Commentary: grading the credibility of molecular evidence for complex diseases

Gene and schizophrenia in the pregenome and postgenome-wide association studies era: a bibliometric analysis and network visualization

This study aimed to perform a bibliometric analysis on genetic studies in schizophrenia in the pregenome-wide association studies (GWAS) and post-GWAS era. We searched the literature on genes and schizophrenia using the Scopus database. The documents increased with time, especially after the human genome project and International HapMap Project, with the highest citation in 2008. The top occurrence author keywords were discovered to be different in the pre-GWAS and post-GWAS eras, reflecting the progress of genetic studies connected to schizophrenia. Emerging keywords highlighted a trend towards an application of precision medicine, showing an interplay of environmental exposures as well as genetic factors in schizophrenia pathogenesis, progression, and response to therapy. In conclusion, the gene and schizophrenia literature has grown rapidly after the human genome project, and the temporal variation in the author keywords pattern reflects the trend of genetic studies related to schizophrenia in the pre-GWAS and post-GWAS era.

Associating complex traits with genetic variants: polygenic risk scores, pleiotropy and endophenotypes

Genotype-phenotype causal modeling has evolved significantly since Johannsen's and Wright's original designs were published. The development of genomewide assays to interrogate and detect possible causal variants associated with complex traits has expanded the scope of genotype-phenotype research considerably. Clusters of causal variants discovered by genomewide assays and associated with complex traits have been used to develop polygenic risk scores to predict clinical diagnoses of multidimensional human disorders. However, genomewide investigations have met with many challenges to their research designs and statistical complexities which have hindered the reliability and validity of their predictions. Findings linked to differences in heritability estimates between causal clusters and complex traits among unrelated individuals remain a research area of some controversy. Causal models developed from case-control studies as opposed to experiments, as well as other issues concerning the genotype-phenotype causal model and the extent to which various forms of pleiotropy and the concept of the endophenotype add to its complexity, will be reviewed.

Exposure-wide epidemiology: revisiting Bradford Hill

Fifty years after Bradford Hill published his extremely influential criteria to offer some guides for separating causation from association, we have accumulated millions of papers and extensive data on observational research that depends on epidemiologic methods and principles. This allows us to re-examine the accumulated empirical evidence for the nine criteria, and to re-approach epidemiology through the lens of exposure-wide approaches. The lecture discusses the evolution of these exposure-wide approaches and tries to use the evidence from meta-epidemiologic assessments to reassess each of the nine criteria and whether they work well as guides for causation. I argue that of the nine criteria, experiment remains important and consistency (replication) is also very essential. Temporality also makes sense, but it is often difficult to document. Of the other six criteria, strength mostly does not work and may even have to be inversed: small and even tiny effects are more plausible than large effects; when large effects are seen, they are mostly transient and almost always represent biases and errors. There is little evidence for specificity in causation in nature. Biological gradient is often unclear how it should it modeled and thus difficult to prove. Coherence remains usually unclear how to operationalize. Finally, plausibility as well as analogy do not work well in most fields of investigation, and their invocation has been mostly detrimental, although exceptions may exist.

C282Y and H63D Polymorphisms in Hemochromatosis Gene and Risk of Parkinson's Disease: A Meta-Analysis

OBJECTIVE

A meta-analysis was performed to better clarify the association between hemochromatosis (HFE) gene and the risk of Parkinson's disease (PD).

METHODS

Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated from fixed- and random-effect models. Heterogeneity among studies was evaluated using the I(2) and Q test. Egger's test was used to estimate the publication bias.

RESULTS

We identified 8 articles with 9 independent studies for this meta-analysis. The present meta-analysis showed no significant association of Y allele with the risk of PD in dominant (OR = 0.87, 95% CI = 0.70-1.09), recessive (OR = 1.58, 95% CI = 0.61-4.10), and codominant (OR = 0.88, 95% CI = 0.72-1.09) models for C282Y. There were also no significant associations of D allele with the risk of PD in dominant (OR = 1.04, 95% CI = 0.87-1.24), recessive (OR = 1.23, 95% CI = 0.70-2.18), and codominant (OR = 1.04, 95% CI = 0.89-1.22) genetic models for H63D. No publication bias was detected.

CONCLUSION

The meta-analysis indicated that C282Y and H63D polymorphisms in the HFE gene might not be associated with PD.

