Candidate Gene Hypothesis Research Articles

No Evidence That Schizophrenia Candidate Genes Are More Associated With Schizophrenia Than Noncandidate Genes

BackgroundA recent analysis of 25 historical candidate gene polymorphisms for schizophrenia in the largest genome-wide association study conducted to date suggested that these commonly studied variants were no more associated with the disorder than would be expected by chance. However, the same study identified other variants within those candidate genes that demonstrated genome-wide significant associations with schizophrenia. As such, it is possible that variants within historic schizophrenia candidate genes are associated with schizophrenia at levels above those expected by chance, even if the most-studied specific polymorphisms are not. MethodsThe present study used association statistics from the largest schizophrenia genome-wide association study conducted to date as input to a gene set analysis to investigate whether variants within schizophrenia candidate genes are enriched for association with schizophrenia. ResultsAs a group, variants in the most-studied candidate genes were no more associated with schizophrenia than were variants in control sets of noncandidate genes. While a small subset of candidate genes did appear to be significantly associated with schizophrenia, these genes were not particularly noteworthy given the large number of more strongly associated noncandidate genes. ConclusionsThe history of schizophrenia research should serve as a cautionary tale to candidate gene investigators examining other phenotypes: our findings indicate that the most investigated candidate gene hypotheses of schizophrenia are not well supported by genome-wide association studies, and it is likely that this will be the case for other complex traits as well.

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.

Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology.

Unraveling genomic complexity at a quantitative disease resistance locus in maize.

Multiple disease resistance has important implications for plant fitness, given the selection pressure that many pathogens exert directly on natural plant populations and indirectly via crop improvement programs. Evidence of a locus conditioning resistance to multiple pathogens was found in bin 1.06 of the maize genome with the allele from inbred line "Tx303" conditioning quantitative resistance to northern leaf blight (NLB) and qualitative resistance to Stewart's wilt. To dissect the genetic basis of resistance in this region and to refine candidate gene hypotheses, we mapped resistance to the two diseases. Both resistance phenotypes were localized to overlapping regions, with the Stewart's wilt interval refined to a 95.9-kb segment containing three genes and the NLB interval to a 3.60-Mb segment containing 117 genes. Regions of the introgression showed little to no recombination, suggesting structural differences between the inbred lines Tx303 and "B73," the parents of the fine-mapping population. We examined copy number variation across the region using next-generation sequencing data, and found large variation in read depth in Tx303 across the region relative to the reference genome of B73. In the fine-mapping region, association mapping for NLB implicated candidate genes, including a putative zinc finger and pan1. We tested mutant alleles and found that pan1 is a susceptibility gene for NLB and Stewart's wilt. Our data strongly suggest that structural variation plays an important role in resistance conditioned by this region, and pan1, a gene conditioning susceptibility for NLB, may underlie the QTL.

OX1 and OX2 orexin/hypocretin receptor pharmacogenetics

Orexin/hypocretin peptide mutations are rare in humans. Even though human narcolepsy is associated with orexin deficiency, this is only extremely rarely due to mutations in the gene coding prepro-orexin, the precursor for both orexin peptides. In contrast, coding and non-coding variants of the OX1 and OX2 orexin receptors have been identified in many human populations; sometimes, these have been associated with disease phenotype, although most confer a relatively low risk. In most cases, these studies have been based on a candidate gene hypothesis that predicts the involvement of orexins in the relevant pathophysiological processes. In the current review, the known human OX1/HCRTR1 and OX2/HCRTR2 genetic variants/polymorphisms as well as studies concerning their involvement in disorders such as narcolepsy, excessive daytime sleepiness, cluster headache, polydipsia-hyponatremia in schizophrenia, and affective disorders are discussed. In most cases, the functional cellular or pharmacological correlates of orexin variants have not been investigated—with the exception of the possible impact of an amino acid 10 Pro/Ser variant of OX2 on orexin potency—leaving conclusions on the nature of the receptor variant effects speculative. Nevertheless, we present perspectives that could shape the basis for further studies. The pharmacology and other properties of the orexin receptor variants are discussed in the context of GPCR signaling. Since orexinergic therapeutics are emerging, the impact of receptor variants on the affinity or potency of ligands deserves consideration. This perspective (pharmacogenetics) is also discussed in the review.

