Single Genetic Effect Research Articles

Spit for Science and the Limits of Applied Psychiatric Genetics

The research program Spit For Science was launched at Virginia Commonwealth University (VCU) in 2011. Since then, more than 10,000 freshmen have been enrolled in the program, filling out extensive questionnaires about their drinking, general substance use, and related behaviors, and also contributing saliva for genotyping. The goals of the program, as initially stated by the investigators, were to find the genes underlying the heritability of alcohol use and related behaviors, and in addition to put genetic knowledge to work in ways that might aid university administrators and mental health professionals in the prevention and treatment of substance abuse. We review every empirical paper involving genetic data that has emerged from the program, and reach a surprising conclusion: the study has never identified a single genetic effect of more than trivial magnitude. Although the quantitative results of the studies were reported transparently, the theoretical ramifications of the negligible results have never been acknowledged. To the contrary, most of the papers ignore the tiny effects, reaching optimistic conclusions about the prospects for future genetic explanations of alcohol use. We explore the implications of these results for the broader prospects of applied psychiatric genetics.

Genetic and functional evidence for a role for SLC11A1 in susceptibility to otitis media in early childhood in a Western Australian population

Otitis media (OM) is a common disease in early childhood characterised by inflammation of the middle ear. Susceptibility to recurrent acute OM (rAOM; ⩾3 episodes AOM in 6months) and chronic OM with effusion (COME; middle ear effusion ⩾3months) is 40–70% heritable. Three bacterial pathogens commonly associated with OM, Streptococcus pneumoniae (Sp), non-typeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mc), have been observed within adenoids and as facultative intracellular pathogens that invade and survive in mononuclear cells. Case/pseudo-control conditional logistic regression analysis of variants in the SLC11A1 gene, initially identified for its role in resistance to intra-macrophage pathogens in mice, revealed association with OM at four polymorphisms (Pbest=0.025) in 531 families (660 affected children) from the Western Australian Family Study of Otitis Media. This included association at the functional promoter GTn polymorphism (rs34448891) with alleles that regulate high (allele 3; odds ratio=1.2, 95% CI 1.00–1.44, P=0.04) versus low (allele 2; odds ratio=0.83, 95% CI 0.69–0.99, P=0.04) SLC11A1 expression. Haplotype and stepwise conditional logistic regression analyses support a single genetic effect in the proximal region of SLC11A1, with the haplotype 3_C_C_G across rs34448891_rs2276631_rs3731865_rs2695343 significantly (P=0.008) over-transmitted to affected offspring. Stratified analysis showed no association with OM in children who had undergone adenoidectomy (296 children), whereas children with adenoids intact (364 children) showed improved significance at the GTn polymorphism (allele 3: odds ratio=1.38, 95% CI=1.10–1.75, P=0.006). Quantitative RT/PCR demonstrated high expression of SLC11A1 in mononuclear cells isolated from adenoid tissue, with a trend for decreased expression with increasing copies of GTn allele 2. Expression of SLC11A1 was enhanced at 12 (P=1.2×10−3) and 24h (P<1.0×10−4) after infection of Mono-Mac-6 cells with NTHi. This study identifies SLC11A1 as a novel candidate for OM susceptibility, particularly in children with adenoids intact. Further analysis in other cohorts is required to validate these observations.

Interpreting joint SNP analysis results: when are two distinct signals really two distinct signals?

