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Results for “Genetic causality”

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PubMed2004

A twin study of genetic and environmental influences on tobacco initiation, regular tobacco use and nicotine dependence.

BACKGROUND: Numerous twin studies have reported significant genetic contributions to the variability of tobacco initiation (TI), while fewer studies have shown similar results for the persistence of smoking behavior, or nicotine dependence (ND). As the development of ND requires regular tobacco use (RTU) which in turn requires TI, a conditional approach is necessary. METHOD: We used structural equation modeling of multi-step conditional processes to examine the relationship between genetic and environmental risk factors for TI, RTU and ND. The tobacco variables were assessed by personal interview in female, male and opposite-sex twin pairs from the population-based Virginia Twin Registry. RESULTS: The results suggested that the liabilities to TI, RTU and ND were correlated. Over 80 % of the variance in liability to TI and RTU were shared, and a smaller proportion was shared between RTU and ND. The heritabilities were estimated at 75 %, 80 % and 60 % respectively for TI, RTU and ND. The variance specific to liability to RTU was entirely accounted for by additive genetic factors. Only a modest part of the heritability in liability of ND was due to genetic factors specific to ND. Shared environmental factors were not significant. No sex differences were found for the sources of variation or causal paths, but prevalences were significantly greater in males versus females. CONCLUSIONS: This study showed significant overlap in the contribution of genetic factors to individual differences in TI, RTU and ND. Furthermore, there was evidence for significant additional genetic factors specific to RTU and ND.

Adult↗
PubMed2006

[Methods of the announcement of amyotrophic lateral sclerosis diagnosis in familial forms].

Between 10 percent and 20 percent of amyotrophic lateral sclerosis cases are familial (FALS). The announcement of a diagnosis of ALS to a patient having relatives already affected with this disease must take into account the familial history and should focus on the improvement in management of ALS patients. Diagnosis of FALS implicitly raises the notion of genetic factors and the possibility for an heritability of the disease (risk of ALS for relatives). Although it is possible to search for mutations in SOD1 gene in ALS patients and asymptomatic relatives, the incomplete penetrance of the disease, the low percentage (10 to 20 percent) of FALS linked to SOD1 mutation and the existence of non causal SOD1 mutations complicate the conclusions of genetic investigations concerning the real risk for a relative with a SOD1 mutation to develop ALS.

Amyotrophic Lateral Sclerosis↗
PubMed1998

Loci predisposing to autoimmunity in MRL-Fas lpr and C57BL/6-Faslpr mice.

Background genes determine the incidence and severity of lymphoaccumulation and histopathologic manifestations of systemic autoimmunity in mice homozygous for the apoptosis-defective Faslpr mutation. By interval mapping of 274 F2 mice intercrossed between MRL-Faslpr (severe disease) and C57BL/6-Faslpr (minimal disease), four loci were identified with significant linkage to lymphadenopathy and/ or splenomegaly on chromosomes 4, 5, 7, and 10, which were named lupus in (MRL-Faslpr x B6-Faslpr)F2 cross1-4 (Lmb1-4), respectively. Lmb1, -2, and -3 were also linked to the production of anti-dsDNA antibodies, but not glomerulonephritis, whereas Lmb4 was associated with glomerulonephritis. Lmb2, -3, and -4 were inherited from the MRL background, but interestingly, Lmb1 was derived from the C57BL16-Faslpr. Nevertheless, each locus, regardless of the strain of origin, appeared to act in an additive manner, although certain combinations were more effective. Only a single suggestive locus on chromosome 1 could be correlated with arthritis. The identification of loci with highly significant linkage to disease manifestations in Faslpr strains will make it possible to map and clone new genetic defects contributing to autoimmunity.

Animals↗
PubMed2025

Interstrain Recombinants of Human Cytomegalovirus Reveal Complex Genetic Correlates and Epistasis Influencing Glycoprotein Display, Virion Infectivity and Spread Characteristics.