Individual Uncertainty and the Uncertainty of Science: The Impact of Perceived Conflict and General Self-Efficacy on the Perception of Tentativeness and Credibility of Scientific Information

We examined in two empirical studies how situational and personal aspects of uncertainty influence laypeople’s understanding of the uncertainty of scientific information, with focus on the detection of tentativeness and perception of scientific credibility. In the first study (N = 48), we investigated the impact of a perceived conflict due to contradicting information as a situational, text-inherent aspect of uncertainty. The aim of the second study (N = 61) was to explore the role of general self-efficacy as an intra-personal uncertainty factor. In Study 1, participants read one of two versions of an introductory text in a between-group design. This text provided them with an overview about the neurosurgical procedure of deep brain stimulation (DBS). The text expressed a positive attitude toward DBS in one experimental condition or focused on the negative aspects of this method in the other condition. Then participants in both conditions read the same text that dealt with a study about DBS as experimental treatment in a small sample of patients with major depression. Perceived conflict between the two texts was found to increase the perception of tentativeness and to decrease the perception of scientific credibility, implicating that text-inherent aspects have significant effects on critical appraisal. The results of Study 2 demonstrated that participants with higher general self-efficacy detected the tentativeness to a lesser degree and assumed a higher level of scientific credibility, indicating a more naïve understanding of scientific information. This appears to be contradictory to large parts of previous findings that showed positive effects of high self-efficacy on learning. Both studies showed that perceived tentativeness and perceived scientific credibility of medical information contradicted each other. We conclude that there is a need for supporting laypeople in understanding the uncertainty of scientific information and that scientific writers should consider how to present scientific results when compiling pertinent texts.

Evaluating historical candidate genes for schizophrenia

Prior to the genome-wide association era, candidate gene studies were a major approach in schizophrenia genetics. In this invited review, we consider the current status of 25 historical candidate genes for schizophrenia (for example, COMT, DISC1, DTNBP1 and NRG1). The initial study for 24 of these genes explicitly evaluated common variant hypotheses about schizophrenia. Our evaluation included a meta-analysis of the candidate gene literature, incorporation of the results of the largest genomic study yet published for schizophrenia, ratings from informed researchers who have published on these genes, and ratings from 24 schizophrenia geneticists. On the basis of current empirical evidence and mostly consensual assessments of informed opinion, it appears that the historical candidate gene literature did not yield clear insights into the genetic basis of schizophrenia. A likely reason why historical candidate gene studies did not achieve their primary aims is inadequate statistical power. However, the considerable efforts embodied in these early studies unquestionably set the stage for current successes in genomic approaches to schizophrenia.

Association of rs6265 and rs2030324 polymorphisms in brain-derived neurotrophic factor gene with Alzheimer's disease: a meta-analysis

Background

The association between polymorphisms rs6265 and rs2030324 in brain-derived neurotrophic factor (BDNF) and Alzheimer’s disease (AD) has been widely reported, but the results remain controversial.

Methods

A comprehensive search of Pubmed, Web of Science, China National Knowledge Infrastructure (CNKI), Wanfang Med Online and China Biology Medical literature database (CBM) was performed. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using fixed or random-effects models. We excluded the studies with OR>3.0 or OR<0.3 for sensitive analysis. Subgroup analysis by ethnicity, form of AD and gender was carried out. Meta-regression was conducted to explore the potential sources of between-study heterogeneity.

Results

29 articles with 7548 cases and 7334 controls concerning rs6265 and 22 articles with 5796 cases and 5706 controls concerning rs2030324 were included in this meta-analysis. The combined evidence suggested rs6265 contributing significantly to the increased risk of AD in females (codominant: fixed-effects model (FEM): OR = 1.13, 95% CI = 1.04–1.23; dominant: FEM: OR = 1.17, 95% CI = 1.05–1.31), especially for Caucasian females (codominant: FEM: OR = 1.18, 95% CI = 1.03–1.34; dominant: FEM: OR = 1.18, 95% CI = 1.01–1.37) and female late-onset Alzheimer’s disease (LOAD) patients (codominant: FEM: OR = 1.22, 95% CI = 1.05–1.41; dominant: FEM: OR = 1.23, 95% CI = 1.03–1.46). No evidence indicated an association between rs2030324 with AD in codominant (random-effects model (REM): OR = 1.06, 95% CI = 0.89–1.26) and dominant (REM: OR = 1.05, 95% CI = 0.86–1.27) models.

Conclusion

This meta-analysis suggested A allele of rs6265 might increase the risk of AD in Caucasian females and female LOAD patients. In addition, no evidence indicated an association between rs2030324 with AD. Further studies are needed to confirm these results.

