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PubMed2026

Robust inference and correlates from genetic associations with personality.

Personality traits describe stable differences in how people think, feel and behave, and how they interact with and experience their social and physical environments1,2. Many questions remain unanswered about associations between DNA and personality traits, such as their robustness, their generalizability and the biological and social pathways through which they act. Here we meta-analyse data across 46 cohorts comprising 611,037 to 1.14 million participants with European-like and African-like genomes for genome-wide association studies (GWAS) of the Big Five personality traits (extraversion, agreeableness, conscientiousness, neuroticism and openness to experience), and data from up to 50,725 participants for within-family GWAS. We identify 1,260 lead genetic variants associated with personality, including 824 novel variants3. Common genetic variants explain a moderate 4.8-9.3% of the variance in measures of each trait, and 9.3-13.3% among instruments with typical measurement reliability. Genetic associations with personality are highly consistent but not identical across geography, reporter (self versus close other), age group and measurement instrument, and we find minimal spousal assortment for personality in recent history. In contrast to many other social and behavioural traits4,5, within-family GWAS and polygenic index analyses indicate that genetic associations with personality are minimally confounded by the shared family environment. Polygenic prediction, genetic correlation and Mendelian randomization analyses indicate that personality traits have widespread, potentially causal associations with consequential behaviours and life outcomes. Overall, we find that the genetic architecture of personality is robustly generalizable, minimally confounded and widely relevant to human experience.

Journal Article↗
PubMed2025

Differential methylation of a retrotransposon upstream of a MYB gene causes variegation of lettuce leaves, which is abolished by the presence of an (AT)5 repeat in the promoter.

Variegation, a common phenomenon in plants, can be the result of several genetic, developmental, and physiological factors. Leaves of some lettuce cultivars exhibit dramatic red variegation; however, the genetic mechanisms underlying this variegation remain unknown. In this study, we cloned the causal gene for variegation on lettuce leaves and elucidated the underlying molecular mechanisms. Genetic analysis revealed that the polymorphism of variegated versus uniformly red leaves is caused by an "AT" repeat in the promoter of the RLL2A gene encoding a MYB transcription factor. Complementation tests demonstrated that the RLL2A allele (RLL2AV) with (AT)n repeat numbers other than five led to variegated leaves. RLL2AV was expressed in the red spots but not in neighboring green regions. This expression pattern was in concert with a relatively low level of methylation in a retrotransposon inserted in -761 bp of the gene in the red spots compared to high methylation of the retrotransposon in the green region. The presence of (AT)5 in the promoter region, however, stabilized the expression of RLL2A, resulting in uniformly red leaves. In summary, we identified a novel promoter mechanism controlling variegation through inconsistent levels of methylation and showed that the presence of a simple sequence repeat of specific size could stabilize gene expression.

Promoter Regions, Genetic↗
PubMed2006

The molecular genetics of cognition: dopamine, COMT and BDNF.

The important contribution of genetic factors to the development of cognition and intelligence is widely acknowledged, but identification of these genes has proven to be difficult. Given a variety of evidence implicating the prefrontal cortex and its dopaminergic circuits in cognition, most of the research conducted to date has focused on genes regulating dopaminergic function. Here we review the genetic association studies carried out on catechol-O-methyltransferase (COMT) and the dopamine receptor genes, D1, D2 and D4. In addition, the evidence implicating another promising candidate gene, brain-derived neurotrophic factor (BDNF) in neuropsychological function, is assessed. Both the COMT val158met polymorphism and the BDNF val66met variant appear to influence cognitive function, but the specific neurocognitive processes involved continue to be a matter of debate. Part of the difficulty is distinguishing between false positives, pleiotropy and the influence of a general intelligence factor, g. Also at issue is the complexity of the relevant neuromolecular pathways, which make the inference of simple causal relationships difficult. The implications of molecular genetic cognitive research for psychiatry are discussed in light of these data.

Animals↗
PubMed1996

[Gene therapy of neurologic diseases. Experimental approaches and clinical perspectives].