Most of the nucleotide diversity in the human cytomegalovirus (HCMV) genome is due to approximately 17 genes with 2-14 alleles each. These allelic genes are interspersed among longer stretches of highly conserved sequences with signatures of extensive recombination that would shuffle the allelic genes into a vast number of allelic haplotypes. Bacterial artificial chromosome clones derived from 3 independent clinical isolates (TB40/e (TB), TR and Merlin (ME)) display dramatic differences in the abundance of entry-mediating glycoproteins gH/gL/gO and gH/gL/UL128-131, virion infectivity and efficiency of cell-free and cell-to-cell modes of spread. Of these, TB and ME are the most phenotypically different and share only 2 of the 17 allelic genes. A set of recombinant HCMV was generated by coinfecting cells with TB and ME and restriction fragment length polymorphism (RFLP) analyses demonstrated complex crossover patterns. Most recombinants were either "TB-like" with much more gH/gL/gO than gH/gL/UL128-131, or "ME-like" with much more gH/gL/UL128-131. This correlated with a TB or ME UL128 sequence, consistent with a G/T polymorphism affecting UL128 pre-mRNA splicing. One recombinant had a gH/gL/gO:gH/gL/UL128-131 ratio of 0.8, suggesting genetic determinants beyond UL128. Virion infectivity correlated with TB versus ME-like glycoprotein display, but intragroup variability indicated additional factors and variability in spread efficiency and the contribution of cell-free and cell-to-cell spread modes indicated an influence of characteristics beyond virion infectivity. Results suggest that the relationships among these three phenotypes are not strictly causal and that all three phenotypes are genetically complex and influenced by epistasis among polymorphic loci across the genome.

Journal Article↗
PubMed2026

Deciphering miRNA-mediated genetic architecture of immune cell subsets in hypertrophic scars and keloids: A 2-step Mendelian randomization study unveiling causal associations.

This study aimed to investigate the potential causal roles of specific circulating microRNAs (miRNAs) and immune cell subsets in the pathogenesis of hypertrophic scars and keloids using a 2-step Mendelian randomization framework. We employed a 2-sample Mendelian randomization approach to evaluate the causal relationships between miRNAs, immune cell genotypes, and scar phenotypes. The analysis integrated miRNA expression quantitative trait loci, immune cell genome-wide association studies, and scar datasets. A 2-step mediation analysis was conducted to assess the indirect effects of miRNAs on scars through immune cell genotypes, using inverse variance weighted methods and complementary sensitivity analyses to ensure robustness. Our analysis identified significant associations between specific miRNAs and scar phenotypes. Notably, miR-6887-5p exhibited a total effect on keloid formation risk (β = 0.324, 95% confidence interval [CI]: 0.073-0.576) and a direct effect (β = 0.283, 95% CI: 0.027, 0.538), with a marginally significant mediation effect through B-cell activating factor receptor on CD20- CD38- B cells (β = 0.042, 95% CI: -0.001, 0.084, P = .047). For hypertrophic scars, miR-345-5p demonstrated a significant total effect (β = -0.501, 95% CI: -0.903, -0.099) and direct effect (β = -0.469, 95% CI: -0.872, -0.066), with a significant mediation effect through CD28+ CD45RA- CD8dim T cell percentage (β = -0.032, 95% CI: -0.062, -0.002, P = .034). miR-4801 showed a significant total effect (β = -0.246, 95% CI: -0.429, -0.064) and direct effect (β = -0.218, 95% CI: -0.402, -0.033), with a marginally significant mediation effect through T cell absolute count (β = -0.028, 95% CI: -0.057, -0.000, P = .043). These findings highlight the interplay between miRNAs and immune cell subsets in scar pathogenesis. This study provides preliminary evidence for the causal roles of specific miRNAs and immune cell subsets in scar formation, emphasizing the potential of miRNA-immune cell axes as therapeutic targets. While the identified associations offer important insights into the molecular mechanisms of scar heterogeneity, further validation through mechanistic studies and clinical trials is necessary to translate these genetic insights into clinical interventions.

Humans↗
PubMed2026

Genome-wide discovery reveals 30 loci for choroidal thickness and uncovers potential causal links with angle-closure glaucoma.

