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1.
Behav Genet ; 2019 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-31493278

RESUMO

There is increasing interest within the genetics community in estimating the relative contribution of parental genetic effects on offspring phenotypes. Here we describe the user-friendly M-GCTA software package used to estimate the proportion of phenotypic variance explained by maternal (or alternatively paternal) and offspring genotypes on offspring phenotypes. The tool requires large studies where genome-wide genotype data are available on mother- (or alternatively father-) offspring pairs. The software includes several options for data cleaning and quality control, including the ability to detect and automatically remove cryptically related pairs of individuals. It also allows users to construct genetic relationship matrices indexing genetic similarity across the genome between parents and offspring, enabling the estimation of variance explained by maternal (or alternatively paternal) and offspring genetic effects. We evaluated the performance of the software using a range of data simulations and estimated the computing time and memory requirements. We demonstrate the use of M-GCTA on previously analyzed birth weight data from two large population based birth cohorts, the Avon Longitudinal Study of Parents and Children (ALSPAC) and the Norwegian Mother and Child Cohort Study (MoBa). We show how genetic variation in birth weight is predominantly explained by fetal genetic rather than maternal genetic sources of variation.

2.
JAMA ; 2019 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-31475726

RESUMO

Importance: The relationship between exposure to lower low-density lipoprotein cholesterol (LDL-C) and lower systolic blood pressure (SBP) with the risk of cardiovascular disease has not been reliably quantified. Objective: To assess the association of lifetime exposure to the combination of both lower LDL-C and lower SBP with the lifetime risk of cardiovascular disease. Design, Setting, and Participants: Among 438 952 participants enrolled in the UK Biobank between 2006 and 2010 and followed up through 2018, genetic LDL-C and SBP scores were used as instruments to divide participants into groups with lifetime exposure to lower LDL-C, lower SBP, or both. Differences in plasma LDL-C, SBP, and cardiovascular event rates between the groups were compared to estimate associations with lifetime risk of cardiovascular disease. Exposures: Differences in plasma LDL-C and SBP compared with participants with both genetic scores below the median. Genetic risk scores higher than the median were associated with lower LDL-C and lower SBP. Main Outcomes and Measures: Odds ratio (OR) for major coronary events, defined as coronary death, nonfatal myocardial infarction, or coronary revascularization. Results: The mean age of the 438 952 participants was 65.2 years (range, 40.4-80.0 years), 54.1% were women, and 24 980 experienced a first major coronary event. Compared with the reference group, participants with LDL-C genetic scores higher than the median had 14.7-mg/dL lower LDL-C levels and an OR of 0.73 for major coronary events (95% CI, 0.70-0.75; P < .001). Participants with SBP genetic scores higher than the median had 2.9-mm Hg lower SBP and an OR of 0.82 for major coronary events (95% CI, 0.79-0.85, P < .001). Participants in the group with both genetic scores higher than the median had 13.9-mg/dL lower LDL-C, 3.1-mm Hg lower SBP, and an OR of 0.61 for major coronary events (95% CI, 0.59-0.64; P < .001). In a 4 × 4 factorial analysis, exposure to increasing genetic risk scores and lower LDL-C levels and SBP was associated with dose-dependent lower risks of major coronary events. In a meta-regression analysis, combined exposure to 38.67-mg/dL lower LDL-C and 10-mm Hg lower SBP was associated with an OR of 0.22 for major coronary events (95% CI, 0.17-0.26; P < .001), and 0.32 for cardiovascular death (95% CI, 0.25-0.40; P < .001). Conclusions and Relevance: Lifelong genetic exposure to lower levels of low-density lipoprotein cholesterol and lower systolic blood pressure was associated with lower cardiovascular risk. However, these findings cannot be assumed to represent the magnitude of benefit achievable from treatment of these risk factors.