Association of A561C and G98T polymorphisms in E-selectin gene with coronary artery disease: a meta-analysis

Objective

E-selectin (SELE) mediates the rolling and adhesion of leukocytes on activated endothelial cells and plays a critial role in the pathogenesis of coronary artery disease (CAD). Associatons between the A561C and G98T polymorphisms of the SELE gene and CAD risk were investigated broadly, but the results were inconsistent. In the present study, we performed a meta-analysis to systematically evaluate the associations between the two polymorphisms and the risk of CAD.

Methods

Comprehensive research was conducted to identify relevant studies. The fixed or random effect model was selected based on the heterogeneity among studies, which was evaluated with Q-test and Ι². Meta-regression was used to explore the potential sources of between-study heterogeneity. Peters's linear regression test was used to estimate the publication bias.

Results

Overall, 24 articles involving 3694 cases and 3469 controls were included. After excluding articles deviating from Hardy–Weinberg equilibrium in controls and sensitive analysis, our meta-analysis showed a significant association between the A561C ploymprphism and CAD in dominant (OR  = 1.84, 95% CI  = 1.56–2.16) and codominant (OR  = 1.74, 95% CI  = 1.49–2.03) models. As for the G98T polymorphism, significantly increased CAD risk was observed in dominant (OR  = 1.47, 95% CI  = 1.16–1.87) and codominant (OR  = 1.48, 95% CI  = 1.18–1.86) models, but after subgroup analysis, the association was not significant among Caucasians in dominant (OR  = 1.58, 95% CI  = 0.73–3.41) and codominant (OR  = 1.58, 95% CI  = 0.79–3.20) models.

Conclusions

Despite some limitations, our meta-analysis suggested that the SELE gene polymorphisms (A561C, G98T) were significantly associated with increased risk of CAD. However, after subgroup analysis no significant association was found among Caucasians for the G98T polymorphism, which may be due to the small sample size and other confounding factors. Future investigations with multicenter, large-scale, and multi-ethnic groups are needed.

Endothelial NO synthase gene polymorphisms and risk of ischemic stroke in Asian population: a meta-analysis

Background

The association between polymorphism 4b/a, T-786C and G894T in endothelial NO synthase gene (eNOS) and ischemic stroke (IS) remains controversial in Asian. A meta-analysis was performed to better clarify the association between eNOS gene and IS risk.

Methods

Based on the search of PubMed, Web of Science (ISI), CNKI (National Knowledge Infrastructure), Wan Fang Med Online and CBM (Chinese Biology Medical Literature Database) databases, all eligible case-control or cohort studies were identified. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) from fixed and random effect models were calculated. Heterogeneity among studies was evaluated using the I². Meta-regression was used to explore the potential sources of between-study heterogeneity. Begg's test was used to estimate publication bias.

Results

Our study included 27 articles, contained 28 independent case–control studies, involved a total of 3,742 cases and 3,691 controls about 4b/a, 1,800 cases and 1,751 controls about T-786C and 2,747 cases and 2,872 controls about G894T. A significant association of 4a allele with increased risk of IS was found in dominant (FEM: OR = 1.498, 95% CI = 1.329–1.689), recessive (FEM: OR = 2.132, 95% CI = 1.383–3.286) and codominant (REM: OR = 1.456, 95% CI = 1.235–1.716) models. For T-786C and G894T, there were significant associations with dominant and codominant genetic models, but not with recessive genetic model.

Conclusions

The meta-analysis indicated that eNOS gene 4b/a, T-786C, G894T polymorphism might be associated with IS.