The choroid is critical for maintaining vision and implicated in several ocular diseases, being the sole source of nutrients and waste removal for the outer retina. Genetic discovery can help elucidate the pathways through which choroidal features influence disease risk. Our meta-analysis of genome-wide association studies (n= 78,682 participants) identified 30 genomic regions, including 20 novel loci, associated with choroidal thickness. Findings suggest inflammatory and vascular processes drive choroidal thickness, with overlapping mechanisms shared with refractive error. Genome-wide independently significant SNPs accounted for 18.7% of the genetic variance in choroidal thickness. Mendelian randomisation analyses showed a causal effect of age-related macular degeneration on choroidal thickness, and suggest a bidirectional causal effect between choroidal thickness and primary angle-closure glaucoma. These findings provide insight into the shared genetic architecture and biological pathways linking choroidal thickness and related diseases.

Canadian Longitudinal Study on Aging↗
PubMed2006

Genetic complexity of Alzheimer's disease: successes and challenges.

About 1% of Alzheimer's Disease (AD) cases have an early-onset autosomal dominant familial form of the disease, genetic analyses of which have found three causal genes: amyloid beta-protein precursor (AbetaPP), presenilin 1 (PS1) and presenilin 2 (PS2). The APOE gene is the only robustly replicated risk factor for the common form of AD with onset after 65 years of age. In at least half of the AD cases, there is no known cause of the disease. Here we provide an overview on known AD-linked genes and discuss the strategies of searching for novel AD genetic risk factors.

Alzheimer Disease↗
PubMed2006

['Migraine and a hole in the heart': causal relationship between migraine and patent foramen ovale not established].

The relationship between patent foramen ovale (PFO) and migraine is controversial. A common genetic background seems possible, but there is no evidence for a causal relationship. Despite the lack of evidence, PFO closure is recommended in many countries as a remedy for migraine. At present, PFO closure for migraine should only be carried out under strictly controlled clinical trial conditions.

Genetic Predisposition to Disease↗
PubMed2023

Pervasive correlations between causal disease effects of proximal SNPs vary with functional annotations and implicate stabilizing selection.

The genetic architecture of human diseases and complex traits has been extensively studied, but little is known about the relationship of causal disease effect sizes between proximal SNPs, which have largely been assumed to be independent. We introduce a new method, LD SNP-pair effect correlation regression (LDSPEC), to estimate the correlation of causal disease effect sizes of derived alleles between proximal SNPs, depending on their allele frequencies, LD, and functional annotations; LDSPEC produced robust estimates in simulations across various genetic architectures. We applied LDSPEC to 70 diseases and complex traits from the UK Biobank (average N=306K), meta-analyzing results across diseases/traits. We detected significantly nonzero effect correlations for proximal SNP pairs (e.g., -0.37±0.09 for low-frequency positive-LD 0-100bp SNP pairs) that decayed with distance (e.g., -0.07±0.01 for low-frequency positive-LD 1-10kb), varied with allele frequency (e.g., -0.15±0.04 for common positive-LD 0-100bp), and varied with LD between SNPs (e.g., +0.12±0.05 for common negative-LD 0-100bp) (because we consider derived alleles, positive-LD and negative-LD SNP pairs may yield very different results). We further determined that SNP pairs with shared functions had stronger effect correlations that spanned longer genomic distances, e.g., -0.37±0.08 for low-frequency positive-LD same-gene promoter SNP pairs (average genomic distance of 47kb (due to alternative splicing)) and -0.32±0.04 for low-frequency positive-LD H3K27ac 0-1kb SNP pairs. Consequently, SNP-heritability estimates were substantially smaller than estimates of the sum of causal effect size variances across all SNPs (ratio of 0.87±0.02 across diseases/traits), particularly for certain functional annotations (e.g., 0.78±0.01 for common Super enhancer SNPs)-even though these quantities are widely assumed to be equal. We recapitulated our findings via forward simulations with an evolutionary model involving stabilizing selection, implicating the action of linkage masking, whereby haplotypes containing linked SNPs with opposite effects on disease have reduced effects on fitness and escape negative selection.

Journal Article↗
PubMed2023

Pervasive correlations between causal disease effects of proximal SNPs vary with functional annotations and implicate stabilizing selection.