4.
Hum Mol Genet ; 2019 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-31276585

RESUMO

Immune mediated diseases (IMDs) arise when tolerance is lost and chronic inflammation is targeted towards healthy tissues. Despite their growing prevalence, therapies to treat IMDs are lacking. Cytokines and their receptors orchestrate inflammatory responses by regulating elaborate signaling networks across multiple cell-types; this makes it challenging to pinpoint therapeutically relevant drivers of IMDs. We developed an analytical framework which integrates Mendelian randomization (MR) and multiple-trait colocalization (moloc) analyses to highlight putative cell-specific drivers of IMDs. MR evaluated causal associations between the levels of 10 circulating cytokines and 9 IMDs within human populations. Subsequently, we undertook moloc analyses to assess whether IMD trait, cytokine protein and corresponding gene expression are driven by a shared causal variant. Moreover, we leveraged gene expression data from 3 separate cell-types (monocytes, neutrophils and T cells) to discern whether associations may be attributed to cell-type specific drivers of disease. MR analyses supported a causal role for IL-18 in inflammatory bowel disease (IBD) (P = 1.17 x 10-4) and eczema/dermatitis (P = 2.81 x 10-3), as well as associations between IL-2rα and IL-6R with several other IMDs. Multiple-trait colocalization strengthened evidence of a causal association for these results, as well as providing evidence of a monocyte and neutrophil-driven role for IL-18 in IBD pathogenesis. In contrast, IL-2rα and IL-6R associations were found to be T cell specific. Our analytical pipeline can help to elucidate putative molecular pathways in the pathogeneses of IMDs, which could be applied to other disease contexts.

6.
BMJ ; 365: l2327, 2019 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-31243001

RESUMO

OBJECTIVE: To examine whether sleep traits have a causal effect on risk of breast cancer. DESIGN: Mendelian randomisation study. SETTING: UK Biobank prospective cohort study and Breast Cancer Association Consortium (BCAC) case-control genome-wide association study. PARTICIPANTS: 156 848 women in the multivariable regression and one sample mendelian randomisation (MR) analysis in UK Biobank (7784 with a breast cancer diagnosis) and 122 977 breast cancer cases and 105 974 controls from BCAC in the two sample MR analysis. EXPOSURES: Self reported chronotype (morning or evening preference), insomnia symptoms, and sleep duration in multivariable regression, and genetic variants robustly associated with these sleep traits. MAIN OUTCOME MEASURE: Breast cancer diagnosis. RESULTS: In multivariable regression analysis using UK Biobank data on breast cancer incidence, morning preference was inversely associated with breast cancer (hazard ratio 0.95, 95% confidence interval 0.93 to 0.98 per category increase), whereas there was little evidence for an association between sleep duration and insomnia symptoms. Using 341 single nucleotide polymorphisms (SNPs) associated with chronotype, 91 SNPs associated with sleep duration, and 57 SNPs associated with insomnia symptoms, one sample MR analysis in UK Biobank provided some supportive evidence for a protective effect of morning preference on breast cancer risk (0.85, 0.70, 1.03 per category increase) but imprecise estimates for sleep duration and insomnia symptoms. Two sample MR using data from BCAC supported findings for a protective effect of morning preference (inverse variance weighted odds ratio 0.88, 95% confidence interval 0.82 to 0.93 per category increase) and adverse effect of increased sleep duration (1.19, 1.02 to 1.39 per hour increase) on breast cancer risk (both oestrogen receptor positive and oestrogen receptor negative), whereas evidence for insomnia symptoms was inconsistent. Results were largely robust to sensitivity analyses accounting for horizontal pleiotropy. CONCLUSIONS: Findings showed consistent evidence for a protective effect of morning preference and suggestive evidence for an adverse effect of increased sleep duration on breast cancer risk.


