed, although to a lower extent, when erm(C) and erm(A) were cloned into S. aureus RN4220. We conclude that erm(C) and erm(A) have different genetic potentials for selection of clindamycin-resistant mutants. By the disk diffusion method, erm(C) and erm(A) isolates could be distinguished on the basis of high- and low-level resistance to oleandomycin, respectively.     

HLA-DQB1*02 and DQB1*06:03P are associated with peanut allergy

Peanut allergy (PA) is a common and serious food allergy and its prevalence has increased in the past decade. Although there is strong evidence of inheritance, the genetic causes of this disease are not well understood. Previously, a large-scale genome-wide association study described an association between human leukocyte antigen (HLA)-DQB1 and asthma; the aim of this study was to evaluate the association between HLA-DQB1 and PA. Genotypic and allelic profiles were established for 311 Caucasian members of a well-described Canadian group of children with PA and 226 Caucasian controls. Firth''s logistic regression analyses showed associations between HLA-DQB1 alleles and PA for DQB1*02 (P=1.1 × 10⁻⁸, odds ratio (OR)=0.09 (CI=0.03–0.23)) and DQB1*06:03P alleles (P=2.1 × 10⁻², OR=2.82 (CI=1.48–5.45)). This study of HLA in PA demonstrates specific association between two allelic groups of the HLA-DQB1 gene (DQB1*02 and DQB1*06:03P) and PA, highlighting its possible role in the development of this disease.     

Homozygosity analysis in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) may appear to be familial or sporadic, with recognised dominant and recessive inheritance in a proportion of cases. Sporadic ALS may be caused by rare homozygous recessive mutations. We studied patients and controls from the UK and a multinational pooled analysis of GWAS data on homozygosity in ALS to determine any potential recessive variant leading to the disease. Six-hundred and twenty ALS and 5169 controls were studied in the UK cohort. A total of 7646 homozygosity segments with length >2 Mb were identified, and 3568 rare segments remained after filtering ‘common'' segments. The mean total of the autosomal genome with homozygosity segments was longer in ALS than in controls (unfiltered segments, P=0.05). Two-thousand and seventeen ALS and 6918 controls were studied in the pooled analysis. There were more regions of homozygosity segments per case (P=1 × 10⁻⁵), a greater proportion of cases harboured homozygosity (P=2 × 10⁻⁵), a longer average length of segment (P=1 × 10⁻⁵), a longer total genome coverage (P=1 × 10⁻⁵), and a higher rate of these segments overlapped with RefSeq gene regions (P=1 × 10⁻⁵), in ALS patients than controls. Positive associations were found in three regions. The most significant was in the chromosome 21 SOD1 region, and also chromosome 1 2.9–4.8 Mb, and chromosome 5 in the 65 Mb region. There are more than twenty potential genes in these regions. These findings point to further possible rare recessive genetic causes of ALS, which are not identified as common variants in GWAS.     

Common polygenic variation in coeliac disease and confirmation of ZNF335 and NIFA as disease susceptibility loci

Coeliac disease (CD) is a chronic immune-mediated disease triggered by the ingestion of gluten. It has an estimated prevalence of approximately 1% in European populations. Specific HLA-DQA1 and HLA-DQB1 alleles are established coeliac susceptibility genes and are required for the presentation of gliadin to the immune system resulting in damage to the intestinal mucosa. In the largest association analysis of CD to date, 39 non-HLA risk loci were identified, 13 of which were new, in a sample of 12 014 individuals with CD and 12 228 controls using the Immunochip genotyping platform. Including the HLA, this brings the total number of known CD loci to 40. We have replicated this study in an independent Irish CD case–control population of 425 CD and 453 controls using the Immunochip platform. Using a binomial sign test, we show that the direction of the effects of previously described risk alleles were highly correlated with those reported in the Irish population, (P=2.2 × 10⁻¹⁶). Using the Polygene Risk Score (PRS) approach, we estimated that up to 35% of the genetic variance could be explained by loci present on the Immunochip (P=9 × 10⁻⁷⁵). When this is limited to non-HLA loci, we explain a maximum of 4.5% of the genetic variance (P=3.6 × 10⁻¹⁸). Finally, we performed a meta-analysis of our data with the previous reports, identifying two further loci harbouring the ZNF335 and NIFA genes which now exceed genome-wide significance, taking the total number of CD susceptibility loci to 42.     

