Linkage analysis using co-phenotypes in the BRIGHT study reveals novel potential susceptibility loci for hypertension

Polymorphisms in genes involved in T-cell co-stimulation are associated with blood pressure in women

In recent years, conclusive data have emerged on a relationship between immune system, especially the T-cell, and blood pressure (BP). The objective of the present study was to determine the association between BP and four polymorphisms in CD80, CD86, CD28 and CTLA4 genes that code for key proteins in the T-cell co-stimulation process, in a female cohort. To that end, an association study in a cohort of 934 women over 40 years old from two hospitals was done. Raw data showed a significant association between the SNP rs1129055 of CD86 gene and BP. Analyzing this association against inheritance patterns, higher SBP (p < 0.000) and DBP (p = 0.005) values were observed in AA than in GG/GA genotype subjects in the largest sample cohort (Hospital 1). In multivariate linear regression studies, with adjustment for presumed independent predictors of BP, the SNP of the CD86 gene remained a predictor of SBP (p = 0.001) and DBP (p = 0.006), as did the SNP rs867234 of the CD80 gene for DBP (p < 0.000), both resisting the Bonferroni correction for multiple comparisons. As conclusion, we report a robust association between the SNP rs1129055 of CD86 gene and BP. The SNP rs867234 of CD80 gene was also shown to be a strong predictor of DBP.

Identification of IGF1, SLC4A4, WWOX, and SFMBT1 as hypertension susceptibility genes in Han Chinese with a genome-wide gene-based association study

Hypertension is a complex disorder with high prevalence rates all over the world. We conducted the first genome-wide gene-based association scan for hypertension in a Han Chinese population. By analyzing genome-wide single-nucleotide-polymorphism data of 400 matched pairs of young-onset hypertensive patients and normotensive controls genotyped with the Illumina HumanHap550-Duo BeadChip, 100 susceptibility genes for hypertension were identified and also validated with permutation tests. Seventeen of the 100 genes exhibited differential allelic and expression distributions between patient and control groups. These genes provided a good molecular signature for classifying hypertensive patients and normotensive controls. Among the 17 genes, IGF1, SLC4A4, WWOX, and SFMBT1 were not only identified by our gene-based association scan and gene expression analysis but were also replicated by a gene-based association analysis of the Hong Kong Hypertension Study. Moreover, cis-acting expression quantitative trait loci associated with the differentially expressed genes were found and linked to hypertension. IGF1, which encodes insulin-like growth factor 1, is associated with cardiovascular disorders, metabolic syndrome, decreased body weight/size, and changes of insulin levels in mice. SLC4A4, which encodes the electrogenic sodium bicarbonate cotransporter 1, is associated with decreased body weight/size and abnormal ion homeostasis in mice. WWOX, which encodes the WW domain-containing protein, is related to hypoglycemia and hyperphosphatemia. SFMBT1, which encodes the scm-like with four MBT domains protein 1, is a novel hypertension gene. GRB14, TMEM56 and KIAA1797 exhibited highly significant differential allelic and expressed distributions between hypertensive patients and normotensive controls. GRB14 was also found relevant to blood pressure in a previous genetic association study in East Asian populations. TMEM56 and KIAA1797 may be specific to Taiwanese populations, because they were not validated by the two replication studies. Identification of these genes enriches the collection of hypertension susceptibility genes, thereby shedding light on the etiology of hypertension in Han Chinese populations.

Association of TGF-beta1 gene polymorphisms in exon1 and blood levels with essential hypertension

AIMS

Based on a case-control study, we investigated the relationship between +869T/C and +915G/C gene polymorphisms in transforming growth factor-beta1 (TGF-beta1), protein levels and essential hypertension (EH) in the Kazakh and Han Chinese populations selected from the Boertonggu countryside of Shawan region in the Xinjiang Uygur Autonomous Region of China (n=1600). The polymorphisms of TGF-beta1 and the blood levels were detected using polymerase chain reaction-restriction fragment length polymorphism assays and sandwich ELISA, respectively.

MAJOR FINDINGS

An association was found between +869C-allele with higher risk of EH in these two populations. We also found that the CG haplotype of the two polymorphisms was associated with EH in the Kazakh EH patients. The levels of TGF-beta(1) in the blood were positively correlated with diastolic blood pressure both in the Kazakh and Han EH patients. Levels of the TGF-beta1 protein in the Kazakh EH patients were significantly higher than those in the Han EH patients.