Assuntos
Neoplasias da Mama/epidemiologia , Neoplasias da Mama/etiologia , Sono , Adulto , Idoso , Estudos de Casos e Controles , Ritmo Circadiano , Comorbidade , Fatores de Confusão (Epidemiologia) , Feminino , Estudo de Associação Genômica Ampla , Humanos , Incidência , Análise da Randomização Mendeliana , Pessoa de Meia-Idade , Análise Multivariada , Estudos Prospectivos , Fatores de Risco , Distúrbios do Início e da Manutenção do Sono/epidemiologia , Fatores de Tempo , Reino Unido/epidemiologia
7.
Am J Epidemiol ; 2019 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-31241132

RESUMO

Genetic predisposition may affect neurodevelopmental outcomes of prenatal methylmercury exposure. We examined suspected heterogeneities for modification of exposure-related neurodevelopment in children from the Avon Longitudinal Study of Parents and Children (ALSPAC, 1991-2000), Bristol, United Kingdom. A subgroup (n = 1127 from a pilot study and 1045 from the present study) was identified based on the availability of the mercury concentration of cord tissue as a measure of prenatal methylmercury exposure, data on 247 single-nucleotide polymorphisms (SNPs), as well as the Wechsler Intelligence Scale for Children Intelligence Quotient (IQ) scores. Log10-transformed mercury concentration was positively associated with IQ, but adjustment confounding cofactors attenuated this association. Enhanced interaction with methylmercury was replicated in the new study for the minor allele of rs1042838 (progesterone receptor) (Beta; 95% Confidence Interval) = (-11.8; -23.0, -0.6) (P-for-interaction = 0.004) and weakly for rs662 (paraoxonase 1) (-3.6; -11.4, 4.3) (P = 0.117). In the joint sample, new interacting single-nucleotide polymorphisms (SNPs) were discovered in relation to superoxide dismutase 2, ATP binding cassette subfamily A member 1, and metallothionein 1M genes. While the low-level prenatal exposure to methylmercury was not associated with child cognition, progesterone receptor rs1042838 minor alleles revealed a negative association of mercury exposure with IQ.

8.
Cell ; 177(3): 587-596.e9, 2019 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-31002795

RESUMO

Severe obesity is a rapidly growing global health threat. Although often attributed to unhealthy lifestyle choices or environmental factors, obesity is known to be heritable and highly polygenic; the majority of inherited susceptibility is related to the cumulative effect of many common DNA variants. Here we derive and validate a new polygenic predictor comprised of 2.1 million common variants to quantify this susceptibility and test this predictor in more than 300,000 individuals ranging from middle age to birth. Among middle-aged adults, we observe a 13-kg gradient in weight and a 25-fold gradient in risk of severe obesity across polygenic score deciles. In a longitudinal birth cohort, we note minimal differences in birthweight across score deciles, but a significant gradient emerged in early childhood and reached 12 kg by 18 years of age. This new approach to quantify inherited susceptibility to obesity affords new opportunities for clinical prevention and mechanistic assessment.

9.
Am J Epidemiol ; 2019 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-30877306

RESUMO

In the last third of the 20th century aetiological epidemiology within high-income country academia shifted its primary concern from attempting to tackle the apparent epidemic of "non-communicable disease" to an increasing focus on developing statistical and causal inference methodologies. This move was mutually constitutive with the failure of applied epidemiology to make major progress, with many of the advances in understanding the causes of "non-communicable diseases" coming from outside the discipline, whilst ironically revealing the infectious origins of several major conditions. Conversely, there were many examples of epidemiological studies promoting ineffective interventions, and little evident attempt to account for such failure. Major advances in concrete understanding of disease aetiology have been driven by a willingness to learn about, and incorporate, developments in biology and other cognate disciplines into epidemiology. If fundamental epidemiological principles regarding the rooting of disease risk within populations are retained, the combination of recent methodological developments with increased biological understanding and data sciences capability should herald in a fruitful post-"Modern Epidemiology" world.

