Use Of Intermediate Phenotypes Research Articles

Deconstructing ARDS Variability: Platelet Count, an ARDS Intermediate Phenotype and Novel Mediator of Genetic Effects in ARDS.

Genome-wide association studies (GWASs) in acute respiratory distress syndrome (ARDS) have been hampered by the heterogeneity of the clinical phenotypes and the large sample size requirement. As the limitations of these studies to uncover the complex genetic architecture of ARDS are evident, new approaches intended to reduce data complexity need to be applied. Intermediate phenotypes are mechanism-related manifestations of the disease, located closer to the genetic substrate than to disease phenotype, and therefore able to reflect more directly and more strongly the effect of causal genes. The dissection of complex phenotypes into less complex intermediate phenotypes is a valuable strategy to facilitate the discovery of those genetic variants whose effect is not strong enough to be detected as markers of disease in traditional GWASs. Genetic causal inference methodologies can be then applied to estimate the implication of the intermediate trait in the causal circuit between genes and disease. By following this strategy, platelet count, a relevant intermediate quantitative trait in ARDS, has been recently identified as a novel mediator in the genetic contribution to ARDS risk and mortality. The use of intermediate phenotypes and causal inference are emerging methodological and statistical strategies that can help to overcome the limitations of traditional GWASs in ARDS. Moreover, these approaches can provide evidence for the mechanisms linking genes to ARDS and help to prioritize therapeutic targets for the treatment of this devastating syndrome.

An initial investigation of associations between dopamine-linked genetic variation and smoking motives in African Americans

Nicotine dependence (ND) is a heterogeneous phenotype with complex genetic influences that may vary across ethnicities. The use of intermediate phenotypes may clarify genetic influences and reveal specific etiological pathways. Prior work in European Americans has found that the four Primary Dependence Motives (PDM) subscales (Automaticity, Craving, Loss of Control, and Tolerance) of the Wisconsin Inventory of Smoking Motives represent core features of nicotine dependence and are promising intermediate phenotypes for understanding genetic pathways to ND. However, no studies have examined PDM as an intermediate phenotype in African American smokers, an ethnic population that displays unique patterns of smoking and genetic variation. In the current study, 268 African American daily smokers completed a phenotypic assessment and provided a sample of DNA. Associations among haplotypes in the NCAM1-TTC12-ANKK1-DRD2 gene cluster, a dopamine-related gene region associated with ND, PDM intermediate phenotypes, and ND were examined. Dopamine-related genetic variation in the DBH and COMT genes was also considered on an exploratory basis. Mediational analysis was used to test the indirect pathway from genetic variation to smoking motives to nicotine dependence. NCAM1-TTC12-ANKK1-DRD2 region variation was significantly associated with the Automaticity subscale and, further, Automaticity significantly mediated associations among NCAM1-TTC12-ANKK1-DRD2 cluster variants and ND. DBH was also significantly associated with Automaticity, Craving, and Tolerance; Automaticity and Tolerance also served as mediators of the DBH–ND relationship. These results suggest that PDM, Automaticity in particular, may be a viable intermediate phenotype for understanding dopamine-related genetic influences on ND in African American smokers. Findings support a model in which putatively dopaminergic variants exert influence on ND through an effect on patterns of automatic routinized smoking.

Genetic Variants Associated With Development of TMD and Its Intermediate Phenotypes: The Genetic Architecture of TMD in the OPPERA Prospective Cohort Study