GPX1 gene Pro200Leu polymorphism, erythrocyte GPX activity, and cancer risk

A meta-analysis was conducted to assess the effect of glutathione peroxidase1 (GPX1) gene Pro200Leu (rs1050450) polymorphism on cancer risk. A comprehensive search was performed to identify all studies on the association of GPX1 gene Pro200Leu polymorphism with cancer risk. The fixed or random effect pooled measure was selected based on homogeneity test among studies. Heterogeneity among studies was evaluated using the I (2). Potential sources of between-study heterogeneity were explored by meta-regression and the sensitivity analysis. Publication bias was estimated using Egger's linear regression test. 35 published articles with 36 results were identified involving 16,920 cases and 19,946 controls. Results from the articles that both obeyed Hardy-Weinberg equilibrium in controls and met high quality design, showed no significant association of GPX1 gene Pro200Leu polymorphism with cancer risk in any of dominant (OR = 1.05, 95 %CI = 0.98-1.12), recessive (OR = 1.04 (0.95-1.13), and TT versus CC (OR = 1.05, 95 %CI = 0.97-1.15) models, and the findings were consistent considering the stratified analysis by cancer type. However, multivariate-adjusted ORs from articles that both obeyed Hardy-Weinberg equilibrium in controls and met high quality design, showed a significant association considering dominant (OR = 1.22, 95 %CI = 1.06-1.41), TT versus CC (OR = 1.16, 95 %CI = 1.02-1.32) models, and a marginally significant association was found considering TC versus CC (OR = 1.11, 95 %CI = 0.99-1.25) model. And compared with the CC genotype, the erythrocyte GPX activity was significantly lower for TT genotype: the standardized mean difference (SMD) = -0.37, 95 %CI = (-0.624, -0.118), and CT genotype: SMD = -0.19, 95 %CI = (-0.37, -0.002). The association of GPX1 gene Pro200Leu polymorphism with cancer risk might be influenced by confounders.

Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus

Diseases such as type 2 diabetes (T2D) result from environmental and genetic factors, and risk varies considerably in the population. T2D-related genetic loci discovered to date explain only a small portion of the T2D heritability. Some heritability may be due to gene–environment interactions. However, documenting these interactions has been difficult due to low availability of concurrent genetic and environmental measures, selection bias, and challenges in controlling for multiple hypothesis testing. Through genome-wide association studies (GWAS), investigators have identified over 90 single nucleotide polymorphisms (SNPs) associated to T2D. Using a method analogous to GWAS [environment-wide association study (EWAS)], we found five environmental factors associated with the disease. By focusing on risk factors that emerge from GWAS and EWAS, it is possible to overcome difficulties in uncovering gene–environment interactions. Using data from the National Health and Nutrition Examination Survey (NHANES), we screened 18 SNPs and 5 serum-based environmental factors for interaction in association to T2D. We controlled for multiple hypotheses using false discovery rate (FDR) and Bonferroni correction and found four interactions with FDR <20 %. The interaction between rs13266634 (SLC30A8) and trans-β-carotene withstood Bonferroni correction (corrected p = 0.006, FDR <1.5 %). The per-risk-allele effect sizes in subjects with low levels of trans-β-carotene were 40 % greater than the marginal effect size [odds ratio (OR) 1.8, 95 % CI 1.3–2.6]. We hypothesize that impaired function driven by rs13266634 increases T2D risk when combined with serum levels of nutrients. Unbiased consideration of environmental and genetic factors may help identify larger and more relevant effect sizes for disease associations.

Correlation of Asp299Gly and Thr399Ile polymorphisms in toll-like receptor 4 gene with digestive cancer risk: A meta-analysis

The aim of this meta-analysis was to evaluate the correlation between the Asp299Gly and Thr399Ile polymorphisms in the toll-like receptor 4 (TLR4) gene and the risk of digestive cancer. A comprehensive search in PubMed, Web of Science (ISI), the China National Knowledge Infrastructure (CNKI), the Database of Chinese Scientific and Technical Periodicals (VIP) and the China Biology Medical (CBM) literature databases, including all the studies until May 25 2012, was conducted in order to investigate the abovementioned correlation. Statistical analysis was performed using STATA version 10.1. A total of 12 case-control studies were identified comprising 1,877 cancer patients and 3,181 controls for Asp299Gly polymorphism, and 8 case-control studies with 1,062 cancer patients and 1,867 controls for Thr399Ile polymorphism. Following sensitivity analysis and excluding studies that deviated from the Hardy-Weinberg equilibrium (HWE) in the controls, this meta-analysis demonstrated a significant correlation between the G allele of the Asp299Gly polymorphism and increased risk of gastric cancer in dominant [fixed-effect model (FEM): odds ratio (OR), 1.772; 95% confidence interval (CI), 1.340-2.343] and codominant (FEM: OR, 1.761, CI, 1.347-2.301) models. However, no significant correlation was detected for overall digestive and colorectal cancer. Furthermore, following the sensitivity analysis and exclusion of studies deviating from HWE in controls, no significant effect of the T allele of Thr399Ile polymorphism on overall digestive, gastric and colorectal cancer risk was demonstrated. This study suggests that the G allele of the TLR4 Asp299Gly polymorphism might be correlated with an increased risk of gastric cancer. However, this result needs to be further investigated by future studies.

