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Gene-environment and gene-gene interaction studies in the molecular genetic analysis of asthma and atopy.

Asthma is a complex trait for which genetic predisposition is fundamental in disease aetiology, but poorly understood. Unravelling the genetic aetiology is complicated by the tremendous influence of the environment over disease expression. For this reason, asthma is multifactorial, in that disease expression is influenced by interactions between multiple major and minor genes, and modulated by interacting non-genetic factors (e.g. environment). 'Parent of origin' effects may be both genetic and environmental in aetiology, and have been observed in a number of population studies on asthma. The primary focus of this review is to evaluate the current approaches used in identifying the interrelationship between (1) certain environmental factors (e.g. allergen exposure, maternal inheritance) and genetic susceptibility to asthma and its associated phenotypes; and (2) candidate genes in chromosomal regions that have been linked to asthma and atopy in ongoing, molecular genetics studies.

Asthma↗

Genetic localization of interacting modifiers affecting severity in a murine model of polycystic kidney disease.

Genetic analysis of mouse disease models provides a means to investigate how modifying loci cause variation in phenotypic expression. We have shown that polycystic kidney disease (PKD) progression in the juvenile cystic kidney (jck) mutation can be influenced by an epistatic interaction between alleles of different strain backgrounds and we localized one of these loci to chromosome 1. Using a chromosome 1 congenic strain, we improved the genetic analysis and mapped the interacting locus to proximal chromosome 4, with a highly significant lod association of 5.5. Re-analysis of the original F(2) cross reveals that in this cohort, while the lod association of the chromosome 4 locus alone is not significant, its effect is apparent when analyzed in combination with the chromosome 1 locus. This result suggests that correlation of paired genotype data with phenotype data will be an effective means to detect epistatic interactions contributing to complex traits, and that these associations can be tested using appropriate congenic lines.

Alleles↗

Linkage disequilibrium mapping using single nucleotide polymorphisms--which population?

There is considerable interest in the potential of single nucleotide polymorphisms (SNPs) for mapping complex traits which are determined by genes of small individual effect (oligogenes). It is thought likely that many oligogenes are themselves common polymorphisms, perhaps biallelic, for which there is effectively neutral selection reflected in late age of onset. The extent of detectable linkage disequilibrium between SNP x SNP pairs and SNP x oligogene pairs is of considerable interest, particularly in the context of identifying 'favourable' populations. Unfortunately data are sparse and few populations have been extensively sampled. Polymorphisms with the appropriate characteristics that have been studied are blood groups in the Rhesus and MNS systems for which there are extensive data on four pairs of biallelics. These might be regarded as surrogates for SNP-SNP or SNP-oligogene pairs. By developing and applying an approach, previously used for major genes, to evaluate association (rho) in SNP haplotypes, it is evident that, with some exceptions, there is little difference between isolates and large populations. Furthermore it is apparent that there is useful linkage disequilibrium even for the MN-Ss locus pair (0.195 cM apart), in both large populations and isolates. This is somewhat more favourable to linkage disequilibrium mapping than a recent simulation suggests.

Alleles↗

The genetics of human epilepsies.

INTRODUCTION: Genetic causes contribute to many different forms of human epilepsies. Genetic analyses obviously represent a very powerful tool to study this highly heterogeneous pathology. The identification of the genes involved in various epileptic syndromes could prove useful in elucidating the basic mechanisms of epilepsies. This review summarise the recent progress that have been made in the localisation and/or identification of many epilepsy genes. METHODS: The MEDLINE database as well as different other scientific sources were screened. RESULTS: While the genes responsible for several progressive epilepsies have now been identified, it is unlikely that they play a role in the aetiology of true idiopathic epilepsies. Although the majority of idiopathic epilepsies are inherited as complex traits, most studies performed to date have led to the identification of several genetic loci underlying rare epileptic syndromes inherited in a Mendelian pattern. Four genes encoding neurotransmitter- or voltage-gated ion channel subunits have been identified in various idiopathic epilepsies. The epilepsies could thus be considered as one of many paroxysmal disorders that are due to mutations in ion channel genes. CONCLUSION: Effort is still needed to identify the genes responsible for the large variety of other epileptic disorders inherited as Mendelian traits and evaluate the role of these genes in the more common and polygenic forms. Defining the genetic bases of the latter will also require that exhaustive association and sib-pair studies to be performed. These studies may help understand the pathophysiology of human epilepsies, will lead to better genetic counselling in affected families, and represent the first step towards the discovery of new therapeutic targets and methods.