PRINCIPAL CONCLUSION

These results suggest that the TGF-beta1 +869 C allele is potentially a genetic factor of EH in these two ethnicities, the CG haplotype can be a genetic marker of EH in the Kazakh Chinese and the high concentration of TGF-beta1 is possibly associated with EH, especially in the Kazakh population.

Genetics of hypertension: from experimental animals to humans

Essential hypertension affects 20 to 30% of the population worldwide and contributes significantly to cardiovascular mortality and morbidity. Heridability of blood pressure is around 15 to 40% but there are also substantial environmental factors affecting blood pressure variability. It is assumed that blood pressure is under the control of a large number of genes each of which has only relatively mild effects. It has therefore been difficult to discover the genes that contribute to blood pressure variation using traditional approaches including candidate gene studies and linkage studies. Animal models of hypertension, particularly in the rat, have led to the discovery of quantitative trait loci harbouring one or several hypertension related genes, but translation of these findings into human essential hypertension remains challenging. Recent development of genotyping technology made large scale genome-wide association studies possible. This approach and the study of monogenic forms of hypertension has led to the discovery of novel and robust candidate genes for human essential hypertension, many of which require functional analysis in experimental models.

Genetics of hypertension. Current status

Genetics of hypertension is complex with no known single gene playing a major role, but rather many genes each with mild effects reacting to different environmental stimuli contribute to blood pressure. The heritable component of blood pressure has been documented in familial and twin studies suggesting that 30%-50% of the variance of blood pressure readings are attributable to genetic heritability and about 50% to environmental factors. Early studies in hypertension identified specific enzymes, channels and receptors implicating sodium handling in the regulation of blood pressure including genes involved with the renin-angiotensin-aldosterone system controlling blood pressure and salt-water homeostasis, proteins in hormonal regulation of blood pressure (enzymes and receptors of the mineralo- and glucocorticoid pathways) and proteins coded by genes involved in the structure and/or regulation of vascular tone (endothelins and their receptors). The field of molecular genetics has revolutionized the study of hypertension by identifying single gene syndromes or Mendelian forms and several candidate genes for blood pressure variance. Genes have been localized to at least 20 chromosome regions. For example, recent genome-wide association studies (GWAS) of common genetic variants found 13 single nucleotide polymorphisms (SNPs) or variants in systolic and 20 for diastolic blood pressure readings representing different genes and genetic heterogeneity. Further understanding of the genetics of hypertension will require the use of advances in bioinformatics tools and genetic technology [e.g., SNP, exon and noncoding (micro) RNA arrays]. New approaches will allow for identification of not only single genes, but other interacting genes contributing to hypertension by merging multiple genetic data sets (structural and functional) from individuals with hypertension and development of new molecular targets for study and treatment.

IGF2 gene variants and risk of hypertension in obese children and adolescents

Obese children have a great risk of hypertension and cardiovascular morbidity in adults. The insulin-like growth factor type II (IGF-II) regulates glucose homeostasis, cardiovascular functions, and lipid metabolism. IGF2 gene variants have shown a strong association with weight, body mass index (BMI), and metabolic profile in adults. We performed the molecular screening of two IGF2 polymorphisms (6815 A/T, 820 G/A), in 227 obese children to evaluate the potential association between IGF2 variants with either obesity or high blood pressure (assessed with a 24-h holter system) or both. A second cohort of age-, sex-, and BMI-matched children were enrolled to confirm any eventual association. We observed a significant association between the 6815 A/T IGF2 gene variant and high systolic blood pressure in obese children. Homozygote subjects for the T6815 allele showed, even in 24-h measurements, a higher risk to develop hypertension than those carrying the A6815 allele (OR = 3.7, 95% CI: 1.59-8.66). This result was confirmed in the second cohort (OR = 4.1, 95% CI: 1.41-6.50). Any statistically significant difference in terms of BMI between the genotype groups was observed. Our results suggest that IGF2 gene variants are involved in the blood pressure regulation in obese children.