The genetic architecture of human diseases and complex traits has been extensively studied, but little is known about the relationship of causal disease effect sizes between proximal SNPs, which have largely been assumed to be independent. We introduce a new method, LD SNP-pair effect correlation regression (LDSPEC), to estimate the correlation of causal disease effect sizes of derived alleles between proximal SNPs, depending on their allele frequencies, LD, and functional annotations; LDSPEC produced robust estimates in simulations across various genetic architectures. We applied LDSPEC to 70 diseases and complex traits from the UK Biobank (average N=306K), meta-analyzing results across diseases/traits. We detected significantly nonzero effect correlations for proximal SNP pairs (e.g., -0.37±0.09 for low-frequency positive-LD 0-100bp SNP pairs) that decayed with distance (e.g., -0.07±0.01 for low-frequency positive-LD 1-10kb), varied with allele frequency (e.g., -0.15±0.04 for common positive-LD 0-100bp), and varied with LD between SNPs (e.g., +0.12±0.05 for common negative-LD 0-100bp) (because we consider derived alleles, positive-LD and negative-LD SNP pairs may yield very different results). We further determined that SNP pairs with shared functions had stronger effect correlations that spanned longer genomic distances, e.g., -0.37±0.08 for low-frequency positive-LD same-gene promoter SNP pairs (average genomic distance of 47kb (due to alternative splicing)) and -0.32±0.04 for low-frequency positive-LD H3K27ac 0-1kb SNP pairs. Consequently, SNP-heritability estimates were substantially smaller than estimates of the sum of causal effect size variances across all SNPs (ratio of 0.87±0.02 across diseases/traits), particularly for certain functional annotations (e.g., 0.78±0.01 for common Super enhancer SNPs)-even though these quantities are widely assumed to be equal. We recapitulated our findings via forward simulations with an evolutionary model involving stabilizing selection, implicating the action of linkage masking, whereby haplotypes containing linked SNPs with opposite effects on disease have reduced effects on fitness and escape negative selection.

Journal Article↗
PubMed1998

[Diagnosis of hypertrophic cardiomyopathy. Validation of criteria using genetics].

Our understanding of the genetics of hypertrophic cardiomyopathy has progressed significantly over the last few years. Seven genes have been identified as being responsible for familiar forms of the disease. This information has been useful, mainly in the elucidation of the physiopathology but clinical implications are also beginning to see the light of day. One example is the assessment of the pertinence of traditional diagnostic criteria. The originality of these studies lies in the analysis of familial hypertrophic cardiomyopathies in which the causal mutation has been identified, using the genetic status of the individual as the reference. The conventional diagnostic criteria then appear to be very specific but not very sensitive, inciting further analysis of additional criteria which might improve the diagnostic performance of routine investigations. This also opens the door to a comprehensive revision of the diagnostic criteria of this disease.

Cardiomegaly↗
PubMed2002

Genome scan among Nigerians linking blood pressure to chromosomes 2, 3, and 19.

An understanding of the genetic influences on hypertension would help unravel the pathophysiology of this complex disorder and improve our understanding of causal mechanisms. Contemporary technology makes it possible to examine enough genetic markers to support a generalized search across the entire genome for candidate regions. In the present study, a family set was recruited from southwest Nigeria, and 378 microsatellite markers were typed on 792 individuals in 196 families. Multipoint variance component analysis identified linkage signals (logarithm of the odds [LOD] 1.74, P<0.0023) for systolic blood pressure on 19p (D19S714) and 19q (D19S246), whereas for diastolic blood pressure, linkage was observed on 2p (D2S1790), 3p (D3S1304), 5q (D5S1462), 7p (D7S3046), 7q (D7S821), and 10q (D10S1221). Other regions of interest (1.18<LOD<1.74, 0.0023<P<0.01) were found on chromosomes 1, 6, 8, 9, and 11. These results provide additional evidence of linkage between blood pressure and several genomic regions reported in previous studies. Some of these regions additionally harbor hypertension candidate genes. Although evidence of linkage for blood pressure has been very slow to accumulate, even in comparison to other complex traits, the sum of current evidence appears to implicate, in particular, 2p, 3p, and 19p. Study designs that make it possible to confirm these results with association analysis and narrow the genomic interval are needed in order to make progress in this field.

Adolescent↗
PubMed2003

Association of multidrug resistance in epilepsy with a polymorphism in the drug-transporter gene ABCB1.