Animals↗

A genetic epidemiological study of hereditary prostate cancer (HPC) in Finland: frequent HPCX linkage in families with late-onset disease.

Several predisposition loci for hereditary prostate cancer (HPC) have been suggested, including HPC1 at 1q24-q25 (OMIM #601518) and HPCX at Xq27-q28 (OMIM #300147). Genetically homogeneous populations, such as that of Finland, and distinct subsets of families may help to minimize the genetic heterogeneity that complicates the genetic dissection of complex traits. Here, the role of the HPC1, and HPCX loci in a series of Finnish prostate cancer families was studied, especially in subgroups of families defined by age, number of affected cases, and the mode of disease transmission. DNA samples were collected from 57 Finnish HPC families with at least two living prostate cancer patients. Linkage analysis was carried out with 39 microsatellite markers for the HPC1 region and 22 markers for the HPCX region. The maximum two-point LOD score for the HPCX was 2.05 (marker DXS1205, at theta = 0.14), whereas HPC1 LOD scores were all negative. In HOMOG3R analyses, significant evidence of heterogeneity was observed. Subgroup analyses performed to explore the nature of this heterogeneity indicated that families with no male-to-male (NMM) transmission and a late age of diagnosis (>65 years) accounted for most of the HPCX-linked cases. The maximum HPCX LOD score in this subgroup was 3.12 (theta = 0.001). Nonparametric sibling pair analyses gave a peak LOD score of 3.04 (P < 0.000093) for the NMM transmission subgroup. No subgroup showed any positivity for HPC1. This study suggests that the HPCX-linked prostate cancer families represent a distinct subgroup characterized by NMM transmission of disease and late age of diagnosis.

Age of Onset↗

Building a multigenic model of breast cancer susceptibility: CYP17 and HSD17B1 are two important candidates.

We conducted a nested case-control study to evaluate whether polymorphisms in two genes involved in estrogen metabolism, CYP17 and HSD17B1, were useful in developing a breast cancer risk model that could help discriminate women who are at higher risk of breast cancer. If polymorphisms in these genes affect the level of circulating estrogens, they may directly influence breast cancer risk. The base population for this study is a multiethnic cohort study that includes African-American, Non-Latina White, Japanese, Latina, and Native Hawaiian women. For this analysis, 1508 randomly selected controls and 850 incident breast cancer cases of the first four ethnic groups who agreed to provide a blood specimen were included (76 and 80% response rates, respectively). The CYP17 A2 allele and the HSD17B1 A allele were considered "high-risk" alleles. Subjects were then classified according to number of high-risk alleles. After adjusting for age, weight, and ethnicity, we found that carrying one or more high-risk alleles increases the risk of advanced breast cancer in a dose-response fashion. The risk among women carrying four high-risk alleles was 2.21 [95% confidence interval (CI), 0.98-5.00; P for trend = 0.03] compared with those who carried none. This risk was largely limited to women who were not taking hormone replacement therapy (relative risk, 2.60; 95% CI, 0.95-7.14) and was most pronounced among those weighing 170 pounds or less (RR, 3.05; 95% CI, 1.29-7.25). These findings suggest that breast cancer risk has a strong genetic component and supports the theory that the underlying mechanism of "complex traits" can be understood using a multigenic model of candidate genes.

17-Hydroxysteroid Dehydrogenases↗

Genetic susceptibility in infectious diseases.

The outcome of infectious disease varies tremendously between individuals due to a number of factors and may therefore be viewed by the geneticist as complex traits. The identification of genes which influence disease outcome is, at present, a resource-intensive project and therefore should not be undertaken without clear evidence, preferably from twin studies, that the genetic contribution is significant. Although three principal techniques are available for the identification of disease susceptibility alleles, they are not applicable to all infectious diseases for logistical reasons. Whether a candidate polymorphic gene is identified through allele sharing studies, from interspecific crosses or taken from the currently available candidate list, the final evaluation will require carefully conducted disease association studies. As we move into the post genomic era, the identification of candidate polymorphisms and the characterization of their functional significance will rapidly increase, which will make the analysis of disease susceptibility in infectious diseases steadily more tractable.

Alleles↗

Genetic and nongenetic factors associated with variation of plasma levels of insulin-like growth factor-I and insulin-like growth factor-binding protein-3 in healthy premenopausal women.