The dystrophin gene and cognitive function in the general population

The aim of our study is to investigate whether single-nucleotide dystrophin gene (DMD) variants associate with variability in cognitive functions in healthy populations. The study included 1240 participants from the Erasmus Rucphen family (ERF) study and 1464 individuals from the Rotterdam Study (RS). The participants whose exomes were sequenced and who were assessed for various cognitive traits were included in the analysis. To determine the association between DMD variants and cognitive ability, linear (mixed) modeling with adjustment for age, sex and education was used. Moreover, Sequence Kernel Association Test (SKAT) was used to test the overall association of the rare genetic variants present in the DMD with cognitive traits. Although no DMD variant surpassed the prespecified significance threshold (P<1 × 10⁻⁴), rs147546024:A>G showed strong association (β=1.786, P-value=2.56 × 10⁻⁴) with block-design test in the ERF study, while another variant rs1800273:G>A showed suggestive association (β=−0.465, P-value=0.002) with Mini-Mental State Examination test in the RS. Both variants are highly conserved, although rs147546024:A>G is an intronic variant, whereas rs1800273:G>A is a missense variant in the DMD which has a predicted damaging effect on the protein. Further gene-based analysis of DMD revealed suggestive association (P-values=0.087 and 0.074) with general cognitive ability in both cohorts. In conclusion, both single variant and gene-based analyses suggest the existence of variants in the DMD which may affect cognitive functioning in the general populations.     

Cultivation of Virulent Treponema pallidum in Tissue Culture

In a series of seven experiments, the virulent Nichols strain of Treponema pallidum was shown to attach and replicate on the surface of tissue culture cells of cottontail rabbit epithelium (Sf1Ep) growing in conventional monolayer cultures under an atmosphere of 1.5% oxygen. Five days after inoculation of 10⁶T. pallidum, the number of treponemes had increased to between 8 × 10⁶ and 2.59 × 10⁷. The viability of harvested organisms ranged from 86 to 97%. The number of T. pallidum continued to increase, generally reaching a plateau between days 9 and 12 of incubation, with increases ranging up to 100-fold and averaging 49-fold. There appeared to be a ceiling of multiplication of about 2 × 10⁸ irrespective of the inoculum, which ranged from 10⁶ to 10⁸T. pallidum. Concurrent deoxyribonucleic acid assays were performed on the cultures containing T. pallidum to obtain further evidence of replication. Significant increases in treponemal deoxyribonucleic acid were observed when the inocula ranged from 10⁶ to 10⁷, with the greatest increases, as might be expected, being in the former group. There was also excellent correlation in the amount of deoxyribonucleic acid per treponeme; the averages for the 10⁶, 2.5 × 10⁶, and 10⁷ groups were 3.46 × 10⁻¹⁴, 3.28 × 10⁻¹⁴, and 2.79 × 10⁻¹⁴ g per treponeme, respectively (3.14 ± 0.72 × 10⁻¹⁴ g per treponeme). In each experiment, organisms were harvested from the group inoculated with 10⁶T. pallidum after 7 days of incubation to test for virulence. In all instances, the organisms were virulent; erythematous, indurated, treponeme-containing lesions were produced from an average of six to seven organisms. Scanning electron microscopy revealed that during the course of replication many microcolonies of treponemes formed on the surface of the cells.     

The functional activities of IgG and IgM anti-A and anti-B

The rate constants for association and dissociation, and the equilibrium constants, were determined for ¹²⁵I-labelled anti-A and anti-B of both IgG and IgM molecular types. The following results and conclusions were obtained:

1. The equilibrium constants were within the range 06×10⁸–13.0×10⁸ l/mole, and were of the same order for both IgG and IgM antibodies.

2. The initial rate constants for association were in the range 2.1×10⁵–4.8×10⁵ l/mole/sec, and the energy of activation (E_a) 6700–9000 cal/mole. These results indicate that the rate of association is approaching the limit set by the rate of diffusion of the reactants.

3. The initial rate constants for dissociation were 1 × 10^-4–5 × 10^-4/sec and E_a = 20,000–36,000 cal/mole. These latter values suggest that more than one bond must be broken simultaneously during dissociation.

4. Ionic strength and pH changes have only a minor effect on the constants; this indicates absence of ionic groups on A and B antigen sites.

5. The changes in enthalpy were –5400 to –21,800 cal/mole; the reactions are mainly enthalpy driven and this accounts for the fact that anti-A and anti-B agglutination titres increase as the temperature is decresed.

6. There was heterogeneity of the values of the standard change in free energy, enthalpy and entropy within each example of antibody.

7. The approximate concentrations of antibody at the end-points of the agglutination titres were: for IgG antibody, 0.2 μg/ml; for IgM antibody, 0.01 μg/ml.

     

A sequence variant on 17q21 is associated with age at onset and severity of asthma

A sequence variant (rs7216389-T) near the ORMDL3 gene on chromosome 17q21 was recently found to be associated with childhood asthma. We sought to evaluate the effect of rs7216389-T on asthma subphenotypes and its correlation with expression levels of neighboring genes. The association of rs7216389-T with asthma was replicated in six European and one Asian study cohort (N=4917 cases N=34 589 controls). In addition, we found that the association of rs7216389-T was confined to cases with early onset of asthma, particularly in early childhood (age: 0–5 years OR=1.51, P=6.89·10⁻⁹) and adolescence (age: 14–17 years OR=1.71, P=5.47·10⁻⁹). A weaker association was observed for onset between 6 and 13 years of age (OR=1.17, P=0.035), but none for adult-onset asthma (OR=1.07, P=0.12). Cases were further stratified by sex, asthma severity and atopy status. An association with greater asthma severity was observed among early-onset asthma cases (P=0.0012), but no association with sex or atopy status was observed among the asthma cases. An association between sequence variants and the expression of genes in the 17q21 region was assessed in white blood cell RNA samples collected from Icelandic individuals (n=743). rs7216389 associated with the expression of GSDMB and ORMDL3 genes. However, other sequence variants showing a weaker association with asthma compared with that of rs7216389 were more strongly associated with the expression of both genes. Thus, the contribution of rs7216389-T to the development of asthma is unlikely to operate only through an impact on the expression of ORMDL3 or GSDMB genes.     