So far, it has not been possible to treat many neurological conditions causally. However, in the past few years underlying genetic defects have been characterized for a substantial number of neurodegenerative disorders. Experimental methods have been developed that allow for efficient gene transfer into defined regions of the mammalian CNS. Such techniques can be applied to deliver genes into target cells of a recipient organism or to transfer genetically modified cells into defined regions of the CNS. Candidate genes for gene therapy are those encoding for neurotrophins and neurotransmitters for symptomatic therapy and, in the case of neurodegenerative disorders with localized gene defects, the wild-type allele as a causal treatment approach. In this review article, we describe some of the most widely used strategies for gene transfer to the CNS. We also report on the results obtained with animal models for human disease, and discuss both the chances and problems of gene therapy approaches in clinical medicine.

Animals↗
PubMed2026

Causal associations between hormone replacement therapy and brain structure: Evidence from large-scale Mendelian randomization and double machine learning.

BACKGROUND: Hormone replacement therapy (HRT) is widely prescribed for the management of hormone deficiency, particularly during menopause, yet its causal effects on human brain structure remain incompletely understood. Observational studies have reported heterogeneous associations, underscoring the need for robust causal inference. METHODS: We applied an integrated causal framework combining two-sample Mendelian Randomization (MR) and Double Machine Learning (DML) to evaluate the effects of four HRT-related exposures-age at initiation, age at cessation, ever-use of HRT, and a composite medication-based phenotype-on 1366 brain imaging-derived phenotypes from the UK Biobank. Genetic instruments were derived from large-scale GWAS summary statistics, and causal estimates were validated using non-parametric DML models with cross-fitting and performance evaluation. RESULTS: Genetic instruments for age at HRT initiation, age at cessation, and ever-use of HRT were strong (median F-statistics 16.29-36.66). MR analyses identified a causal association between later initiation of HRT and lower orientation dispersion in the right inferior cerebellar peduncle (ubm-a-542; primary finding, no pleiotropy detected). An additional association with the left tapetum FA (ubm-a-243) was identified but exhibited significant directional horizontal pleiotropy (MR-Egger intercept P = 0.001) and is excluded from primary conclusions (Supplementary Note S2). Later cessation of HRT was associated with increased cortical thickness in the left middle occipital gyrus, reduced surface area in the left frontopolar cortex, and increased orientation dispersion in the splenium of the corpus callosum. Ever-use of HRT was causally linked to larger volumes of the right inferior frontal gyrus and right nucleus accumbens. These associations were corroborated by independent DML validation, which provided causally debiased estimates robust to high-dimensional confounding. Results for ukb-b-8080 (median F = 1.45) are provided in Supplementary Note S1 only; weak-instrument bias precludes causal inference. CONCLUSIONS: This study provides genetic-instrument-based and machine-learning-validated evidence for causal associations between HRT exposure-particularly its timing and lifetime use-and specific features of human brain structure, including white-matter microarchitecture, cortical thickness, and regional brain volume. These findings are FDR-controlled within exposures and independently replicated by DML, but require replication in external neuroimaging GWAS cohorts to establish definitive causal conclusions. They highlight the neurobiological relevance of sex steroid exposure and inform future research on brain aging and personalized hormone-based interventions.

Humans↗
PubMed2006

[Integration of genetic factors into epidemiological studies].

During the last two decades, genetic epidemiology has been established in parallel to the area of classical epidemiology. This paper presents some essentials of the epidemiology of genetic factors. It begins with a discussion of complex diseases that are characterized by an involvement of several genes. The problems that are attached to modeling gene-gene and gene-environment interactions and their integration into causal pathways are elucidated and the role of genetic factors in the etiology of complex diseases is investigated. Classical and new epidemiological study designs that allow an integration of genetic data are introduced. The introduction of this data is partly motivated by the danger of bias due to genetic heterogeneity (population stratification) in classical designs. The problem of replication of study results is discussed and the concept of Mendelian randomization is presented.