Association Study of 167 Candidate Genes for Schizophrenia Selected by a Multi-Domain Evidence-Based Prioritization Algorithm and Neurodevelopmental Hypothesis

Integrating evidence from multiple domains is useful in prioritizing disease candidate genes for subsequent testing. We ranked all known human genes (n = 3819) under linkage peaks in the Irish Study of High-Density Schizophrenia Families using three different evidence domains: 1) a meta-analysis of microarray gene expression results using the Stanley Brain collection, 2) a schizophrenia protein-protein interaction network, and 3) a systematic literature search. Each gene was assigned a domain-specific p-value and ranked after evaluating the evidence within each domain. For comparison to this ranking process, a large-scale candidate gene hypothesis was also tested by including genes with Gene Ontology terms related to neurodevelopment. Subsequently, genotypes of 3725 SNPs in 167 genes from a custom Illumina iSelect array were used to evaluate the top ranked vs. hypothesis selected genes. Seventy-three genes were both highly ranked and involved in neurodevelopment (category 1) while 42 and 52 genes were exclusive to neurodevelopment (category 2) or highly ranked (category 3), respectively. The most significant associations were observed in genes PRKG1, PRKCE, and CNTN4 but no individual SNPs were significant after correction for multiple testing. Comparison of the approaches showed an excess of significant tests using the hypothesis-driven neurodevelopment category. Random selection of similar sized genes from two independent genome-wide association studies (GWAS) of schizophrenia showed the excess was unlikely by chance. In a further meta-analysis of three GWAS datasets, four candidate SNPs reached nominal significance. Although gene ranking using integrated sources of prior information did not enrich for significant results in the current experiment, gene selection using an a priori hypothesis (neurodevelopment) was superior to random selection. As such, further development of gene ranking strategies using more carefully selected sources of information is warranted.

Rare Missense Mutations in the Calcium Channel β2 Subunit Gene of Autistic Patients Reduce Time-Dependent Inactivation of CaV1.2

Loss of function of voltage-dependent L-type calcium channels (VDCC) in patients with Timothy syndrome results in a multiorgan dysfunction including lethal arrhythmias, immune deficiency, skeleton-dysplasia, syndactylia and autism. This single gene disorder serves as a model disease for autism spectrum disease (ASD), giving insights in a possible pathophysiology. A point mutation in the pore-forming calcium channel subunit CaV1.2 gene is involved in the development of the Timothy syndrome and leads to incomplete inactivation of the L-type calcium currents (Splawski et al., Cell 2004;119:19-31). Functionally similar biophysical effects can be induced by the influence of auxiliary VDCC β subunits (Herzig et al., FASEB J. 2007;21:1527-38; Jangsangthong et al., Pflugers Arch. 2010;459:399-411).Supported by findings in a meta-analysis of linkage data of ASD patients (Trikalinos et al., Mol Psychiatry. 2006;11:29-36), we are investigating a function-based candidate gene hypothesis linking the β2 subunit gene (CACNB2) with ASD. We performed a case control study sequencing all exons and flanking introns of CACNB2 in 155 patients. We found three rare missense mutations in ASD patients, but not in 259 unaffected controls. All three occur at highly conserved positions and might alter protein function; additionally one mutation probably introduces a new phosphorylation site. Until now, we characterized two of these mutations and a phosphorylation-mimicking mutant in electrophysiological studies. All variants show a decelerated and incomplete time-dependent inactivation of the co-transfected CaV1.2 subunit. So far two variants exhibit a significant increased slope factor of voltage-dependent steady-state inactivation.We here present mutations in the β2 subunit gene of ASD patients that result in a retardation of inactivation behavior, thus phenocopying the monogenic Timothy syndrome mutations of CaV1.2. β2 subunit mutations may influence neuronal function or development in some ASD patients.

Haplotypes of the porcine peroxisome proliferator-activated receptor delta gene are associated with backfat thickness.