In genetic association studies, much effort has focused on moving beyond the initial single-nucleotide polymorphism (SNP)-by-SNP analysis. One approach is to reanalyze a chromosomal region where an association has been detected, jointly analyzing the SNP thought to best represent that association with each additional SNP in the region. Such joint analyses may help identify additional, statistically independent association signals. However, it is possible for a single genetic effect to produce joint SNP results that would typically be interpreted as two distinct effects (e.g., both SNPs are significant in the joint model). We present a general approach that can (1) identify conditions under which a single variant could produce a given joint SNP result, and (2) use these conditions to identify variants from a list of known SNPs (e.g., 1000 Genomes) as candidates that could produce the observed signal. We apply this method to our previously reported joint result for smoking involving rs16969968 and rs588765 in CHRNA5. We demonstrate that it is theoretically possible for a joint SNP result suggestive of two independent signals to be produced by a single causal variant. Furthermore, this variant need not be highly correlated with the two tested SNPs or have a large odds ratio. Our method aids in interpretation of joint SNP results by identifying new candidate variants for biological causation that would be missed by traditional approaches. Also, it can connect association findings that may seem disparate due to lack of high correlations among the associated SNPs.

Genetics of Asthma Exacerbations: A Candidate Gene and Genome-Wide Association Study

RationaleExacerbations are a major cause of asthma morbidity and account for a large proportion of asthma healthcare costs. Discovering genetic markers of susceptibility to exacerbations could result in more targeted interventions.MethodsUsing data from four clinical trials (ADA109055/ADA109057/ SFA103153/I13106870) 701 samples were analyzed to conduct a genome-wide association study (GWAS) and an analysis of 50 markers from 18 candidate genes. Exacerbation cases were defined as subjects requiring treatment with systemic corticosteroids, an emergency room visit, or hospitalization for acute asthma symptoms. Controls were subjects without exacerbations. Meta-analysis was used to combine logistic regression results across studies. Principal components derived from genome-wide genetic markers accounted for ancestral diversity.ResultsNo genetic markers from candidate gene or GWAS analyses met pre-specified significance criteria (2.0x10−4 and 4.1x10−8, respectively) for association with asthma exacerbations. However, results from two candidate genes merited additional consideration. Although the direction of effect differed among studies, correlated coding variants in the IL-4 receptor gene (IL4R), a gene previously associated with asthma exacerbations, had the lowest meta-p-values across three studies (p <0.005). A single genetic effect was detected for interferon β1 (IFNB1) with exacerbations in the study that recruited only African-Americans (p<0.002).ConclusionsWhile no genetic markers met the pre-specified statistical criteria, two genes of interest were identified. The IL4R results may support previous findings of association with the IL-4/IL-13 pathway. Similarly, IFNB1 findings in African-Americans are consistent with innate immunity pathways contributing to asthma exacerbation susceptibility. Further studies are required to understand exacerbation associations. RationaleExacerbations are a major cause of asthma morbidity and account for a large proportion of asthma healthcare costs. Discovering genetic markers of susceptibility to exacerbations could result in more targeted interventions. Exacerbations are a major cause of asthma morbidity and account for a large proportion of asthma healthcare costs. Discovering genetic markers of susceptibility to exacerbations could result in more targeted interventions. MethodsUsing data from four clinical trials (ADA109055/ADA109057/ SFA103153/I13106870) 701 samples were analyzed to conduct a genome-wide association study (GWAS) and an analysis of 50 markers from 18 candidate genes. Exacerbation cases were defined as subjects requiring treatment with systemic corticosteroids, an emergency room visit, or hospitalization for acute asthma symptoms. Controls were subjects without exacerbations. Meta-analysis was used to combine logistic regression results across studies. Principal components derived from genome-wide genetic markers accounted for ancestral diversity. Using data from four clinical trials (ADA109055/ADA109057/ SFA103153/I13106870) 701 samples were analyzed to conduct a genome-wide association study (GWAS) and an analysis of 50 markers from 18 candidate genes. Exacerbation cases were defined as subjects requiring treatment with systemic corticosteroids, an emergency room visit, or hospitalization for acute asthma symptoms. Controls were subjects without exacerbations. Meta-analysis was used to combine logistic regression results across studies. Principal components derived from genome-wide genetic markers accounted for ancestral diversity. ResultsNo genetic markers from candidate gene or GWAS analyses met pre-specified significance criteria (2.0x10−4 and 4.1x10−8, respectively) for association with asthma exacerbations. However, results from two candidate genes merited additional consideration. Although the direction of effect differed among studies, correlated coding variants in the IL-4 receptor gene (IL4R), a gene previously associated with asthma exacerbations, had the lowest meta-p-values across three studies (p <0.005). A single genetic effect was detected for interferon β1 (IFNB1) with exacerbations in the study that recruited only African-Americans (p<0.002). No genetic markers from candidate gene or GWAS analyses met pre-specified significance criteria (2.0x10−4 and 4.1x10−8, respectively) for association with asthma exacerbations. However, results from two candidate genes merited additional consideration. Although the direction of effect differed among studies, correlated coding variants in the IL-4 receptor gene (IL4R), a gene previously associated with asthma exacerbations, had the lowest meta-p-values across three studies (p <0.005). A single genetic effect was detected for interferon β1 (IFNB1) with exacerbations in the study that recruited only African-Americans (p<0.002). ConclusionsWhile no genetic markers met the pre-specified statistical criteria, two genes of interest were identified. The IL4R results may support previous findings of association with the IL-4/IL-13 pathway. Similarly, IFNB1 findings in African-Americans are consistent with innate immunity pathways contributing to asthma exacerbation susceptibility. Further studies are required to understand exacerbation associations. While no genetic markers met the pre-specified statistical criteria, two genes of interest were identified. The IL4R results may support previous findings of association with the IL-4/IL-13 pathway. Similarly, IFNB1 findings in African-Americans are consistent with innate immunity pathways contributing to asthma exacerbation susceptibility. Further studies are required to understand exacerbation associations.