Circulating levels of insulin-like growth factor-I (IGF-I) and insulin-like growth factor-binding protein 3 (IGFBP-3) vary considerably between normal individuals. Recent epidemiological studies have provided evidence that these levels are predictive of risk of several common cancers. To evaluate possible sources of variation of the levels of circulating IGF-I and IGFBP-3 in females, we studied specific candidate genetic and nongenetic factors in 311 nulliparous, premenopausal Caucasian women, 17-35 years of age. Women who used oral contraceptives (OC) had reduced levels of IGF-I (269 versus 301 ng/ml; P = 0.001 adjusted for age) and increased levels of IGFBP-3 (4213 versus 4009 ng/ml; P = 0.002, adjusted for age) compared with nonusers. The ratio of IGF-I:IGFBP-3 was associated with the dose of estrogen contained in the OC (P(trend) = 0.006, adjusted for age). We identified a novel single bp polymorphism in the promoter region of the gene encoding IGFBP-3. This polymorphism was related to the level of IGFBP-3 in the circulation. Mean IGFBP-3 levels were 4390, 4130, and 3840 ng/ml for the AA, AC, and CC genotypes, respectively (P(trend) = 0.006, adjusted for age and OC use). We observed no effect of a recently described polymorphism in the promoter region of the gene encoding IGF-I on the plasma IGF-I level, but there was evidence for a modifying effect of this locus on the influence of OC on the IGF-I level. Our results support the view that circulating IGF-I levels and IGFBP-3 levels are complex traits and are influenced by a number of interacting genetic and nongenetic factors.

Adolescent↗

Predictive genetic testing -- new possibilities in determination of risk of complex diseases.

Predictive genetic testing offers the possibility to statistically determine the risk of inheriting a complex phenotype by establishing an individual s genotype for metabolic polymorphisms. Here we discuss the conditions under which a predictive test may be offered to a patient and the problems connected with it. Examples of predictive genetic testing for multifactorial diseases and drug responses are given. We describe in detail the association of the C677T polymorphism of methylentetrahydrofolate reductase gene with hyperhomocystinemia and folate levels, as an independent risk factor for cardiovascular disease, and the association of a polymorphism of the promoter of the 5-lipoxygenase gene and the response to leukotriene inhibitors in asthma. Prospective development of genomic medicine and its use in the study of complex traits will hopefully bring significant benefit to the population and enhance the prevention and therapy of common diseases.

Cardiovascular Diseases↗

[Genes and kidney disease. Candidate genes].

Molecular biology techniques have provided important advances in the search for causal relationships in complex diseases supporting traditional epidemiologic studies. Genetic epidemiology allows us to detect genetic variants that could be related to the onset and progression of different diseases. In cardiovascular and renal diseases, this approach linking traditional risk factors to new described ones and those allelic variants, which contribute to the development of these manifestations permits a better understanding of individual disease susceptibility. This is usually afforded through case-control studies evaluating allelic variants of candidate genes previously associated with the disease. Even in this candidate gene search, association-based methods are more powerful than linkage studies in complex traits if we assume that some of the typed polymorphisms are causative although with subtle phenotypic effects. Some brief examples may illustrate the progress in the understanding of renal and cardiovascular diseases.

DNA↗

Global gene expression analysis of developing neocortex using SAGE.

The mammalian brain is estimated to contain about a hundred billion neurons, making it the most complex biological structure on earth. Trying to understand the assembly and function of this elaborate organ is a formidable task. Yet the information to build a brain is encoded by no more than a subset of the 80,000 genes present in the genome, a more manageable number. This review describes the use of SAGE technology (Serial Analysis of Gene Expression) to decode the genetic repertoire of genes that are differentially expressed in time and in space during development of the neocortex, the part of the mammalian brain responsible for complex traits. We demonstrate that SAGE is not only powerful for generating comprehensive molecular portraits from the developing cortex but can also assist in discovering new genes.

Animals↗

The application of molecular markers in the process of selection.

Molecular markers are modern diagnostic tools, which may help breeders to solve practical problems. They facilitate cultivar identification, the determination of genetic similarities among breeding stocks and enable the calculation of polymorphism level, heterozygosity or self-pollination rate. But the main expectation with respect to molecular markers is their potential use in marker-assisted selection (MAS). There are four major strategies of finding a molecular marker tightly linked to a target gene of agronomic importance. The first approach takes advantage of the nearly isogenic lines (NILs) which are differentiated only by the allelic sets in the gene of interest and in the adjacent chromosomal region. The second strategy involves bulked segregant analysis (BSA) for identification of markers linked to a single gene. The third involves the genetic dissection of more complex traits, which leads to the identification of quantitative trait loci (QTL) and their markers. The fourth strategy of marker identification includes computer databases (sequence and mapping data). The usefulness of these strategies is discussed in this paper. Some consequences of the application of BSA for gene tagging are described.