Child μ-opioid receptor gene variant influences parent-child relations

Variation in the μ-opioid receptor gene has been associated with early social behavior in mice and rhesus macaques. The current study tested whether the functional OPRM1 A118G predicted various indices of social relations in children. The sample included 226 subjects of self-reported European ancestry (44% female; mean age 13.6, SD=2.2) who were part of a larger representative study of children aged 9-17 years in rural North Carolina. Multiple aspects of recent (past 3 months) parent-child relationship were assessed using the Child and Adolescent Psychiatric Assessment. Parent problems were coded based upon a lifetime history of mental health problems, substance abuse, or criminality. Child genotype interacted with parent behavior such that there were no genotype differences for those with low levels of parent problems; however, when a history of parent problems was reported, the G allele carriers had more enjoyment of parent-child interactions (mean ratio (MR)=3.5, 95% CI=1.6, 8.0) and fewer arguments (MR=3.1, 95% CI=1.1, 8.9). These findings suggest a role for the OPRM1 gene in the genetic architecture of social relations in humans. In summary, a variant in the μ-opioid receptor gene (118G) was associated with improved parent-child relations, but only in the context of a significant disruption in parental functioning.

Lower prevalence of common filaggrin mutations in a community sample of atopic eczema: is disease severity important?

BACKGROUND

Recent studies have shown an association of loss-of-function mutations in the filaggrin gene (FLG) with ichthyosis vulgaris and atopic eczema (AE). Case selection may have distorted the hitherto reported prevalence of FLG mutations and their relation to atopic disease. The aim of the study was to determine the true population prevalence of FLG mutations in unselected children with and without reported physician diagnoses of asthma, allergic rhinitis and AE and their relationship with family history of atopic disease.

METHODS

We used a nested case-control design by sampling children with reported doctor's diagnoses of AE, asthma and allergic rhinitis and randomly selected controls from a larger cross-sectional study (n = 1263). Most common FLG mutations R501X, 2282del4, and R2447X were screened in DNA extracted from defrosted urine samples. The relationship of the combined FLG variants with atopic diseases and with reported family history of AE, asthma, and rhinitis was assessed.

RESULTS

In the patient group one homozygote (R501X/R501X), 4 compound heterozygotes (3 R501X/2282del4, one 2282del4/R2447X), and 17 heterozygotes (10 R501X/wt, 5 2282del4/wt, and 2 R2447X/wt), in the control group 9 heterozygotes (5 R501X/wt, 4 2282del4/wt) were detected. The combined prevalence of FLG loss-of-function alleles was 5% in the control group and 9% in the atopic sample. In a subgroup analysis, the combination of allergic rhinitis and AE showed a significant relationship with FLG mutations, OR = 3.7 (1.01-12.67, p = 0.024). Likewise, significant relations with reported family history of asthma, OR = 4.35 (1.78-10.62, p = 0.0012), allergic rhinitis, OR = 2.33 (1.49-3.63, p = 0.0002), and AE, OR = 5.08 (2.78-9.30, p ≤ 0.0001) were observed. In contrast to clinical studies with higher percentages of severely affected persons, FLG mutations here showed a moderate association with atopic disease.

CONCLUSIONS

Case selection may be responsible for overestimating the prevalence of FLG mutations in atopic disease.

Effectiveness of strategies to increase the validity of findings from association studies: size vs. replication

Background

The capacity of multiple comparisons to produce false positive findings in genetic association studies is abundantly clear. To address this issue, the concept of false positive report probability (FPRP) measures "the probability of no true association between a genetic variant and disease given a statistically significant finding". This concept involves the notion of prior probability of an association between a genetic variant and a disease, making it difficult to achieve acceptable levels for the FPRP when the prior probability is low. Increasing the sample size is of limited efficiency to improve the situation.

Methods

To further clarify this problem, the concept of true report probability (TRP) is introduced by analogy to the positive predictive value (PPV) of diagnostic testing. The approach is extended to consider the effects of replication studies. The formula for the TRP after k replication studies is mathematically derived and shown to be only dependent on prior probability, alpha, power, and number of replication studies.

Results

Case-control association studies are used to illustrate the TRP concept for replication strategies. Based on power considerations, a relationship is derived between TRP after k replication studies and sample size of each individual study. That relationship enables study designers optimization of study plans. Further, it is demonstrated that replication is efficient in increasing the TRP even in the case of low prior probability of an association and without requiring very large sample sizes for each individual study.