Genetic risk factors are believed to combine with environmental exposures and contribute to the risk of developing temporomandibular disorder (TMD). In this prospective cohort study, 2,737 people without TMD were assessed for common genetic variation in 358 genes known to contribute to nociceptive pathways, inflammation, and affective distress. During a median follow-up period of 2.8 years, 260 people developed first-onset TMD. Hazard ratios were computed as measures of association between 2,924 single-nucleotide polymorphisms and TMD incidence. After correction for multiple testing, no single single-nucleotide polymorphism was significantly associated with risk of onset TMD. However, several single-nucleotide polymorphisms exceeded Bonferroni correction for multiple comparison or false discovery rate thresholds (.05, .1, or .2) for association with intermediate phenotypes shown to be predictive of TMD onset. Nonspecific orofacial symptoms were associated with voltage-gated sodium channel, type I, alpha subunit (SCN1A, rs6432860, P = 2.77 × 10−5) and angiotensin I–converting enzyme 2 (ACE2, rs1514280, P = 4.86 × 10−5); global psychological symptoms with prostaglandin-endoperoxide synthase 1 (PTGS1, rs3842803, P = 2.79 × 10−6); stress and negative affectivity with amyloid-β (A4) precursor protein (APP, rs466448, P = 4.29 × 10−5); and heat pain temporal summation with multiple PDZ domain protein (MPDZ, rs10809907, P = 3.05 × 10−5). The use of intermediate phenotypes for complex pain diseases revealed new genetic pathways influencing risk of TMD. PerspectiveThis article reports the findings of a large candidate gene association study of first-onset TMD and related intermediate phenotypes in the OPPERA Study. Although no genetic markers predicted TMD onset, several genetic risk factors for clinical, psychological, and sensory phenotypes associated with TMD onset were observed.

Does COMT genotype influence the effects of d‐amphetamine on executive functioning?

In a widely cited study, Mattay et al. reported that amphetamine (0.25 mg/kg oral, or 17 mg for a 68 kg individual) impaired behavioral and brain indices of executive functioning, measured using the Wisconsin Card Sorting Task (WCST) and N-Back working memory task, in 6 individuals homozygous for the met allele of the val158met polymorphism in the catechol-O-methyltransferase (COMT) gene, whereas it improved executive functioning in 10 individuals homozygous for the more active val allele. We attempted to replicate their behavioral findings in a larger sample, using similar executive functioning tasks and a broader range of amphetamine doses. Over four sessions, n = 200 healthy normal adults received oral placebo, d-amphetamine 5, 10, and 20 mg (average of 0.07, 0.15 and 0.29 mg/kg), under counterbalanced double-blind conditions and completed WCST and N-back tests of executive functioning. Amphetamine had typical effects on blood pressure and processing speed but did not affect executive functioning. COMT genotype (val158met) was not related to executive functioning under placebo or amphetamine conditions, even when we compared only the homozygous val/val and met/met genotypes at the highest dose of amphetamine (20 mg). Thus, we were not able to replicate the behavioral interaction between COMT and amphetamine seen in Mattay et al. We discuss possible differences between the studies and the implications of our findings for the use of COMT genotyping to predict clinical responses to dopaminergic drugs, and the use of intermediate phenotypes in genetic research.

No effect of polymorphisms in the non-duplicated region of the CHRNA7 gene on sensory gating P50 ratios in patients with schizophrenia and bipolar disorder

Previous research has reported that bipolar disorder and schizophrenic patients evidence sensory gating deficits. The use of intermediate phenotypes may facilitate genetic studies. Four single nucleotide polymorphisms (SNPs) located on the non-duplicated region of the alpha-7 nicotinic receptor gene (CHRNA7) were genotyped in 95 healthy subjects, 127 bipolar disorder and 153 schizophrenic patients. We evaluated the association of these polymorphisms with P50 evoked potential measures. Our results do not support a role for the candidate gene in this neurophysiological disturbance.