10.
Neurology ; 92(16): e1803-e1810, 2019 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-30894442

RESUMO

OBJECTIVE: To investigate the potential for a causal effect of age at puberty on multiple sclerosis (MS) susceptibility using a mendelian randomization (MR) approach. METHODS: We used 372 genetic variants strongly associated with age at menarche in a genome-wide association study (GWAS) involving 329,245 women. The genetic architecture of pubertal timing across both sexes is highly correlated (genetic correlation [r g] = 0.75, p = 1.2 × 10-79), allowing these variants to provide reliable insight into pubertal timing in males as well. The effect of pubertal timing on risk of MS was measured with summary statistics from a GWAS of 14,802 cases with MS and 26,703 controls from the International Multiple Sclerosis Genetics Consortium. Multivariable MR controlling for effects of body mass index (BMI) using genetic data from additional consortia investigated whether pubertal effects on MS were dependent on weight status. RESULTS: A 1-year increase in genetically predicted age at puberty decreased odds of MS by 8% (odds ratio [OR] 0.92, 95% confidence interval [CI] 0.86-0.99, p = 0.03). However, multivariable MR analysis showed that after accounting for effects on adult BMI, the association of age at puberty with MS susceptibility attenuated (OR 0.96, 95% CI 0.88-1.04, p = 0.36). Similar results were obtained when childhood BMI was incorporated. Sensitivity analyses provided no evidence of major bias from genetic pleiotropy. CONCLUSIONS: We found support for an association between higher age at puberty and decreased risk of MS with a magnitude comparable to that reported in observational studies. This effect appears to be largely mediated by the strong association between age at puberty and obesity. A large causal effect of pubertal timing independent of BMI is unlikely.

11.
Epidemiology ; 30(2): 246-255, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30721168

RESUMO

BACKGROUND: Childhood and adolescent mortality accounts for a substantial proportion of years lost prematurely. Reducing childhood and adolescent mortality relies on knowing characteristics of those at elevated risk of dying young. We therefore aimed to identify such characteristics; our main hypothesis is that psychosocial adversity in infancy is linked to increased mortality rates in childhood and adolescence. METHODS: We conducted a register-based cohort study involving all 1,549,581 children born to Danish-born parents in Denmark between 1 January 1981 and 31 December 2010. For each infant, we extracted data relevant to Rutter's indicators of adversity (low social class, parents not cohabiting, large family size, paternal criminality, maternal mental disorder, and placement in out-of-home care). Follow-up began on the cohort member's first birthday. We estimated the association between adversity score (the number of Rutter's indicators of adversity present in infancy) and death via. Cox regression. RESULTS: During follow-up (18,874,589 person-years), 2,081 boys and 1,420 girls died before or on their 18th birthday. The hazard ratios for death were 2.3 (95% CI = 1.9, 2.9) and 2.1 (95% CI = 1.6, 2.7) for boys and girls with adversity scores of 3-6 compared with those with a score of 0. These associations were driven by causes of death with known links to psychosocial adversity. CONCLUSION: While absolute mortality rates were low, infants with adversity scores of 3-6 were approximately twice as likely to die prematurely compared with infants with adversity scores of 0. Whether these associations generalize to other countries should be subjected to further study.


Assuntos
Mortalidade da Criança/tendências , Características da Família , Classe Social , Adolescente , Criança , Criança Acolhida , Pré-Escolar , Estudos de Coortes , Dinamarca/epidemiologia , Feminino , Humanos , Lactente , Masculino , Saúde Mental , Mortalidade , Comportamento Paterno
12.
Eur Respir J ; 53(4)2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30765504

RESUMO

RATIONALE: We aimed to identify differentially methylated regions (DMRs) in cord blood DNA associated with childhood lung function, asthma and chronic obstructive pulmonary disease (COPD) across the life course. METHODS: We meta-analysed epigenome-wide data of 1688 children from five cohorts to identify cord blood DMRs and their annotated genes, in relation to forced expiratory volume in 1 s (FEV1), FEV1/forced vital capacity (FVC) ratio and forced expiratory flow at 75% of FVC at ages 7-13 years. Identified DMRs were explored for associations with childhood asthma, adult lung function and COPD, gene expression and involvement in biological processes. RESULTS: We identified 59 DMRs associated with childhood lung function, of which 18 were associated with childhood asthma and nine with COPD in adulthood. Genes annotated to the top 10 identified DMRs were HOXA5, PAOX, LINC00602, ABCA7, PER3, CLCA1, VENTX, NUDT12, PTPRN2 and TCL1A. Differential gene expression in blood was observed for 32 DMRs in childhood and 18 in adulthood. Genes related with 16 identified DMRs were associated with respiratory developmental or pathogenic pathways. INTERPRETATION: Our findings suggest that the epigenetic status of the newborn affects respiratory health and disease across the life course.