Case-Control Studies↗
PubMed2006

Polymorphisms of the vitamin D receptor gene predict the onset of surgical menopause in Caucasian females.

We tested association of four single nucleotide polymorphisms (SNPs) of the vitamin D receptor gene (VDR) with age at surgical and natural menopause in a sample of Caucasians composed of 153 women with surgical and 260 with natural menopause. A significant association was observed between age at surgical menopause and two SNPs, rs1544410 (BsmI) and rs731236 (TaqI) (p < 0.05). For rs1544410, homozygotes of the minor allele, AA, had about two-fold higher risk of surgical menopause than homozygotes of the major allele, GG (95% confidence ratio (CI) 1.09-3.82). For rs731236, the CC subjects had a greater chance of surgical menopause than the TT subjects (odds ratio = 2.01, 95% CI 1.07-3.78). Since rs1544410 and rs731236 are in strong linkage disequilibrium, the haplotypes based on these two loci were also tested. The haplotype AC was highly significantly associated with age at surgical menopause (p = 0.008). Women with this haplotype had surgical menopause on average 2.8 years earlier than non-carriers. These results reveal the potential effect of the VDR gene on ovaries and uterus, and suggest that its SNPs can be used as predictors of genetic susceptibility for early surgical menopause and respective causal health problems.

Age of Onset↗
PubMed2000

Genetic variation in coronary heart disease and myocardial infarction: methodological overview and clinical evidence.

The precise molecular mechanisrms that lead to coronary artery disease (CAD) and myocardial infarction (MI) are not understood, despite a wealth of knowledge on predisposing risk factors and pathomechanisms. CAD and MI are complex genetic diseases; neither the environment alone nor a single gene cause disease, but a mix of environmental and genetic factors lead to atherosclerosis of the coronary arteries and subsequent manifestation of clinical disease. The biological complexity of atherosclerotic disease results from unknown or unpredictable interactions of many genetic and environmental factors which, by themselves, have only been partially identified. According to current knowledge, genetic variations in causative or susceptihility genes form the basis of molecular mechanisms that, together with environmental impact, lead to CAD/MI and determine its clinical course. Linkage analysis, which follows 'disease' alleles in families, or genetic association in a population of unrelated individuals are tools used in the search for chromosomal loci and candidate genes that are involved in these complex diseases. Progress in sequencing and mapping of the human genorne and efforts to identify all of the expected one million single nucleotide polymorphisms (SNPs) expected to be present in mankind will allow new approaches such as genome-wide association studies. The contribution of the current state of knowledge on genetic variation in man towards the dissection of CAD/MI as complex traits is sobering. Raised expectations with regard to the power of molecular genetic studies as compared to the traditional pathophysiological experimental approaches, lack of precise clinical phenotyping, lack of functional characterisation of gene variants, and the vast number of yet undetected genes may provide some explanation. Except for certain polymorphisms in lipid genes (i.e., apolipoprotein E [apo E]) or rare genetic variations (i.e., LDL receptor), which have a causal effect on both the intermediate (LDL-cholesterol level in plasma) and the clinical phenotypes (CAD/MI), the role of most gene polymorphisms is controversial or unknown. Despite the enormous progress in sequencing the human genome and in molecular genetic and bioinformatic techniques during the past decade, the progress in mapping and identifying genes responsible for complex traits such as CAD/MI has been modest and presents a formidable challenge to medical research in the 21st century.

Coronary Disease↗
PubMed2006

A common haplotype of interferon regulatory factor 5 (IRF5) regulates splicing and expression and is associated with increased risk of systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by activation of the type I interferon (IFN) pathway. Here we convincingly replicate association of the IFN regulatory factor 5 (IRF5) rs2004640 T allele with SLE in four independent case-control cohorts (P = 4.4 x 10(-16)) and by family-based transmission disequilibrium test analysis (P = 0.0006). The rs2004640 T allele creates a 5' donor splice site in an alternate exon 1 of IRF5, allowing expression of several unique IRF5 isoforms. We also identify an independent cis-acting variant associated with elevated expression of IRF5 and linked to the exon 1B splice site. Haplotypes carrying the variant associated with elevated expression and lacking the exon 1B donor site do not confer risk of SLE. Thus, a common IRF5 haplotype driving elevated expression of multiple unique isoforms of IRF5 is an important genetic risk factor for SLE, establishing a causal role for type I IFN pathway genes in human autoimmunity.