BackgroundPeroxisome proliferator-activated receptor delta belongs to the nuclear receptor superfamily of ligand-inducible transcription factors. It is a key regulator of lipid metabolism. The peroxisome proliferator-activated receptor delta gene (PPARD) has been assigned to a region on porcine chromosome 7, which harbours a quantitative trait locus for backfat. Thus, PPARD is considered a functional and positional candidate gene for backfat thickness. The purpose of this study was to test this candidate gene hypothesis in a cross of breeds that were highly divergent in lipid deposition characteristics.ResultsScreening for genetic variation in porcine PPARD revealed only silent mutations. Nevertheless, significant associations between PPARD haplotypes and backfat thickness were observed in the F2 generation of the Mangalitsa × Piétrain cross as well as a commercial German Landrace population. Haplotype 5 is associated with increased backfat in F2 Mangalitsa × Piétrain pigs, whereas haplotype 4 is associated with lower backfat thickness in the German Landrace population. Haplotype 4 and 5 carry the same alleles at all but one SNP. Interestingly, the opposite effects of PPARD haplotypes 4 and 5 on backfat thickness are reflected by opposite effects of these two haplotypes on PPAR-δ mRNA levels. Haplotype 4 significantly increases PPAR-δ mRNA levels, whereas haplotype 5 decreases mRNA levels of PPAR-δ.ConclusionThis study provides evidence for an association between PPARD and backfat thickness. The association is substantiated by mRNA quantification. Further studies are required to clarify, whether the observed associations are caused by PPARD or are the result of linkage disequilibrium with a causal variant in a neighbouring gene.

Inspiratory timing differences and regulation of Gria2 gene variation: a candidate gene hypothesis.

Individual variation in eupneic breathing pattern has been shown in human subjects and laboratory animal models. Genetic predisposition is one of several factors proposed as the basis for the variation among individuals. It is unclear, however, which genes may determine diversity in breathing pattern and by what mechanism(s) genetic factors play a role. Our laboratory has addressed these questions using variation among inbred mouse strains as genetic models of differential respiratory control mechanisms. This report summarizes a series of studies that considers the role of the Gria2 gene, which encodes an ionotropic glutamate receptor subunit, in determining strain variation in eupneic breathing pattern.

Isolation and Genetic Mapping of a Non‐Lethal Rice (Oryza sativa L.) low phytic acid 1 Mutation

Phytic acid (myo‐inositol 1,2,3,4,5,6 hexakisphosphate) is the most abundant form of phosphorus (P) in seeds and is virtually indigestible by humans or non‐ruminant livestock. It was hypothesized that one class of maize (Zea mays L.) and barley (Hordeum vulgare L.) low phytic acid mutations, designated lpa1, interrupt myo‐inositol supply during seed development and may be mutations of the myo‐inositol 1‐phosphate synthase (MIPS) gene. This study describes the isolation, inheritance, and genetic mapping of the first rice lpa1 mutation and reexamines the MIPS/lpa1 candidate gene hypothesis in rice. Grain from 3632 rice M2 lines, derived from gamma‐irradiated seed, was screened for the lpa phenotype. Two mutations, one lethal and one non‐lethal, were identified. The non‐lethal mutation is phenotypically similar to maize and barley lpa1 mutants and was designated rice lpa1‐1 Homozygosity for rice lpa1‐1 reduces the phytic acid portion of seed P from 71 to 39% and increases the inorganic portion of seed P from 5 to 32%, with little effect on total seed P. This rice lpa1 mutation was mapped to a 2.2‐cM interval on chromosome 2L. A single‐copy rice MIPS gene was mapped to a locus on rice chromosome 3 that is orthologous to MIPS loci on maize chromosome 1S (near maize lpa1) and barley chromosome 4H. Unlike maize lpa1, the rice and barley lpa1 mutations loci are clearly distinguishable from this canonical MIPS gene. No relationship can be inferred between the maize, barley, and rice lpa1 loci. Although this canonical MIPS gene may be an appropriate target for controlling seed phytic acid synthesis, modifications of other genes (e.g., maize lpa2, barley lpa1, barley lpa2, and rice lpa1) may also be useful in reducing grain phytic acid and improving the nutritional value of cereal grains and/or milling by‐products.

Genetic variation of the glutamate transporter EAAT2 gene and vulnerability to alcohol dependence.