BACKGROUND: One third of patients with epilepsy have drug-resistant epilepsy, which is associated with an increased risk of death and debilitating psychosocial consequences. Because this form is resistant to multiple antiepileptic drugs, the mode of resistance must be nonspecific, involving drug-efflux transporters such as ATP-binding cassette sub-family B member 1 (ABCB1, also known as MDR1 and P-glycoprotein 170). We hypothesized that the CC genotype at the ABCB1 C3435T polymorphism, which is associated with increased expression of the protein, influences the response to antiepileptic-drug treatment. METHODS: ABCB1 3435 was genotyped in 315 patients with epilepsy, classified as drug-resistant in 200 and drug-responsive in 115, and 200 control subjects without epilepsy. Recently devised methods were used to control for population stratification, and linkage disequilibrium was calculated across the gene. RESULTS: As compared with patients with drug-responsive epilepsy, patients with drug-resistant epilepsy were more likely to have the CC genotype at ABCB1 3435 than the TT genotype (odds ratio, 2.66; 95 percent confidence interval, 1.32 to 5.38; P=0.006). There was no genetic stratification between the two groups of patients. The polymorphism fell within an extensive block of linkage disequilibrium spanning much or all of the gene, implying that the polymorphism may not itself be causal but rather may be linked with the causal variant. CONCLUSIONS: These pharmacogenomic results identify a genetic factor associated with resistance to antiepileptic drugs.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2006

Role of discs large homolog 5.

In 2004, an association of genetic variation in the discs large homolog 5 (DLG5) gene with inflammatory bowel disease (IBD) was described in two large European study samples. The initial report of DLG5 as a novel IBD susceptibility gene sparked a multitude of studies investigating its effect on CD and IBD, respectively, leading to controversial findings and ongoing discussions concerning the validity of the initial association finding and its role in the aetiology of Crohn disease. This review aims to summarize the current state of knowledge and to place the reported findings in the context of current concepts of complex diseases. This includes aspects of statistical power, phenotype differences and genetic heterogeneity between different populations as well as gene-gene and gene-environment interactions.

Asian People↗
PubMed2024

A functional genomic framework to elucidate novel causal metabolic dysfunction-associated fatty liver disease genes.

BACKGROUND AND AIMS: Metabolic dysfunction-associated fatty liver disease (MASLD) is the most prevalent chronic liver pathology in western countries, with serious public health consequences. Efforts to identify causal genes for MASLD have been hampered by the relative paucity of human data from gold standard magnetic resonance quantification of hepatic fat. To overcome insufficient sample size, genome-wide association studies using MASLD surrogate phenotypes have been used, but only a small number of loci have been identified to date. In this study, we combined genome-wide association studies of MASLD composite surrogate phenotypes with genetic colocalization studies followed by functional in vitro screens to identify bona fide causal genes for MASLD. APPROACH AND RESULTS: We used the UK Biobank to explore the associations of our novel MASLD score, and genetic colocalization to prioritize putative causal genes for in vitro validation. We created a functional genomic framework to study MASLD genes in vitro using CRISPRi. Our data identify VKORC1 , TNKS , LYPLAL1 , and GPAM as regulators of lipid accumulation in hepatocytes and suggest the involvement of VKORC1 in the lipid storage related to the development of MASLD. CONCLUSIONS: Complementary genetic and genomic approaches are useful for the identification of MASLD genes. Our data supports VKORC1 as a bona fide MASLD gene. We have established a functional genomic framework to study at scale putative novel MASLD genes from human genetic association studies.

Humans↗
PubMed2002

Genetics of parkinsonism.

Parkinson's disease (PD) was noted to have a familial component as early as 1880 (Leroux, 1880). More recently, the discovery of several genetic factors influencing parkinsonism has emphasized the importance of heredity in PD. The clinical spectrum of familial parkinsonism is wide; it includes not only PD, but also dementia with Lewy bodies (DLB), progressive supranuclear palsy (PSP), essential tremor, and other disorders. In the general population, it is likely that PD results from combined genetic and environmental factors, most of which are not yet known. The discovery of causal mutations in the gene for alpha-synuclein, parkin, and of genetic linkages to chromosomes 2p4, 4p5, and three loci on 1q6-8 have revolutionized PD research. This review focuses on recent progress in the Mendelian genetics of PD and those diseases in which parkinsonism is a prominent feature, and considers how these discoveries modify our beliefs regarding the etiology and pathogenesis of these disorders.

Chromosome Mapping↗