Alleles↗

Molecular pathogenesis of primary hyperparathyroidism.

This article will primarily focus on the molecular pathogenesis of common, sporadic (nonfamilial) parathyroid adenomas; two genes currently have established roles in the development of these tumors. The cyclin D1/PRAD1 gene was identified as a clonally activated oncogene in parathyroid adenomas and has subsequently been established as a major contributor to human neoplasia. Overexpression of cyclin D1, a key regulator of the cell cycle, has been implicated in the pathogenesis of 20-40% of sporadic parathyroid adenomas. That such cyclin D1 overexpression indeed constitutes a stimulus to excessive parathyroid cell proliferation has been confirmed experimentally by the development of a transgenic mouse model with parathyroid-targeted overexpression of cyclin D1. Parathyroid hormone (PTH)-cyclin D1 transgenic mice develop parathyroid hypercellularity, biochemical hyperparathyroidism, and a shifted in vivo parathyroid-calcium setpoint; these mice constitute an animal model of human hyperparathyroidism in which aspects of tumorigenesis, parathyroid secretory setpoint control, and the pathophysiology of the chronic hyperparathyroid state can be further investigated. The MEN1 tumor suppressor is the only other gene to date with an established role in the pathogenesis of sporadic parathyroid adenomatosis. Specific clonal alterations involving somatic mutation and/or deletion of both MEN1 alleles have been demonstrated in about 15-20% of sporadic parathyroid adenomas. Allelic losses on 11q occur in roughly twice this number of adenomas, raising the still-unresolved possibility that an additional tumor suppressor gene on 11q may be the functional target of many of these acquired deletions. A mouse model of MEN1 deficiency causes a phenotype that includes parathyroid hypercellularity albeit unaccompanied by biochemical hyperparathyroidism, and additional mouse models in which menin deficiency is targeted to the parathyroids will likely provide additional important insights. The MEN1 gene product menin may have a role in transcriptional regulation involving JunD; several other menin-interacting proteins have also been identified. The in vivo mechanism of menin's actions, with special attention to its role as a parathyroid oncosuppressor, will be important to establish, as will the potential interrelationships between these pathways and those involving cyclin D1. A number of genes, put forth as candidate tumor suppressors based on their genomic locations, roles in familial disease, and/or other relevant biological functions, have been examined for pathogenetic mutations in sporadic parathyroid tumors with negative results; these include the calcium-sensing receptor protein (CaR), vitamin-D receptor (VDR), and RET. However, the CaR, which when partially or markedly deficient because of germline mutation can cause familial hypocalciuric hypercalcemia or neonatal severe hyperparathyroidism, must still be considered as having a potentially important secondary role in the manifestations of sporadic parathyroid tumors. Future goals include identifying additional parathyroid oncogenes and tumor suppressor genes; exploiting tools of complex trait genetics to ascertain whether development of "sporadic" hyperparathyroidism might be influenced by predisposing polymorphic alleles in the population; obtaining molecular insights into the relationship between proliferative and hormone regulatory abnormalities of hyperparathyroidism; and obtaining molecular insights into the observed association of parathyroid neoplasia with exposure to ionizing irradiation and with the postmenopausal state.

Adenoma↗

Genome-wide linkage analysis of von Willebrand factor plasma levels: results from the GAIT project.

High plasma levels of von Willebrand factor (vWF) have been associated with the risk of thromboembolic disease. As a complex trait, this phenotype must be influenced by genetic and environmental factors. Among the genetic factors, only the ABO gene located on chromosome 9q34 has been clearly linked to the plasma levels of vWF. This locus explains about 30-40% of the genetic variability. Therefore, the source of the majority of the genetic component remains to be identified. To search for these unknown loci, we conducted a genomewide linkage screen for genes affecting normal variation in vWF levels in 21 Spanish families as part of the GAIT (Genetic Analysis of Idiopathic Thrombophilia) Project. The results showed that the strongest linkage signal (LOD =3.46, p = 0.00003) for vWF was found on chromosome 9q34 at the DNA marker D9S290, where the ABO gene is located. Additional suggestive linkage signals were found on chromosomes 2q23.2 (LOD = 1.65, p = 0.003) and 1p36.13 (LOD =1.32, p = 0.007). After refining the linkage analysis, conditional to the ABO genotype, three additional loci on chromosomes 5, 6 and 22 showed LOD scores higher than 1, suggesting the presence of other genes linked to vWF levels. Curiously, no linkage signals were detected in other chromosome regions previously associated with vWF levels (like the structural VWF gene on 12p13.2 or Lewis blood group gene on 19q13). These results indicate that these loci are not important genetic determinants of the normal variation of vWF levels. Our results indicate that the ABO locus is the major genetic determinant of the plasma levels of the vWF in Spanish population. It is possible that there are other potential regions on chromosomes 1, 2, 5, 6 and 22 that influence this thrombosis risk factor. However, the structural vWF gene itself has a very low influence (if any) on the plasma levels of vWF.