Conclusions

True report probability is a comprehensive and straightforward concept for assessing the validity of positive statistical testing results in association studies. By its extension to replication strategies it can be demonstrated in a transparent manner that replication is highly effective in distinguishing spurious from true associations. Based on the generalized TRP method for replication designs, optimal research strategy and sample size planning become possible.

Beyond genome-wide association studies: genetic heterogeneity and individual predisposition to cancer

Genome-wide association studies (GWAS) using population-based designs have identified many genetic loci associated with risk of a range of complex diseases including cancer; however, each locus exerts a very small effect and most heritability remains unexplained. Family-based pedigree studies have also suggested tentative loci linked to increased cancer risk, often characterized by pedigree-specificity. However, comparison between the results of population- and family-based studies shows little concordance. Explanations for this unidentified genetic 'dark matter' of cancer include phenotype ascertainment issues, limited power, gene-gene and gene-environment interactions, population heterogeneity, parent-of-origin-specific effects, and rare and unexplored variants. Many of these reasons converge towards the concept of genetic heterogeneity that might implicate hundreds of genetic variants in regulating cancer risk. Dissecting the dark matter is a challenging task. Further insights can be gained from both population association and pedigree studies.

Genome-wide association study in discordant sibships identifies multiple inherited susceptibility alleles linked to lung cancer

We analyzed a series of young (median age = 52 years) non-smoker lung cancer patients and their unaffected siblings as controls, using a genome-wide 620 901 single-nucleotide polymorphism (SNP) array analysis and a case-control DNA pooling approach. We identified 82 putatively associated SNPs that were retested by individual genotyping followed by use of the sib transmission disequilibrium test, pointing to 36 SNPs associated with lung cancer risk in the discordant sibs series. Analysis of these 36 SNPs in a polygenic model characterized by additive and interchangeable effects of rare alleles revealed a highly statistically significant dosage-dependent association between risk allele carrier status and proportion of cancer cases. Replication of the same 36 SNPs in a population-based series confirmed the association with lung cancer for three SNPs, suggesting that phenocopies and genetic heterogeneity can play a major role in the complex genetics of lung cancer risk in the general population.

Identifying rarer genetic variants for common complex diseases: diseased versus neutral discovery panels

The power of genetic association studies to identify disease susceptibility alleles fundamentally relies on the variants studied. The standard approach is to determine a set of tagging-SNPs (tSNPs) that capture the majority of genomic variation in regions of interest by exploiting local correlation structures. Typically, tSNPs are selected from neutral discovery panels - collections of individuals comprehensively genotyped across a region. We investigated the implications of discovery panel design on tSNP performance in association studies using realistically-simulated sequence data. We found that discovery panels of 24 sequenced 'neutral' individuals (similar to NIEHS or HapMap ENCODE data) were sufficient to select well-powered tSNPs to identify common susceptibility alleles. For less common alleles (0.01-0.05 frequency) we found neutral panels of this size inadequate, particularly if low-frequency variants were removed prior to tSNP selection; superior tSNPs were found using panels of diseased individuals. Only large neutral panels (200 individuals) matched diseased panel performance in selecting well-powered tSNPs to detect both common and rarer alleles. The 1000 Genomes Project initiative may provide larger neutral panels necessary to identify rarer susceptibility alleles in association studies. In the interim, our results suggest investigators can boost power to detect such alleles by sequencing diseased individuals for tSNP selection.

A searchable database of genetic evidence for psychiatric disorders

This paper describes a new bioinformatic tool for use in psychiatric research, "SLEP" (Sullivan Lab Evidence Project). SLEP is a searchable archive of findings from psychiatric genetics that is freely available on the web for non-commercial use (http://slep.unc.edu). Via a simple interface, users can retrieve findings from genome-wide linkage, genome-wide association, and microarray studies for ADHD, autism, bipolar disorder, eating disorders, major depression, nicotine dependence, and schizophrenia. Findings can be save to disk or viewed via a genome browser.

Schizophrenia genetics: the search for a hard lead

PURPOSE OF REVIEW

To describe the rationale for searching for genes for schizophrenia, prior efforts via candidate gene association and genomewide linkage studies, and to set the stage for the numerous genomewide association studies that will emerge by the end of 2008.

RECENT FINDINGS

Genomewide association studies have identified dozens of new and previously unsuspected candidate genes for many biomedical disorders. At least seven new studies of approximately 20,000 cases plus controls are expected to be completed by the end of 2008.

SUMMARY

Current results have few implications for clinical practice or research, and it is possible that this recommendation could be dramatically different in a year.

Examining the co-occurrence of bladder and prostate cancer: a worthwhile investigation?