Genetic Determinants of UV-Susceptibility in Non-Melanoma Skin Cancer

A milieu of cytokines and signaling molecules are involved in the induction of UV-induced immune suppression and thus the etiology of non-melanoma skin cancer (NMSC). Targeting the UV-induced immunosuppression pathway, and using a large population based study of NMSC, we have investigated the risk associated with functional variants in 10 genes (IL10, IL4, IL4R, TNF, TNFR2, HTR2A, HRH2, IL12B, PTGS2, and HAL). The most prominent single genetic effect was observed for IL10. There was increasing risk for both basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) with increasing number of variant IL10 haplotypes (BCC: ptrend = 0.0048; SCC: ptrend = 0.031). Having two IL10 GC haplotypes was associated with increased odds ratios of BCC and SCC (ORBCC = 1.5, 95% CI 1.1–1.9; ORSCC = 1.4, 95% CI 1.0–1.9), and these associations were largely confined to women (ORBCC = 2.2, 95% CI 1.4–3.4; SCC: ORSCC = 1.8, 95% CI 1.1–3.0). To examine how combinations of these variants contribute to risk of BCC and SCC, we used multifactor dimensionality reduction (MDR) and classification and regression trees (CART). Results from both of these methods found that in men, a combination of skin type, burns, IL10, IL4R, and possibly TNFR2 were important in both BCC and SCC. In women, skin type, burns, and IL10 were the most critical risk factors in SCC, with risk of BCC involving these same factors plus genetic variants in HTR2A, IL12B and IL4R. These data suggest differential genetic susceptibility to UV-induced immune suppression and skin cancer risk by gender.

Multiplealpha-synucleingene polymorphisms are associated with Parkinson’s disease in a Norwegian population

Previous studies have found associations between Parkinson's disease (PD) and polymorphisms located within both the alpha-synuclein gene (SNCA) promoter and other gene regions. Our aim was to study SNCA gene markers in a closely matched Norwegian PD population to examine the genetic relationship between different polymorphisms associated with the disease. We genotyped seven single nucleotide polymorphisms (SNPs) located in the SNCA promoter and two SNPs in the 3' gene region and seven microsatellite markers located across the gene in a closely matched series of 236 PD patients and 236 controls. Linkage disequilibrium (LD) structure was examined, and association of single markers and gene haplotypes analyzed. Several markers located across the SNCA gene were associated with PD, including marker alleles associated with disease in previous studies (Rep1 263-bp allele, rs356165 and rs356219). LD between associated marker alleles located across the SNCA gene suggests that a single genetic effect might explain the previous reported association in the promoter and 3' regions.