Interactions Between Genetic Variants in Glucose Transporter Type 9 (SLC2A9) and Dietary Habits in Serum Uric Acid Regulation

Aim

To investigate possible interactions between genetic variants in glucose transporter type 9 (SLC2A9) gene and dietary habits in serum uric acid regulation.

Methods

Participants for this study were recruited from two isolated Croatian island communities of Vis (n = 918) and Korčula (n = 898). Three single nucleotide polymorphisms (SNP) from the SLC2A9 gene (rs1014290, rs6449213, rs737267) were correlated with dietary habits and uric acid.

Results

A significant decrease in uric acid levels was recorded with increasing consumption of milk, sour cream, duck and turkey, and eggs. The only significant interaction was found between potato consumption and rs737267 and a near-significant interaction was found between soft drinks and rs1014290 (interaction P = 0.068). Increased consumption of soft drinks interacting with the TT genotype at rs1014290 increased serum uric acid. No significant interactions were observed between food products consumption and rs6449213.

Conclusion

There is a certain extent of interaction between SLC2A9 and dietary patterns in serum uric acid determination. The metabolic effect of soft drinks seems to be determined by the underlying genotype of rs1014290.Gout is a disorder of purine metabolism that presents as inflammatory arthritis caused by urate crystallizing in joints following chronic hyperuricemia. It affects 1%-2% of the adult population in the Western world, especially elderly men. Diet and, more recently, genetic polymorphisms have been recognized as the most important factors causatively associated with serum uric acid levels and gout (1). High protein intake and purine-rich products, like meat and seafood, have been known to increase serum uric acid and the risk of gout, while vegetables rich in purine content showed no effect (2). On the other hand, the protective effect of certain foods has been identified. For example, dairy products, vitamin C, and coffee have been reported to decrease serum uric acid and prevalence of gout (1).Serum urate concentration is a highly variable trait among humans. It is greatly affected by environmental factors (diet), but shows high heritability of about 60% (3). Not surprisingly, genome-wide association studies identified genetic polymorphisms that substantially affect urate concentrations and gout. Polymorphisms in a transporter gene GLUT9 (SLC2A9) have been shown to explain 1.7%-5.3% of the variance in serum uric acid concentration (4,5). Recently, polymorphisms in 3 additional genes, URAT1 (SLC22CA12), ABCG2, and SLC17A3, have also been associated with uric acid concentrations and the risk of gout (6-8).SLC2A9 was first described as a glucose transporter and only later as a urate transporter. The study investigating whether glucose or fructose influenced urate transport in African clawed frog oocytes (Xenopus laevis) demonstrated that SLC2A9-mediated urate transport was facilitated by glucose and, to a lesser extent, fructose (9). We wanted to investigate if we could observe the same effect in vivo in humans and whether diet in general had a different impact on serum uric acid depending on the genetic background of an individual. To our knowledge, this is the first study on uric acid and gout that investigates genotype-environment interaction, more specifically, the interaction between previously reported genetic polymorphisms in the SLC2A9 gene and diet in humans.     

Genome-wide haplotypic testing in a Finnish cohort identifies a novel association with low-density lipoprotein cholesterol

We performed genome-wide tests for association between haplotype clusters and each of 9 metabolic traits in a cohort of 5402 Northern Finnish individuals genotyped for 330 000 single-nucleotide polymorphisms. The metabolic traits were body mass index, C-reactive protein, diastolic blood pressure, glucose, high-density lipoprotein (HDL), insulin, low-density lipoprotein (LDL), systolic blood pressure, and triglycerides. Haplotype clusters were determined using Beagle. There were LDL-associated clusters in the chromosome 4q13.3-q21.1 region containing the albumin (ALB) and platelet factor 4 (PF4) genes. This region has not been associated with LDL in previous genome-wide association studies. The most significant haplotype cluster in this region was associated with 0.488 mmol/l higher LDL (95% CI: 0.361–0.615 mmol/l, P-value: 6.4 × 10⁻¹⁴). We also observed three previously reported associations: Chromosome 16q13 with HDL, chromosome 1p32.3-p32.2 with LDL and chromosome 19q13.31-q13.32 with LDL. The chromosome 1 and chromosome 4 LDL associations do not reach genome-wide significance in single-marker analyses of these data, illustrating the power of haplotypic association testing.