Association of polymorphisms of SORBS1, GCK and WISP1 with hypertension in community-dwelling Japanese individuals

Although various loci and genes have been implicated in predisposition to hypertension by genetic linkage analyses and candidate gene association studies, the genes that confer susceptibility to this condition remain to be identified definitively. We have now examined the relationships of 22 candidate gene polymorphisms with the prevalence of hypertension and with blood pressure (BP) in a 6-year population-based longitudinal cohort study and observed significant relationships of three polymorphisms of SORBS1, GCK and WISP1 with hypertension. The 2233 subjects (1106 women, 1127 men) were aged 40-79 years and were randomly recruited to a population-based prospective cohort study of aging and age-related diseases in Japan. BP was measured with subjects having rested in the sitting position for at least 15 min. Genotypes for the 682A --> G (Thr228Ala) polymorphism of SORBS1, the -30G --> A polymorphism of GCK and the 2364A --> G polymorphism of WISP1 were determined by melting curve analysis. Longitudinal analysis with a generalized estimating equation revealed that the polymorphisms of SORBS1 and GCK and that of WISP1 were significantly associated with the prevalence of hypertension in women and men, respectively. Longitudinal analysis with a mixed-effect model revealed that the polymorphism of SORBS1 was significantly related to diastolic BP in women and that those of GCK and WISP1 were significantly related to both systolic and diastolic BP in women and men, respectively. These results suggest that SORBS1 and GCK are susceptibility loci for hypertension in Japanese women and that WISP1 is such a locus in men.

A genome-wide search for linkage to chronic kidney disease in a community-based sample: the SAFHS

BACKGROUND

Chronic kidney disease (CKD) phenotypes such as albuminuria measured by urinary albumin creatinine ratio (ACR), elevated serum creatinine (SrCr) and/or decreased creatinine clearance (CrCl) and glomerular filtration rate (eGFR) are major risk factors for renal and cardiovascular diseases. Epidemiological studies have reported that CKD phenotypes cluster in families suggesting a genetic predisposition. However, studies reporting chromosomal regions influencing CKD are very limited. Therefore, the purpose of this study is to identify susceptible chromosomal regions for CKD phenotypes in Mexican American families enrolled in the San Antonio Family Heart Study (SAFHS).

METHODS

We used the variance components decomposition approach (implemented in the software package SOLAR) to perform linkage analysis on 848 participants from 26 families. A total of 417 microsatellite markers were genotyped at an average interval of 10 cM spanning 22 autosomal chromosomes.

RESULTS

All phenotypes were measured by standard procedures. Mean +/- SD values of ACR, SrCr, CrCl and eGFR were 0.06 +/- 0.38, 0.85 +/- 0.72 mg/dl, 129.85 +/- 50.37 ml/min and 99.18 +/- 25.69 ml/min/1.73 m(2) body surface area, respectively. All four CKD phenotypes exhibited significant heritabilities (P < 0.0001). A genome-wide scan showed linkage on chromosome 2p25 for SrCr, CrCl and eGFR. Significant linkage was also detected on chromosome 9q21 for eGFR [logarithm of the odds (LOD) score = 3.87, P = 0.00005] and SrCr (LOD score = 2.6, P = 0.00026). ACR revealed suggestive evidence for linkage to a region on chromosome 20q12 (LOD score = 2.93, P = 0.00020).

CONCLUSION

Findings indicate that chromosomal regions 2p25, 9q21 and 20q12 may have functional relevance to CKD phenotypes in Mexican Americans.

Testing for association on the X chromosome

The problem of testing for genotype–phenotype association with loci on the X chromosome in mixed-sex samples has received surprisingly little attention. A simple test can be constructed by counting alleles, with males contributing a single allele and females 2. This approach does assume not only Hardy–Weinberg equilibrium in the population from which the study subjects are sampled but also, perhaps, an unrealistic alternative hypothesis. This paper proposes 1 and 2 degree-of-freedom tests for association which do not assume Hardy–Weinberg equilibrium and which treat males as homozygous females. The proposed method remains valid when phenotype varies between sexes, provided the allele frequency does not, and avoids the loss of power resulting from stratification by sex in such circumstances.

Current status of genome-wide scanning for hypertension

PURPOSE OF REVIEW

The current review focuses on new trends in genome-wide assessment of the inherited component of blood pressure variation.

RECENT FINDINGS

Systematic linkage and association analyses of a region on chromosome 1q, complemented by gene prioritization with comparative genomic evidence, revealed variants in three genes contributing to tangible increases in blood pressure. The results of one of the first two-dimensional scans were published, confirming the oligogenic epistatic nature of the genetic component of blood pressure determination. Several loci with distinct effects on blood pressure in men and women were reported, enhancing the sexually dimorphic map of complex traits. Novel approaches were applied to extract genetically and clinically distinct subsets of garden-variety hypertension, which appears to be a promising direction to take in deciphering the hypertension genetic puzzle.