13.
Epigenomics ; 11(2): 133-145, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30638414

RESUMO

AIM: To determine if nonsyndromic cleft lip with or without cleft palate (nsCL/P) genetic risk variants influence liability to nsCL/P through gene regulation pathways, such as those involving DNA methylation. MATERIALS & METHODS: nsCL/P genetic summary data and methylation data from four studies were used in conjunction with Mendelian randomization and joint likelihood mapping to investigate potential mediation of nsCL/P genetic variants. RESULTS & CONCLUSION: Evidence was found at VAX1 (10q25.3), LOC146880 (17q23.3) and NTN1 (17p13.1), that liability to nsCL/P and variation in DNA methylation might be driven by the same genetic variant, suggesting that genetic variation at these loci may increase liability to nsCL/P by influencing DNA methylation. Follow-up analyses using different tissues and gene expression data provided further insight into possible biological mechanisms.

14.
Nat Commun ; 10(1): 29, 2019 01 03.
Artigo em Inglês | MEDLINE | ID: mdl-30604766

RESUMO

Chronic kidney disease (CKD) affects ~10% of the global population, with considerable ethnic differences in prevalence and aetiology. We assemble genome-wide association studies of estimated glomerular filtration rate (eGFR), a measure of kidney function that defines CKD, in 312,468 individuals of diverse ancestry. We identify 127 distinct association signals with homogeneous effects on eGFR across ancestries and enrichment in genomic annotations including kidney-specific histone modifications. Fine-mapping reveals 40 high-confidence variants driving eGFR associations and highlights putative causal genes with cell-type specific expression in glomerulus, and in proximal and distal nephron. Mendelian randomisation supports causal effects of eGFR on overall and cause-specific CKD, kidney stone formation, diastolic blood pressure and hypertension. These results define novel molecular mechanisms and putative causal genes for eGFR, offering insight into clinical outcomes and routes to CKD treatment development.


Assuntos
Taxa de Filtração Glomerular/genética , Hipertensão/genética , Cálculos Renais/genética , Rim/fisiopatologia , Insuficiência Renal Crônica/genética , Adulto , Idoso , Pressão Sanguínea/genética , Grupos Étnicos/genética , Feminino , Loci Gênicos/genética , Estudo de Associação Genômica Ampla , Código das Histonas/genética , Histonas/metabolismo , Humanos , Hipertensão/etnologia , Hipertensão/fisiopatologia , Cálculos Renais/etnologia , Cálculos Renais/fisiopatologia , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único , Insuficiência Renal Crônica/etnologia , Insuficiência Renal Crônica/fisiopatologia
15.
Nat Commun ; 10(1): 333, 2019 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-30659178

RESUMO

Large studies use genotype data to discover genetic contributions to complex traits and infer relationships between those traits. Co-incident geographical variation in genotypes and health traits can bias these analyses. Here we show that single genetic variants and genetic scores composed of multiple variants are associated with birth location within UK Biobank and that geographic structure in genotype data cannot be accounted for using routine adjustment for study centre and principal components derived from genotype data. We find that major health outcomes appear geographically structured and that coincident structure in health outcomes and genotype data can yield biased associations. Understanding and accounting for this phenomenon will be important when making inference from genotype data in large studies.