Reduced Dopamine Receptor Sensitivity as an Intermediate Phenotype in Alcohol Dependence and the Role of the COMT Val158Met and DRD2 Taq1A Genotypes

Alcohol dependence is a common neuropsychiatric disorder with high heritability. However, genetic association studies on alcohol dependence are often troubled by nonreplication. The use of intermediate phenotypes may help make clear the mode of action of various candidate genes and improve the reproducibility of genetic association studies. To test central dopamine receptor sensitivity as an intermediate phenotype for alcohol dependence, specifically evaluating the hypothesis that the dopaminergic genes COMT Val158Met and DRD2 Taq1A affect dopamine receptor sensitivity. Case-control pharmacogenetic challenge study. Patients with alcohol dependence admitted for detoxification were compared with healthy control subjects matched for age and level of education. Patients (n = 110) were a consecutive sample, whereas controls (n = 99) were recruited through advertisements in regional newspapers. A dopamine challenge test was subcutaneously administered using the dopamine agonist apomorphine hydrochloride (0.005 mg/kg). Outcome measures were plasma growth hormone levels and results of a continuous performance task. Central dopamine receptor sensitivity is reduced in alcohol dependence, and this is modulated by dopaminergic genes. Specifically, DRD2 Taq1A genotype affected dopamine receptor sensitivity as measured by plasma growth hormone levels, and COMT Val158Met genotype affected dopamine receptor sensitivity as measured by performance on a continuous performance task. In a logistic regression analysis, reduced dopamine receptor sensitivity on both measures predicted alcohol dependence, without an additive effect of the COMT Val158Met and DRD2 Taq1A genotypes. COMT Val158Met and DRD2 Taq1A may affect the intermediate phenotype of central dopamine receptor sensitivity. COMT Val158Met and DRD2 Taq1A may confer their risk of alcohol dependence through reduced dopamine receptor sensitivity in the prefrontal cortex and hindbrain, respectively.

Inherited Risk Factors for Thrombotic Diseases in Children: The Genome-Wide Perspective

As a result of technological advances in the field of high-throughput genomics, there has been a remarkable transition in studying the nature of complex genetic disorders. The genetic analysis of prothrombotic risk factors has shifted from candidate gene to genome-wide association studies (GWAS) in adults. GWAS established a framework in which up to 90% of common genetic variation can be analyzed in a single experiment. Given the ubiquity of the GWAS approach in the adult population, it will become essential for clinicians and researchers in the field of pediatrics to interpret results derived from genetic high-throughput studies. Here, we review the current knowledge regarding genetic factors affecting prothrombotic risk in children and adults. Advantages and pitfalls of the GWAS approach are discussed, including the use of intermediate phenotypes, deep resequencing, and the differences between family-based and association studies. Intelligently designed and well-powered studies incorporating stringent phenotype assessment will contribute to decipher the genetic basis of stroke and venous thrombosis in children.

Genetics Studies in Ischaemic Stroke

Conventional risk factors such as high blood pressure account for a significant proportion of stroke risk, but much stroke risk remains unexplained. Epidemiological evidence suggests genetic predisposition accounts for some of this unexplained risk. Many candidate genes association studies have been performed but have lead to largely disappointing results. The genome-wide association study (GWAS) approach allows novel associations to be identified with as many as one million polymorphisms (genetic variants) across the genome. It has been successfully applied to other complex diseases, including other cardiovascular diseases, but stroke has lagged behind. A number of GWAS projects in stroke are now underway. Genetic variants originally identified using the GWAS approach in atrial fibrillation and coronary artery disease have been shown to also confer an increased risk of stroke. These associations have been with specific subtypes of stroke, emphasising the importance of accurate stroke subtyping. The use of intermediate phenotypes for stroke, such as white matter hyperintensities on MRI and carotid intima-media thickness, is also discussed.