Case-Control Studies↗
PubMedDate not supplied

Genetic manipulation in higher organisms. I. Goldfish ova as materials of operation, mRNA mediated alteration of the liver specific isozymes.

Both crucian and carp egg-mRNAs were found to mediate the transformation of goldfish tail from the double (veil-shaped) to the single (fork-shaped). Livers of these single tailed goldfish were tested for genetic change using lactate dehydrogenase isozymes (LDH) as marker. Electrophoresis of liver extracts on starch gel showed that the liver specific LDH-C4 isozymes of both the egg-mRNA and liver-mRNA injected goldfish resembled the control goldfish except an additional intermediate band. The migration distance of this new band matched the third band of the hybrids (carp X goldfish). These findings lead to the conclusion that carp egg-mRNA contains a fraction partly responsible for liver development. Rat liver was found possessing the cathodally migrating C4 isozymes. Injection of rat liver-mRNA into goldfish eggs resulted in the intensification of the liver specific C4 isozymes. It appears therefore that the input informational molecules (liver-mRNA) and the output molecular products (liver C4 isozymes) are causally related. This causal relationship would pave the way for genetic manipulation in higher organisms.

Animals↗
PubMed1994

The concept of gender identity disorder in childhood and adolescence after 39 years.

The term "gender role" appeared in print first in 1955. The term "gender identity" was used in a press release, November 21, 1966, to announce the new clinic for transsexuals at The Johns Hopkins Hospital. It was disseminated in the media worldwide, and soon entered the vernacular. The definitions of gender and gender identity vary on a doctrinal basis. In popularized and scientifically debased usage, sex is what you are biologically; gender is what you become socially; gender identity is your own sense or conviction of maleness or femaleness; and gender role is the cultural stereotype of what is masculine and feminine. Causality with respect to gender identity disorder is subdivisible into genetic, prenatal hormonal, postnatal social, and postpubertal hormonal determinants, but there is, as yet, no comprehensive and detailed theory of causality. Gender coding in the brain is bipolar. In gender identity disorder, there is discordancy between the natal sex of one's external genitalia and the brain coding of one's gender as masculine or feminine.

Adolescent↗
PubMed2001

Genetic dissection of immunity to mycobacteria: the human model.

Humans are exposed to a variety of environmental mycobacteria (EM), and most children are inoculated with live Bacille Calmette-Guérin (BCG) vaccine. In addition, most of the world's population is occasionally exposed to human-borne mycobacterial species, which are less abundant but more virulent. Although rarely pathogenic, mildly virulent mycobacteria, including BCG and most EM, may cause a variety of clinical diseases. Mycobacterium tuberculosis, M. leprae, and EM M. ulcerans are more virulent, causing tuberculosis, leprosy, and Buruli ulcer, respectively. Remarkably, only a minority of individuals develop clinical disease, even if infected with virulent mycobacteria. The interindividual variability of clinical outcome is thought to result in part from variability in the human genes that control host defense. In this well-defined microbiological and clinical context, the principles of mouse immunology and the methods of human genetics can be combined to facilitate the genetic dissection of immunity to mycobacteria. The natural infections are unique to the human model, not being found in any of the animal models of experimental infection. We review current genetic knowledge concerning the simple and complex inheritance of predisposition to mycobacterial diseases in humans. Rare patients with Mendelian disorders have been found to be vulnerable to BCG, a few EM, and M. tuberculosis. Most cases of presumed Mendelian susceptibility to these and other mycobacterial species remain unexplained. In the general population leprosy and tuberculosis have been shown to be associated with certain human genetic polymorphisms and linked to certain chromosomal regions. The causal vulnerability genes themselves have yet to be identified and their pathogenic alleles immunologically validated. The studies carried out to date have been fruitful, initiating the genetic dissection of protective immunity against a variety of mycobacterial species in natural conditions of infection. The human model has potential uses beyond the study of mycobacterial infections and may well become a model of choice for the investigation of immunity to infectious agents.