ABO Blood-Group System↗

Genetics of suicidal behavior: candidate association genetic approach.

Suicidal behavior runs in families and seemed to be genetically determined in part and independent of the presence of psychiatric disorders. This review presents the current knowledge of candidate gene association studies in the field of suicidology. Concordance for monozygotic twins is about 13% Vs. 0.7% in dizygotics. It seems that there is a relationship to intermediate phenotypes such as impulsivity and aggression. The problem of studying complex traits and of ethnic stratification in heterogeneous population are major concerns in studying genetics of suicide. Family-based methods is one of the strategies to overcome stratification. We found a possible association of tryptophane hydroxylase gene polymorphism with depression and serotonin transporter promoter gene to violence traits by family-based methods. Recent data from the study of COMT. MAO and serotonin receptors genes polymorphisms are controversial at this stage. Future directions for research includes alternative phenotypes, endo-phenotypes and genome scan.

Adolescent↗

[Genetic aspect of essential hypertension].

Essential hypertension affects up to 30% of the adult population; its pathogenesis involves interactions between genetic and environmental factors. Improved understanding of the molecular basis of essential hypertension may facilitate the development of new targeted forms of pharmacological therapy that can be tailored to the needs of individual patients and thereby minimize the risk of morbidity and mortality from cardiovascular diseases. The genetic analysis of complex traits and diseases such as blood pressure and hypertension is difficult because of their polygenic origin, genetic heterogeneity, variable penetrance, unknown modes of inheritance, and variable effects of environmental factors. Molecular variants of the angiotensinogen (AGT) gene, a key component of the renin-angiotensin system, are considered a genetic risk for primary hypertension. Some of the genotypes can be used to identify individual patients who would benefit from a specific anti-hypertensive treatment as well as from a specific life style modification.

Angiotensinogen↗

[Genetics and essential hypertension: candidate genes or screening of the whole genome?].

Essential hypertension is a major cardiovascular risk factor in the industrialised countries. Its hereditary nature has been well established in many familial studies: about 30% of blood pressure variance is thought to be genetically determined. However, the identification of the culprit genes has met with many difficulties: the multitude of genes, the effect of which is difficult to appreciate, the many possible genetic polymorphisms of each gene studied, the very important role of environmental factors (diet, physical activity, etc...) on the blood pressure itself or on the effect of the genes which control the blood pressure. With the exception of some rare caricatural forms of mendelian transmitted hypertension, the search for genes has focused on large case control studies and/or studies of siblings with hypertension. Two main approaches are used with these collections of subjects. The first consists of analysing so-called "candidate" genes which code for proteins whose function is known and which may influence the blood pressure. In the last ten years, many candidate genes have been assessed with often controversial results. The second approach is to carry out, with no a priori, a complete screen of the genome. These more recent studies have also provided contradictory results. To date, the results illustrate the difficulty of genetic analysis of a complex trait and the necessity of more integrated approaches: analysis of combination of polymorphisms, analysis of a phenotype under standardised environmental conditions, analysis of gene-environment interactions.

Case-Control Studies↗

[Twins in biomedical research and the creation of the "National Twin Registry"].

Twins are a valuable resource for the study of complex traits. The twin method is substantially based on the comparison between correlations and concordance in monozygotic (MZ) and dizygotic (DZ) twins and allows several applications in biomedical and molecular genetic research. It allows either the qualitative and quantitative evaluation of the influences that genetic and environmental factors exert on phenotypes or the estimation of trait variability. Moreover, classical genetic linkage analysis is more powerful if performed in DZ twins. However, the twin method has some pitfalls, such as the necessity that collected samples be representative of both twin and general population. For this reason, over the last few years, a number of Countries have established population-based twin registers, which guarantee the maximum level of representation and, consequently, are of extreme value for epidemiological studies. Italy is also implementing a national twin register. The following is the description of the procedure that led to the establishment of the Italian Twin Registry.

Databases, Factual↗