SUMMARY

The current landscape of genome-wide linkage studies of hypertension is acquiring novel facets in an attempt to more appropriately grasp the genomic architecture of hypertension. The advent of genome-wide association investigations, enhanced possibilities of comparative genomics and integration with information on copy number variations and transcriptomics will most likely reshape our view of nature and the evolutionary connotations of genetic variation affecting blood pressure in the near future.

Association of interleukin-6, interleukin-12, and interleukin-10 gene polymorphisms with essential hypertension in Tatars from Russia

Essential hypertension is a common disease with fatal clinical complications. Epidemiological and family studies have confirmed the role of genetic predisposition in its development. Hypertensive patients have been shown to have an altered profile of pro- and anti-inflammatory cytokines. The aim of our investigation was to reveal the association of interleukin-6, interleukin-12, and interleukin-10 gene polymorphisms with essential hypertension and its clinical complications in a Tatar ethnic group from Bashkortostan, Russia. The study involved 362 hypertensive patients and 244 healthy subjects from this Tatar ethnic group (Bashkortostan, Russia). DNA was isolated from whole venous blood using phenol-chloroform extraction by the standard method. IL6 -572 G/C, IL12B 1159 C/A, and IL10 -627 C/A genotypes were typed using polymerase chain reaction followed by restriction enzyme digestion. We found that the IL10 -627 *C/*C genotype was associated with decreased risk of hypertension (OR = 0.64, P = 0.035). IL6 genotypes and allele distribution did not differ significantly between subjects with and without hypertension, but the IL6 -572 *G/*G genotype frequency was found to be significantly higher among those patients who had stroke, compared with normotensive control subjects (P = 0.036). Carriers of the IL12B 1159 *A/*A genotype had a lower risk of stroke (OR = 0.38, P = 0.028). Our study has shown the association between IL10 -627 C/A polymorphism and essential hypertension in the Tatar ethnic group from Bashkortostan, Russia. The IL10 -627*C/*C genotype was found to be protective against hypertension. We also demonstrated that hypertensive patients with the IL12B *A/*A and IL6 *G/*G genotypes had increased risk of stroke. Our results suggest a role for cytokines in cardiovascular disease development in the Tatar ethnic group, but further investigation is needed.

Sequence variation in DOCK9 and heterogeneity in bipolar disorder

BACKGROUND

Linkage of bipolar disorder to a broad region on chromosome 13q has been supported in several studies including a meta-analysis on genome scans. Subsequent reports have shown that variations in the DAOA (G72) locus on 13q33 display association with bipolar disorder but these may not account for all of the linkage evidence in the region.

OBJECTIVE

To identify additional susceptibility loci on 13q32-q33 by linkage disequilibrium mapping and explore the impact of phenotypic heterogeneity on association.

METHODS

In the initial phase, 98 single nucleotide polymorphism (SNPs) located on 13q32-q33 were genotyped on 285 probands with bipolar disorder and their parents were drawn from families in the NIMH Genetics Initiative consortium for bipolar disorder (NIMH1-4) and two other series. Fine scale mapping using one family series (NIMH1-2) as the test sample was targeted on a gene that displayed the highest evidence of association. A secondary analysis of familial component phenotypes of bipolar disorder was conducted.

RESULTS

Three of seven SNPs in DOCK9, a gene that encodes an activator of the Rho-GTPase Cdc42, showed significant excess allelic transmission (P=0.0477-0.00067). Fine scale mapping on DOCK9 yielded evidence of association at nine SNPs in the gene (P=0.02-0.006). Follow-up tests detected excess transmission of the same allele of rs1340 in two out of three other sets of families. The association signals were largely attributable to maternally transmitted alleles (rs1927568: P=0.000083; odds ratio=3.778). A secondary analysis of familial component phenotypes of bipolar disorder detected significant association across multiple DOCK9 markers for racing thoughts, psychosis, delusion during mania and course of illness indicators.

CONCLUSION

These results suggest that DOCK9 contributes to both risk and increased illness severity in bipolar disorder. We found evidence for the effect of phenotypic heterogeneity on association. To our knowledge this is the first report to implicate DOCK9 or the Rho-GTPase pathway in the etiology of bipolar disorder.