Advances in Genomic Analysis of Stroke

As a result of technological advances, the genomic analysis of stroke has shifted from candidate gene association studies to genome-wide association studies (GWAS). Agnostic GWAS evaluate up to 90% of common genetic variation in a single experiment, creating an improved framework for identifying novel genetic leads for biochemical and cellular mechanisms underlying stroke. Given the ubiquity of the GWAS approach, it has become essential for stroke researchers and clinicians to be able to interpret GWAS results. Thus, we review the basic elements of design, methods, presentation, and interpretation of GWAS in the context of stroke research. In 8 recent stroke GWAS reports, no single locus has been identified in 2 GWAS at a genome-wide level of significance. Additionally, no significant association signal between stroke and a locus with previous evidence from candidate gene studies of stroke has been identified yet. Some caveats of the approach and future directions for stroke genomics are discussed, including the use of intermediate phenotypes, Mendelian randomization, phenomics, and deep resequencing. Intelligent, appropriately powered, multidisciplinary studies incorporating knowledge from clinical medicine, epidemiology, genetics, and molecular biology will be required to fully characterize the genomic contributors to stroke.

Pharmacogenetics in Psychiatry - A Useful Clinical Tool or Wishful Thinking for the Future?

More than fifty years of pharmacogenetic research have produced many examples of the impact of inherited variability in the response to psychotropic drugs. These successes, however, have as yet failed to translate into broadly applicable strategies for the improvement of individual drug treatment in psychiatry. One important argument against the widespread adoption of pharmacogenetics as a clinical tool is the lack of evidence showing its impact on medical decision making and on risk benefit ratio for the patients. The individual drug metabolizing capacity is assessed by genotyping drug metabolizing enzymes. The potential implications of information gained from genotyping are dose adjustments according to genotype. However, even when the consequences of genotype on pharmacokinetics are significant and well known, as in the case of many tricyclic antidepressants and several SSRIs, there is still considerable controversy on whether adjustment of dosage driven by genetic information may improve therapeutic efficacy, and/or adverse events is prevented, to an extent of any practical importance in clinical practice. Different types of pharmacogenetic studies may improve our understanding of the functional consequence of a genetic variant in the clinical setting. The use of intermediate phenotypes instead of broad outcome parameters such as drug response or remission might improve our knowledge on what exactly happens if an individual with a specific genotype takes a certain drug. Here, we review the potential impact of an integrated approach, including the assessment of intermediate phenotypes for the effect of genetic polymorphism, the monitoring of therapy progress, and response prediction in depression.

Neural substrates of pleiotropic action of genetic variation in COMT: a meta-analysis

Genetic variation in catechol-O-methyltransferase (COMT), encoding an enzyme critical for prefrontal dopamine flux, has been studied extensively using both behavioral and neuroimaging methods. In behavior, pleiotropic action of a functional Val(158)Met (rs4680) polymorphism on executive cognition and emotional stability has been described and proposed to be of evolutionary significance (the 'warrior/worrier' hypothesis). We conducted a meta-analysis of all available neuroimaging studies of rs4680 to investigate the evidence for a neural substrate of this behavioral pleiotropy. We show significant association between the COMT genotype and prefrontal activation, with large (d=0.73) effect size without evidence for publication bias. Strong and opposing effects were found for executive cognition paradigms (favoring Met allele carriers) and emotional paradigms (favoring Val), providing meta-analytical evidence for a neural substrate for the pleiotropic behavioral effects of COMT genetic variation and validating the use of intermediate phenotypes as a method to bridge between genes and behavior.

Personality endophenotypes for bipolar affective disorder: a family‐based genetic association analysis