Environmental Microbiology↗
PubMed2001

Molecular diagnosis in a child with sudden infant death syndrome.

Although sudden infant death syndrome (SIDS) has been associated with long QT syndrome-a genetic disorder that causes arrhythmia-a causal link has not been shown. We screened genomic DNA from a child who died of SIDS and identified a de-novo mutation in KVLQT1, the gene most frequently associated with long QT syndrome. This mutation (C350T) had already been identified in an unrelated family that was affected by long QT syndrome. These results confirm the hypothesis that some deaths from SIDS are caused by long QT syndrome and support implementation of neonatal electrocardiographic screening.

Adolescent↗
PubMed2026

Causal Relationships Between Oral Microbiota and Inflammatory Skin Diseases.

INTRODUCTION AND AIMS: The oral microbiome has been increasingly linked to systemic inflammation and immune dysregulation, but whether specific oral bacteria causally contribute to inflammatory skin diseases remains unclear due to confounding and reverse causation. This study aimed to assess the causal effects of 43 oral microbiota taxa on the risk of five inflammatory skin diseases using a Mendelian randomization (MR) approach. METHODS: We performed a two-sample MR analysis using genetic instruments for oral microbiota derived from publicly available genome-wide association studies and outcome data from the FinnGen consortium. Causal effects of oral taxa on systemic lupus erythematosus, vitiligo, pemphigus, localized scleroderma, and dermatitis herpetiformis were estimated. The inverse-variance weighted method served as the primary analysis, complemented by sensitivity analyses to evaluate horizontal pleiotropy, heterogeneity, and reverse causality. RESULTS: MR analyses identified several putative causal associations between oral microbiota and inflammatory skin diseases. Genus Granulicatella and an unknown Streptococcus species (ASV0009) showed causal effects on systemic lupus erythematosus. Family Lachnospiraceae_[XIV] and an unknown Rothia species (ASV0016) were associated with vitiligo. Five oral microbiota taxa demonstrated causal associations with pemphigus. Actinomyces species micronuciformis was linked to localized scleroderma. Order Fusobacteriales and an unknown Neisseria species (ASV0004) were associated with dermatitis herpetiformis. No significant heterogeneity or horizontal pleiotropy was detected in sensitivity analyses. CONCLUSION: This MR study provides genetic evidence supporting a causal role of specific oral bacteria in the development of several inflammatory skin diseases, highlighting the oral microbiome as a potential contributor to cutaneous autoimmunity and inflammation. CLINICAL RELEVANCE: Our findings highlight the putative role of the oral microbiome as a plausible candidate for mechanistic and clinical investigations into the prevention or adjunctive management of selected inflammatory skin diseases. However, oral hygiene improvement, targeted antimicrobials, and other microbiota-directed interventions were not directly tested in this MR study and remain hypothetical strategies requiring validation in experimental and clinical studies.

Humans↗
PubMed2026

NLCD: A method to discover nonlinear causal relations among genes.