Glutamate-mediated excitatory pathways play an important role in the pathogenesis of alcohol dependence. The present association study tested the candidate gene hypothesis that variation of the gene encoding the astroglial glutamate transporter EAAT2 confers vulnerability to alcohol dependence. Genotypes of a silent G603A nucleotide exchange in exon 5 of the EAAT2 gene were assessed in 565 subjects of German descent, comprising 342 alcohol-dependent subjects and 223 control subjects. Two more homogeneous subgroups of alcoholics were selected: (1) 112 alcoholics with a history of alcohol withdrawal seizure or delirium; and (2) 54 alcoholics with an antisocial personality disorder. The Tridimensional Personality Questionnaire was applied to assess personality dimensions in 106 alcohol-dependent males. The allele frequencies of the G603A polymorphism did not differ significantly between the control subjects and either the entire sample of alcoholics or the alcoholics with severe physiological withdrawal symptoms. Without correction for multiple testing, there was a significant increase of the frequency of the A603 allele in the antisocial alcoholics compared with either the control subjects [chi2 = 4.587, 1 degree of freedom (df), P = 0.032] or the alcoholics without ASPD (chi2 = 4.968, 1 df, P = 0.026). The personality trait of Harm Avoidance was significantly lower in alcoholics carrying the A603 allele compared with those lacking it (U-test; P = 0.009). These two consistent lines of evidence suggest that genetic variation of the EAAT2 gene confers vulnerability to risk-taking behavior in alcoholics.

Genetic variation of the human μ-opioid receptor and susceptibility to idiopathic absence epilepsy

Pharmacological and autoradiological studies suggest that μ-opioid receptor (OPRM) mediated neurotransmission is involved in the generation of absence seizures. Mutation screening of the human OPRM gene identified a common amino acid substitution polymorphism (Asn40Asp) that differentially modulates the binding affinity of β-endorphin and signal transduction of the receptor. The present association study tested the candidate gene hypothesis that the Asn40Asp substitution polymorphism in the N-terminal OPRM domain confers genetic susceptibility to idiopathic absence epilepsy (IAE). The genotypes of the Asn40Asp polymorphism were assessed by allele-specific polymerase chain reaction in 72 German IAE patients and in 340 ethnically matched control subjects. The frequency of the Asp40 allele was significantly increased in the IAE patients [ f(Asp40)=0.139] compared to the controls [ f(Asp40)=0.078; χ 2=5.467, df=1, P=0.019; OR=2.03; 95%-CI: 1.12–3.68]. This allelic association suggests that the functional Asp40 variant of OPRM modulates neuronal excitability underlying the epileptogenesis of IAE.

Association analysis of exonic variants of the gene encoding the GABAB receptor and idiopathic generalized epilepsy.

The gene encoding the GABAB receptor (GABABR1) maps close to the HLA-F locus on chromosome 6p21.3 in the same region to which a major susceptibility locus for common subtypes of idiopathic generalized epilepsy (IGE), designated as EJM1, has been localized. Moreover, animal models suggest that the GABAB receptor plays a critical role in the epileptogenesis of absence seizures. Accordingly, the present association study tested the candidate gene hypothesis that genetic variants of the human GABABR1 gene confer susceptibility to common subtypes of IGE. Three DNA sequence variants in exons 1a1, 7, and 11 of the GABABR1 gene were assessed by PCR-based restriction fragment length polymorphisms in 248 unrelated probands of German descent, comprising 72 patients with juvenile myoclonic epilepsy (JME), 46 patients with idiopathic absence epilepsy (IAE), and 130 control subjects without a history of epileptic seizures and lack of generalized spike-wave discharges in their electroencephalogram. The results revealed no evidence for an allelic association of any of the GABABR1 sequence variants with either JME or IAE (P > 0.18). Thus, we failed to demonstrate that any of the three exonic GABABR1 variants themselves, or other so-far unidentified mutations, which are in strong linkage disequilibrium with the investigated variants, are involved in the pathogenesis of common IGE subtypes.

Testing candidate gene hypotheses in schizophrenia

Testing candidate gene hypotheses in schizophrenia