Assuntos
Bancos de Espécimes Biológicos , Epidemiologia , Genótipo , Herança Multifatorial , Variação Genética , Estudo de Associação Genômica Ampla , Geografia , Humanos , Fenótipo , Gestantes , Alinhamento de Sequência , Reino Unido
18.
Nat Genet ; 51(2): 230-236, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30664745

RESUMO

Osteoarthritis is the most common musculoskeletal disease and the leading cause of disability globally. Here, we performed a genome-wide association study for osteoarthritis (77,052 cases and 378,169 controls), analyzing four phenotypes: knee osteoarthritis, hip osteoarthritis, knee and/or hip osteoarthritis, and any osteoarthritis. We discovered 64 signals, 52 of them novel, more than doubling the number of established disease loci. Six signals fine-mapped to a single variant. We identified putative effector genes by integrating expression quantitative trait loci (eQTL) colocalization, fine-mapping, and human rare-disease, animal-model, and osteoarthritis tissue expression data. We found enrichment for genes underlying monogenic forms of bone development diseases, and for the collagen formation and extracellular matrix organization biological pathways. Ten of the likely effector genes, including TGFB1 (transforming growth factor beta 1), FGF18 (fibroblast growth factor 18), CTSK (cathepsin K), and IL11 (interleukin 11), have therapeutics approved or in clinical trials, with mechanisms of action supportive of evaluation for efficacy in osteoarthritis.


Assuntos
Predisposição Genética para Doença/genética , Osteoartrite do Quadril/genética , Adulto , Idoso , Bancos de Espécimes Biológicos , Estudos de Casos e Controles , Feminino , Estudo de Associação Genômica Ampla/métodos , Humanos , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Reino Unido
19.
Nat Hum Behav ; 2(11): 867-880, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30525112

RESUMO

Success in school and the labour market relies on more than high intelligence. Associations between "non-cognitive" skills in childhood, such as attention, self-regulation, and perseverance, and later outcomes have been widely investigated. In a systematic review of this literature, we screened 9553 publications, reviewed 554 eligible publications, and interpreted results from 222 better quality publications. Better quality publications comprised randomised experimental and quasi-experimental studies (EQIs), and observational studies that made reasonable attempts to control confounding. For academic achievement outcomes there were 26 EQI publications but only 14 were available for meta-analysis with effects ranging from 0.16 to 0.37SD. However, within sub-domains effects were heterogeneous. The 95% prediction interval for literacy was consistent with negative, null and positive effects (-0.13 to 0.79). Similarly heterogeneous findings were observed for psychosocial, cognitive and language, and health outcomes. Funnel plots of EQIs and observational studies showed asymmetric distributions and potential for small study bias. There is some evidence that non-cognitive skills associate with improved outcomes. However, there is potential for small study and publication bias that may over-estimate true effects, and heterogeneity of effect estimates spanned negative, null and positive effects. The quality of evidence from EQIs under-pinning this field is lower than optimal and more than a third of observational studies made little or no attempt to control confounding. Interventions designed to develop children's non-cognitive skills could potentially improve outcomes. The inter-disciplinary researchers interested in these skills should take a more strategic and rigorous approach to determine which interventions are most effective.

20.
Nat Commun ; 9(1): 4774, 2018 11 14.
Artigo em Inglês | MEDLINE | ID: mdl-30429480

RESUMO

The total number of acquired melanocytic nevi on the skin is strongly correlated with melanoma risk. Here we report a meta-analysis of 11 nevus GWAS from Australia, Netherlands, UK, and USA comprising 52,506 individuals. We confirm known loci including MTAP, PLA2G6, and IRF4, and detect novel SNPs in KITLG and a region of 9q32. In a bivariate analysis combining the nevus results with a recent melanoma GWAS meta-analysis (12,874 cases, 23,203 controls), SNPs near GPRC5A, CYP1B1, PPARGC1B, HDAC4, FAM208B, DOCK8, and SYNE2 reached global significance, and other loci, including MIR146A and OBFC1, reached a suggestive level. Overall, we conclude that most nevus genes affect melanoma risk (KITLG an exception), while many melanoma risk loci do not alter nevus count. For example, variants in TERC and OBFC1 affect both traits, but other telomere length maintenance genes seem to affect melanoma risk only. Our findings implicate multiple pathways in nevogenesis.

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