Functional response: rigorous estimation and sensitivity to genetic variation in prey

Holling's type II functional response is a cornerstone of community ecology and coevolutionary theory. The so‐called disc equation is the most widely used model of the type II response, yet thus far no robust experimental assessment has been achieved in any single system. Fundamental issues that remain to be assessed include whether the assumptions of the disc equation are fulfilled, whether the disc equation yields accurate estimates of predation‐related individual traits, and whether differences in disc equation parameters can capture genetic variation in prey behaviour. This paper provides a rigorous approach to all of these questions. The functional response of the predatory mitePergamasus crassipeson three genetically distinct clones of the springtailFolsomia candidawas measured at six levels of prey density in controlled conditions where prey number and arena size were concomitantly manipulated. A crucial assumption of Holling's disc equation was fulfilled by maintaining a constant prey density for the entire experimental period of predation. The timing of each attack and capture, as well as the duration of the handling time, were recorded by constant observation. We contrasted three different methods to calculate functional response curves: (1) indirect estimation of the disc equation's parameters from the number of prey killed by the end of each experimental run; (2) direct estimation of the parameters via a unique protocol of constant observation; and (3) independently deriving a function based on direct measurements of encounter rate and attack success. The basic assumptions of the disk equation were globally fulfilled. Estimations of the functional response's parameters (type II) were remarkably congruent across approach (1) and (2). A single genetic effect was detected – the relationship between the encounter rate and prey density differed significantly between clones – whereas a direct comparison of functional response across clones failed to reveal genetic variation.

Analysis of polymorphisms affecting immune complex handling in systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a polygenic disorder of dysregulated inflammation. Numerous specific candidate genes have been identified and most relate to the handling of immune complexes or antigen presentation. This is consistent with the classic finding of immune complex deposition in affected end organs. We wished to examine combinatorial effects of polymorphic variants of genes involved in immune complex clearance in susceptibility to lupus. This study examined the occurrence of polymorphisms in genes which encode proteins known to be involved in immune complex handling and clearance. Each polymorphic variant of a complement protein (C2, mannose binding protein and C4), complement receptor (CR1) or Fc receptor (FcgammaRIIA and FcgammaRIIIA) gene is known to affect function adversely. One hundred and sixty SLE patients and 212 control subjects were genotyped using polymerase chain reaction methods. We found an increasing association of SLE with increasing numbers of gene defects. Combinations of severe defects in FcgammaRIIA and FcgammaRIIIA were particularly deleterious for both African American and Caucasian patients, even though only one defective variant was individually statistically significantly associated with SLE. The results of the study suggest that genes may interact in ways that either synergize or modify the effect of a single genetic effect and imply that association studies must be interpreted within the genetic background of the populations.

To type or not to type: the use of unaffected siblings in nonparametric linkage analysis.

Unaffected individuals are often disregarded in nonparametric linkage analysis. Because of the presumed high complexity of genetic interactions and the resulting low penetrance of any single genetic effect, the statistical contribution of unaffected sib pairs is thought to be considerably lower than that of the affected. However, in cases where a large number of unaffected family members are available for genotyping--as is the case in the simulated Genetic Analysis Workshop 12 data set--the relatively low value of the unaffected sibs may be offset by their number. In this paper, I demonstrate that unaffected siblings do contain a significant amount of statistical information, and show that the most powerful method of nonparametric analysis utilizes both affected and unaffected individuals. I also show that selecting the unaffected individuals based on their age is the most cost effective and usually the most powerful strategy.