We investigate the possible reasons for the co-occurrence of bladder and prostate cancer and discuss its clinical relevance. The co-occurrence of bladder and prostate cancer can (partly) be explained by a survival effect and diagnostic bias. Radiotherapy for prostate cancer might be responsible for a significant increase in secondary bladder cancers, with an absolute effect that is small. Existing international consortia should expand to include secondary primary cancers as well as the index tumor. This will facilitate the investigation of common etiology and will help to identify subgroups that are susceptible to treatment-induced carcinogenesis. The prognosis after a diagnosis of both bladder and prostate cancer seems to depend mainly on the prognosis of the bladder tumor.

Ethnic stratification of the association of RGS4 variants with antipsychotic treatment response in schizophrenia

BACKGROUND

Genetic association studies, including a large meta-analysis, report association of regulator of G protein signaling 4 (RGS4) with schizophrenia in the context of heterogeneity. The central role of RGS4 in regulating signaling via Gi/o coupled neurotransmitter receptors led us to hypothesize that there may be RGS4 genotypes predictive of specific disease phenotypes and antipsychotic treatment responses.

METHODS

Subjects were 678 individuals with schizophrenia who participated in the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE). Among the 678 subjects, the inferred ancestries were 198 (29%) "Africa only," 397 (59%) "Europe only," and 83 (12%) "Other." Eight single nucleotide polymorphisms (SNPs) spanning RGS4 were genotyped. Multiple linear regression was used to analyze association of RGS4 markers with Positive and Negative Symptoms Scale (PANSS) scores at baseline and throughout antipsychotic treatment.

RESULTS

Two consecutive markers within RGS4, rs2661319 and rs2842030, were associated with more severe baseline PANSS total score. Treatment with perphenazine was more effective than treatment with quetiapine (p = .010) or ziprasidone (p = .002) in individuals of inferred African ancestry and homozygous for the rs951439 C allele.

CONCLUSIONS

RGS4 genotypes predicted both the severity of baseline symptoms and relative responsiveness to antipsychotic treatment. Although these analyses are exploratory and replication is required, these data provide support for RGS4 in schizophrenia pathogenesis and suggest a functional role for RGS4 in differential antipsychotic treatment efficacy of schizophrenia.

Methods for meta-analysis in genetic association studies: a review of their potential and pitfalls

Meta-analysis offers the opportunity to combine evidence from retrospectively accumulated or prospectively generated data. Meta-analyses may provide summary estimates and can help in detecting and addressing potential inconsistency between the combined datasets. Application of meta-analysis in genetic associations presents considerable potential and several pitfalls. In this review, we present basic principles of meta-analytic methods, adapted for human genome epidemiology. We describe issues that arise in the retrospective or the prospective collection of relevant data through various sources, common traps to consider in the appraisal of evidence and potential biases that may interfere. We describe the relative merits and caveats for common methods used to trace inconsistency across studies along with possible reasons for non-replication of proposed associations. Different statistical models may be employed to combine data and some common misconceptions may arise in the process. Several meta-analysis diagnostics are often applied or misapplied in the literature, and we comment on their use and limitations. An alternative to overcome limitations arising from retrospective combination of data from published studies is to create networks of research teams working in the same field and perform collaborative meta-analyses of individual participant data, ideally on a prospective basis. We discuss the advantages and the challenges inherent in such collaborative approaches. Meta-analysis can be a useful tool in dissecting the genetics of complex diseases and traits, provided its methods are properly applied and interpreted.

DBH -1021C-->T does not modify risk or age at onset in Parkinson's disease

DBH is a candidate gene in Parkinson's disease (PD) and contains a putative functional polymorphism (-1021C-->T) that has been reported to modify PD susceptibility. We examined -1021C-->T in a sample of 1,244 PD patients and 1,186 unrelated control subjects. There was no significant difference in allele (p = 0.14) or genotype (p = 0.26) frequencies between the two groups. A similar result was obtained after pooling our data with those previously published. Furthermore, we found no evidence for an effect of genotype on age at onset among patients. Our findings argue against DBH -1021C-->T as a risk factor or age at onset modifier in PD.

Assessment of cumulative evidence on genetic associations: interim guidelines

Established guidelines for causal inference in epidemiological studies may be inappropriate for genetic associations. A consensus process was used to develop guidance criteria for assessing cumulative epidemiologic evidence in genetic associations. A proposed semi-quantitative index assigns three levels for the amount of evidence, extent of replication, and protection from bias, and also generates a composite assessment of 'strong', 'moderate' or 'weak' epidemiological credibility. In addition, we discuss how additional input and guidance can be derived from biological data. Future empirical research and consensus development are needed to develop an integrated model for combining epidemiological and biological evidence in the rapidly evolving field of investigation of genetic factors.