Genetic analyses of complex conditions such as bipolar disorder (BD) may be facilitated by the use of intermediate phenotypes. Various personality traits are overrepresented in people with BD and their unaffected relatives, and may constitute genetically transmitted risk factors or endophenotypes of the illness. In this study, we administered a battery of seven different personality questionnaires comprising 19 subscales to 31 Caucasian BD families (n = 241). Ten of these personality traits showed significant evidence of heritability and were therefore selected as candidate endophenotypes. In addition, a principal components analysis produced two heritable components (negative affect and appetitive drive), which accounted for a considerable proportion of the variance (29% + 12%) and were also used in the analysis. A family-based quantitative association study was carried out using the orthogonal model from the quantitative transmission disequilibrium tests (QTDT) program. Monte Carlo permutations (M = 500), which allow for non-normal data and provide a global P value, corrected for multiple testing, were used to calculate empirical P values for the within-family component of association. The 3' untranslated region repeat polymorphism of the dopamine transporter gene (SLC6A3) was associated with self-directedness (P < 0.0001) and negative affect (P = 0.010). The short allele of the serotonin transporter gene (SLC6A4) promoter polymorphism showed a trend toward association with higher harm avoidance (P = 0.016) and negative affect (P = 0.028). The catechol-o-methyltransferase val158met polymorphism was weakly associated with the personality traits, 'Spirituality' (P = 0.040) and irritable temperament (P = 0.022). Furthermore, the met allele of the brain-derived neurotrophic factor val66met polymorphism was associated with higher hyperthymic temperament scores. We raise the possibility that the 10R allele of the SLC6A3 repeat polymorphism and the short allele of the SLC6A4 promoter variant constitute risk factors for irritable-aggressive and anxious-dysthymic subtypes of BD, respectively.

Pleiotropic effects of noveltrans-acting loci influencing human sympathochromaffin secretion

Family studies have suggested a genetic contribution to variation in blood pressure, but the genes responsible have thus far eluded identification. The use of intermediate phenotypes associated with hypertension, such as chromogranin plasma concentrations, may assist the discovery of hypertension-predisposing loci. We measured the concentrations of four chromogranin A (CHGA) and B (CHGB) peptides in 742 individuals from 235 nuclear families. The CHGA- and CHGB-derived peptides displayed significant heritability and revealed significant genetic correlations, most strikingly observed between CHGA(361-372) (catestatin) and CHGB(439-451). A 5-cM microsatellite genome scan revealed significant and suggestive evidence for linkage on several chromosomes for three of the peptides. Subsequent bivariate linkage analysis for peptides CHGA(361-372) and CHGB(439-451), which showed evidence for convergent linkage peaks on chromosomes 2, 7, and 13, resulted in increased evidence for linkage to these regions, suggesting pleiotropic effects of these three loci on multiple chromogranin traits. Because CHGA itself is on chromosome 14q32, and CHGB itself is on chromosome 20pter-p12, the pleiotropic regions on chromosomes 2, 7, and 13 must represent trans-acting quantitative trait loci coordinately affecting CHGA/CHGB biosynthesis and/or exocytotic secretion, likely by regulating efferent sympathetic outflow, a conclusion consistent with the in vitro studies presented here of the dual control of both exocytosis and transcription of these peptides by secretory stimuli in chromaffin cells. The results suggest a new approach to heritable autonomic control of circulation and the genetic basis of cardiovascular diseases such as systemic hypertension.

Candidate gene studies in the 21st century: meta‐analysis, mediation, moderation

The results of a large body of candidate gene studies of behavioural and psychiatric phenotypes have been largely inconclusive, with most findings failing to replicate reliably. A variety of approaches that augment the 'traditional' candidate gene approach are discussed, including the use of meta-analysis to combine findings from existing published reports, the investigation of mediating variables (including the use of intermediate phenotypes or endophenotypes) and the awareness of possible moderating influences (such as sex or ethnicity) and gene-environment interactions on genetic associations, possibly via epigenetic mechanisms. Advances in genotyping technology will also allow the routine use of haplotype analysis and linkage disequilibrium mapping. Examples of how these approaches may improve our understanding of how genetic associations with behavioural and psychiatric phenotypes obtain are given.