Distinguishing correlation from causation is a fundamental challenge in many scientific fields, including biology, especially when interventions like randomized controlled trials are infeasible and only observational data are available. Methods based on statistical tests of conditional independence within the Mendelian Randomization framework can detect causality between two observed variables that are each associated with a third instrumental variable. However, these methods for detecting causal relationships between traits (e.g., two gene expression or clinical traits associated with a genetic variant, all observed in the same population) often assume a linear relationship, thereby hindering the discovery of causal gene networks from genomics data. We have developed NLCD, a method for NonLinear Causal Discovery from genomics data based on nonlinear regression modeling and conditional feature importance scoring. NLCD uses these techniques to extend the statistical tests in an existing linear causal discovery method called the Causal Inference Test (CIT). We benchmarked NLCD against current state-of-the-art methods: CIT, Findr, and MRPC. On simulated datasets, NLCD performs comparably to most methods in detecting linear relations (Average AUPRC (Area Under the Precision-Recall Curve) of NLCD&#x2009;=&#x2009;0.94, CIT&#x2009;=&#x2009;0.94, Findr&#x2009;=&#x2009;0.94, and MRPC&#x2009;=&#x2009;0.99), and outperforms them in detecting nonlinear (sine and sawtooth type) relations between two genes (Average AUPRC of NLCD&#x2009;=&#x2009;0.76, CIT&#x2009;=&#x2009;0.60, Findr&#x2009;=&#x2009;0.56, and MRPC&#x2009;=&#x2009;0.73). When tested on a nonlinear subset of a yeast genomic dataset to recover known causal relations involving transcription factors, NLCD and CIT performed comparable to each other and slightly better than Findr and MRPC (Average AUPRC of NLCD&#x2009;=&#x2009;0.82, CIT&#x2009;=&#x2009;0.81, Findr&#x2009;=&#x2009;0.71, and MRPC&#x2009;=&#x2009;0.54). On application to a human genomic dataset, NLCD revealed active causal gene pairs (IRF1 &#x2192; PSME1 and HLA-C &#x2192; HLA-T) in the muscle tissue, and clarified the promises and challenges in discovering causal gene networks in tissues under in vivo human settings.

Humans↗
PubMed1997

QTL analysis to study the association between leaf size and abscisic acid accumulation in droughted rice leaves and comparisons across cereals.

Plants accumulate abscisic acid (ABA) under droughted conditions. Genetic variation in the accumulation of ABA in deteched and partially dehydrated leaves of rice has previously been reported, and this was found to be associated with variation in leaf size (smaller leaves made more ABA). Correlation analysis failed to distinguish clearly between a causal relationship between the two traits and close genetic between loci controlling the traits. Here we present a detailed genetic analysis of ABA accumulation in detached and partially dehydrated rice leaves. using a population of F2 plants generated from the lowland x upland cross IR20 (high-ABA) x 63-83 (low-ABA) which was mapped with RFLP and AFLP markers. Several highly significant quantitative trait loci (QTLs) for ABA accumulation and leaf weight were identified. Only one of the minor QTLs for ABA accumulation (accounting for only 4% of the phenotypic variance) was coincident with any QTLs for leaf size such that the high-ABA allele was associated with smaller leaves. This analysis, therefore, showed that the association previously found between ABA accumulation and leaf size was probably largely due to genetic linkage and not to a direct effect of leaf size on ABA accumulation or vice versa. Because of the importance of ABA accumulation in regulating responses of plants to drought stress and the effects of plant size on the rate of development of stress, QTLs for drought-induced ABA accumulation, leaf size and tiller number were compared between rice and wheat. In particular, a possible location in rice was sought for a homoeologue of the major wheat vernalization responsive gene, Vrn1, as this gene is also associated with major effects on leaf size, tiller number and ABA accumulation in wheat. The likelihood of homoeologous loci regulating ABA accumulation, leaf size and tiller number in the two crops is discussed.

Abscisic Acid↗
PubMed1996

[Genetic epidemiology and frequent multifactorial diseases].

A global approach is required in the search for factors predisposing to multifactorial diseases. The analysis of genotypes must, of course, be integrated in addition to environmental factors and intermediary phenotypes as well as a precise evaluation of different clinical manifestations of the disease. A better understanding of the pathophysiological mechanisms involved is essential for intelligent selection of candidate genes, pertinent analysis of intermediary phenotypes and measurements of factors susceptible to influence the genetic effects. Strategy to identify factors of genetic susceptibility to frequent diseases does not necessarily involve linkage analysis.

Alcoholism↗