Spurious genetic associations

BACKGROUND

Genetic association studies are widely used in biomedical research and yet only a minority of positive findings stand the test of replication. I explored the capacity of association studies to produce false positive findings and the impact of various definitions of replication.

METHODS

Genetically realistic simulation data of a typical genotyping/analytic approach for 10 single nucleotide polymorphisms (SNPs) in COMT, a commonly studied candidate gene.

RESULTS

Candidate gene studies like those simulated here are highly likely to produce one or more false positive findings at alpha < or = .05, the pattern of findings can often be "compelling" or "intriguing," and false positive findings propagate and confuse the literature unless the definition of replication is precise.

CONCLUSIONS

Findings from single association studies constitute "tentative knowledge" and must be interpreted with exceptional caution. For the association method to function as intended, every statistical comparison must be tracked and reported, and integrated replication is essential. Precise replication (the same SNPs, phenotype, and direction of association) is required in the interpretation of multiple association studies.

Molecular evidence-based medicine: evolution and integration of information in the genomic era

Evidence-based medicine and molecular medicine have both been influential in biomedical research in the last 15 years. Despite following largely parallel routes to date, the goals and principles of evidence-based and molecular medicine are complementary and they should be converging. I define molecular evidence-based medicine as the study of medical information that makes sense of the advances of molecular biological disciplines and where errors and biases are properly appreciated and placed in context. Biomedical measurement capacity improves very rapidly. The exponentially growing mass of hypotheses being tested requires a new approach to both statistical and biological inference. Multidimensional biology requires careful exact replication of research findings, but indirect corroboration is often all that is achieved at best. Besides random error, bias remains a major threat. It is often difficult to separate bias from the spirit of scientific inquiry to force data into coherent and 'significant' biological stories. Transparency and public availability of protocols, data, analyses and results may be crucial to make sense of the complex biology of human disease and avoid being flooded by spurious research findings. Research efforts should be integrated across teams in an open, sharing environment. Most research in the future may be designed, performed, and integrated in the public cyberspace.

The GNB3 C825T polymorphism and essential hypertension: a meta-analysis of 34 studies including 14,094 cases and 17,760 controls

OBJECTIVES

The C825T single nucleotide polymorphism of the G-protein beta3 (GNB3) has been implicated in susceptibility to essential hypertension, through the expression of an alternatively spliced truncated variant. In an effort to clarify earlier inconclusive results, we performed a meta-analysis of population-based case-control genetic association studies.

METHODS

Random-effects methods were applied on summary data in order to combine the results of the individual studies.

RESULTS

We identified in total 34 studies, including 14,094 hypertensive cases and 17,760 controls. The TT versus CC + CT contrast yielded an overall odds ratio (OR) of 1.08 [95% confidence interval (CI): 1.01, 1.15], the contrast of TT + CT versus CC, an OR of 1.17 (95% CI: 1.06, 1.29), whereas that of the T allele versus C allele yielded a non-significant OR of 1.05 (95% CI: 0.98, 1.13). There was moderate evidence for a publication bias in the latter two contrasts, which was eliminated after excluding studies not in Hardy-Weinberg equilibrium and those performed on non-normal populations (those with a diagnosis of diabetes, obesity and myocardial infarction). Subgroup analyses revealed that non-significant estimates arose from studies on Asian populations, as opposed to the Caucasian ones. Furthermore, the frequency of the T allele was lower in Caucasians and these populations were found to inhabit higher latitudes.

CONCLUSIONS

The findings are in agreement with a recently proposed causal model for systolic blood pressure, which correlates it with the T allele and the absolute latitude. Further studies are needed in order to fully address questions about the aetiological mechanism of the particular association, as well as to study the effect in populations of African descent.

Genomics meets HIV-1

Genomics is now a core element in the effort to develop a vaccine against HIV-1. Thanks to unprecedented progress in high-throughput genotyping and sequencing, in knowledge about genetic variation in humans, and in evolutionary genomics, it is finally possible to systematically search the genome for common genetic variants that influence the human response to HIV-1. The identification of such variants would help to determine which aspects of the response to the virus are the most promising targets for intervention. However, a key obstacle to progress remains the scarcity of appropriate human cohorts available for genomic research.