Dissecting Hypertension by Obesity Identifies a Locus at 1p36

The elevated arterial pressure that defines essential hypertension is regarded as the manifestation of a diverse array of interacting genetic and environmental causes. As such, hypertension is a heterogeneous disorder in which multiple contributing factors are responsible for the overarching phenotype of high blood pressure that is the primary clinical manifestation observed. Such heterogeneity has undoubtedly hampered efforts to elucidate the genetic basis of essential hypertension. Overweight and obesity are well known to increase the risk of essential hypertension. Yet, there are many hypertensive individuals whose weight is normal. So does obesity hypertension have a different underlying genetic cause than lean hypertension? In the current issue, Pausova et al report finding a locus with suggestive linkage to hypertension and then reanalyzed their data after dividing their families into lean and obese.1 Of considerable interest, the significance of the linkage peak increased for the obese families but disappeared in the case of the families with hypertension who were not obese. The striking contrast in results for each category of hypertension lends strong support to the idea that hypertension of obesity has a different genetic basis than other categories of hypertension. Not only is this finding important in discovery of the genetic basis of obesity hypertension, but it has obvious implications for approaches that might be used to identify the basis for other “intermediate phenotypes” of hypertension. The study by Pausova et al involved 55 extended families from the geographically remote French-Canadian Saguenay/Lac-St-Jean region of Quebec. This relatively small, isolated population has been spared the level of genetic “noise” present in populations elsewhere. As a result, the degree of genetic homogeneity should be elevated and likely contributed to the …

Genetic Association Studies in Stroke

A large number of candidate gene association studies have attempted to identify genes implicated in stroke, but there have been few replicable and robust associations reported. The skantness of replicable associations partly relates to poor study design. Important methodological considerations include adequate sample size, the selection of appropriate controls, careful clinical phenotyping using standardized classification systems, and determining associations with stroke subtypes as well as stroke as a whole. The use of intermediate phenotypes, particularly carotid intima-media thickness and MRI white matter hyperintensities, appears promising. It is essential that positive associations are replicated in independent populations, and appropriate methodology is used in such studies. To be of use for others, association studies should meet certain standards. In particular, genetic association studies should enable replication studies and meta-analyses. This article discusses key methodological aspects and suggests standard criteria for candidate gene studies in stroke.

An association study of angiotensinogen polymorphisms with serum level and hypertension in an African-American population.

To evaluate the association of angiotensinogen (AGT) gene with AGT level and hypertension based on the overall genetic variation of the AGT gene in among African-Americans. All non-rare single nucleotide polymorphisms (SNPs) in AGT were identified by resequencing 24 individuals. Five tagging SNPs were selected based on the pairwised linkage disequilibrium (LD) pattern and were genotyped in 284 individuals. Association studies of AGT level and hypertension were performed using these five tagging SNPs. No significant association with AGT level or hypertension was found in analyses of each of the five single SNPs. However, one of the haplotypes defined by these five SNPs was significantly associated with AGT level (P = 0.046), although this haplotype was not associated with hypertension. Identification of genetic polymorphisms associated with risk of hypertension has been frustratingly difficult. Two strategies adopted to improve precision are the use of intermediate phenotypes and summarization of genetic information using haplotypes. These strategies appeared to yield a modest increase in precision at the AGT locus with respect to the physiological intermediate, but did not lead to significant association of the molecular markers with hypertension. Additional research is required to increase confidence in haplotype mapping as an epidemiological analysis tool.

The genetics of alcoholism and alcohol abuse.

Twin studies have established that there are substantial genetic influences on alcoholism (0.5-0.6) in both men and women. Our knowledge of behaviors predisposing to alcoholism, including anxiety and impulsivity, is advancing rapidly through animal and human studies. Although alcoholism is often comorbid with other substance abuse and psychiatric disorders, recent studies have shown that, with the exception of nicotine, the heritability of alcoholism is largely substance-specific. Increasing understanding of the neurobiology of addiction has identified neural pathways in which genetic variation at candidate genes could influence vulnerability. Some functional variants of these genes have been identified. Recent linkage analyses in humans and rodents have pointed to genomic regions harboring genes that influence alcoholism. Refinement of clinical phenotypes and use of intermediate phenotypes will improve chances of gene identification. All these advances in the understanding of the genetics of alcoholism should facilitate the development of more accurately targeted therapies using molecular diagnostic approaches.