Interpreting analyses of continuous covariates in affected sibling pair linkage studies

Datasets collected for linkage analyses of complex human diseases often include a number of clinical or environmental covariates. In this study, we evaluated the performance of three linkage analysis methods when the relationship between continuous covariates and disease risk or linkage heterogeneity was modeled in three different ways: (1) The covariate distribution is determined by a quantitative trait locus (QTL), which contributes indirectly to the disease risk; (2) the covariate is not genetically determined, but influences the disease risk through statistical interaction with a disease susceptibility locus; (3) the covariate distribution differs in families linked or unlinked to a particular disease susceptibility locus. We analyzed simulated datasets with a regression-based QTL analysis, a nonparametric analysis of the binary affection status, and the ordered subset analysis (OSA). We found that a significant OSA result may be due to a gene that influences variability in the population distribution of a continuous disease risk factor. Conversely, a regression-based QTL analysis may detect the presence of gene-environment (GxE) interaction in a sample of primarily affected individuals. The contribution of unaffected siblings and the size of baseline lod scores may help distinguish between QTL and GxE models. As illustrated by a linkage study of multiplex families with age-related macular degeneration, our findings assist in the interpretation of analysis results in real datasets. They suggest that the side-by-side evaluation of OSA and QTL results may provide important information about the relationship of measured covariates with either disease risk or linkage heterogeneity.

Testing genetic linkage with relative pairs and covariates by quasi-likelihood score statistics

BACKGROUND/AIMS

Genetic linkage analysis of common diseases is complicated by the heterogeneity of genetic and environmental factors that increase disease risk, and possibly interactions among them. Most linkage methods that account for covariates are restricted to sib pairs, with the exception of the conditional logistic regression model [1] implemented in LODPAL in the S.A.G.E. software [2]. Although this model can be applied to arbitrary pedigrees, at times it can be difficult to maximize the likelihood due to model constraints, and it does not account for the dependence among the different types of relative pairs in a pedigree.

METHODS

To overcome these limitations, we developed a new approach based on score statistics for quasi- likelihoods, implemented as weighted least squares. Our methods can be used to test three different hypotheses: (1) a test for linkage without covariates; (2) a test for linkage with covariates, and (3) a test for effects of covariates on identity by descent sharing (i.e., heterogeneity). Furthermore, our methods are robust because they account for the dependence among different relative pairs within a pedigree.

RESULTS AND CONCLUSION

Although application of our methods to a prostate cancer linkage study did not find any critical covariates in our data, the results illustrate the utility and interpretation of our methods, and suggest, nonetheless, that our methods will be useful for a broad range of genetic linkage heterogeneity analyses.

An R package for analysis of whole-genome association studies

OBJECTIVE

To provide data classes and methods to facilitate the analysis of whole genome association studies in the R language for statistical computing.

METHODS

We have implemented data classes in which each genotype call is stored as a single byte. At this density, data for single chromosomes derived from large studies and new high-throughput gene chip platforms can be handled in memory. We use the object-oriented programming model introduced with version 4 of the S-plus package, usually termed 'S4 methods'.

RESULTS

At the current state of development the package only supports population-based studies, although we would hope to provide support for family-based studies soon. Both quantitative and qualitative phenotypes may be analysed. Flexible association testing functions are provided which can carry out single SNP tests which control for potential confounding by quantitative and qualitative covariates. Tests involving several SNPs taken together as 'tags' are also supported. Efficient calculation of pair-wise linkage disequilibrium measures is implemented and data input functions include a function which can download data directly from the international HapMap project website.

Genetics of arterial hypertension and hypotension

Human hypertension affects affects more than 20% of the adult population in industrialized countries, and it is implicated in millions of deaths worldwide each year from stroke, heart failure and ischemic heart disease. Available evidence suggests a major genetic impact on blood pressure regulation. Studies in monogenic hypertension revealed that renal salt and volume regulation systems are predominantly involved in the genesis of these disorders. Mutations here affect the synthesis of mineralocorticoids, the function of the mineralocorticoid receptor, epithelial sodium channels and their regulation by a new class of kinases, termed WNK kinases. It has been learned from monogenic hypotension that almost all ion transporters involved in the renal uptake of Na(+) have a major impact on blood pressure regulation. For essential hypertension as a complex disease, many candidate genes have been analysed. These include components of the renin-angiotensin-aldosterone system, adducin, beta-adrenoceptors, G protein subunits, regulators of G protein signalling (RGS) proteins, Rho kinases and G protein receptor kinases. At present, the individual impact of common polymorphisms in these genes on the observed blood pressure variation, on risk for stroke and as predictors of antihypertensive responses remains small and clinically irrelevant. Nevertheless, these studies have greatly augmented our knowledge on the regulation of renal functions, cellular signal transduction and the integration of both. Together, this provides the basis for the identification of novel drug targets and, hopefully, innovative antihypertensive drugs.