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Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our earlier discovery sample of 101,069 individuals to 293,723 individuals, and a replication study in an independent sample of 111,349 individuals from the UK Biobank. We identify 74 genome-wide significant loci associated with the number of years of schooling completed. Single-nucleotide polymorphisms associated with educational attainment are disproportionately found in genomic regions regulating gene expression in the fetal brain. Candidate genes are preferentially expressed in neural tissue, especially during the prenatal period, and enriched for biological pathways involved in neural development. Our findings demonstrate that, even for a behavioural phenotype that is mostly environmentally determined, a well-powered GWAS identifies replicable associated genetic variants that suggest biologically relevant pathways. Because educational attainment is measured in large numbers of individuals, it will continue to be useful as a proxy phenotype in efforts to characterize the genetic influences of related phenotypes, including cognition and neuropsychiatric diseases.
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Encéfalo/metabolismo , Escolaridade , Feto/metabolismo , Regulação da Expressão Gênica/genética , Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único/genética , Doença de Alzheimer/genética , Transtorno Bipolar/genética , Cognição , Biologia Computacional , Interação Gene-Ambiente , Humanos , Anotação de Sequência Molecular , Esquizofrenia/genética , Reino UnidoRESUMO
The development of high-throughput genomic technologies has impacted many areas of genetic research. While many applications of these technologies focus on the discovery of genes involved in disease from population samples, applications of genomic technologies to an individual's genome or personal genomics have recently gained much interest. One such application is the identification of relatives from genetic data. In this application, genetic information from a set of individuals is collected in a database, and each pair of individuals is compared in order to identify genetic relatives. An inherent issue that arises in the identification of relatives is privacy. In this article, we propose a method for identifying genetic relatives without compromising privacy by taking advantage of novel cryptographic techniques customized for secure and private comparison of genetic information. We demonstrate the utility of these techniques by allowing a pair of individuals to discover whether or not they are related without compromising their genetic information or revealing it to a third party. The idea is that individuals only share enough special-purpose cryptographically protected information with each other to identify whether or not they are relatives, but not enough to expose any information about their genomes. We show in HapMap and 1000 Genomes data that our method can recover first- and second-order genetic relationships and, through simulations, show that our method can identify relationships as distant as third cousins while preserving privacy.
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Privacidade Genética , Pesquisa em Genética , Genoma Humano , Família , Genômica , Projeto HapMap , Projeto Genoma Humano , HumanosRESUMO
We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcripts show a significant tissue-specific expression bias. By identifying candidate functional variants at 718 quantitative trait loci we show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus. These sequences provide a starting point for a new era in the functional analysis of a key model organism.
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Regulação da Expressão Gênica/genética , Variação Genética/genética , Genoma/genética , Camundongos Endogâmicos/genética , Camundongos/genética , Fenótipo , Alelos , Animais , Animais de Laboratório/genética , Genômica , Camundongos/classificação , Camundongos Endogâmicos C57BL/genética , Filogenia , Locos de Características Quantitativas/genéticaRESUMO
The use of mixed models to determine narrow-sense heritability and related quantities such as SNP heritability has received much recent attention. Less attention has been paid to the inherent variability in these estimates. One approach for quantifying variability in estimates of heritability is a frequentist approach, in which heritability is estimated using maximum likelihood and its variance is quantified through an asymptotic normal approximation. An alternative approach is to quantify the uncertainty in heritability through its Bayesian posterior distribution. In this paper, we develop the latter approach, make it computationally efficient and compare it to the frequentist approach. We show theoretically that, for a sufficiently large sample size and intermediate values of heritability, the two approaches provide similar results. Using the Atherosclerosis Risk in Communities cohort, we show empirically that the two approaches can give different results and that the variance/uncertainty can remain large.
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Padrões de Herança , Modelos Genéticos , Característica Quantitativa Herdável , Incerteza , Algoritmos , Aterosclerose/genética , Teorema de Bayes , Estudos de Coortes , Feminino , Genótipo , Humanos , Masculino , Fenótipo , Polimorfismo de Nucleotídeo Único , Grupos Raciais/genética , Fatores de RiscoRESUMO
The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (â¼ 1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome.
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Antimaláricos/farmacologia , Resistência a Medicamentos/genética , Loci Gênicos , Plasmodium falciparum/genética , Etanolaminas/farmacologia , Fluorenos/farmacologia , Dosagem de Genes , Expressão Gênica , Estudos de Associação Genética , Variação Genética , Genótipo , Haplótipos , Desequilíbrio de Ligação , Lumefantrina , Malária Falciparum/parasitologia , Malária Falciparum/prevenção & controle , Mefloquina/farmacologia , Fenantrenos/farmacologia , Plasmodium falciparum/efeitos dos fármacos , Polimorfismo de Nucleotídeo Único , Seleção GenéticaRESUMO
Restless legs syndrome (RLS) affects up to 10% of older adults. Their healthcare is impeded by delayed diagnosis and insufficient treatment. To advance disease prediction and find new entry points for therapy, we performed meta-analyses of genome-wide association studies in 116,647 individuals with RLS (cases) and 1,546,466 controls of European ancestry. The pooled analysis increased the number of risk loci eightfold to 164, including three on chromosome X. Sex-specific meta-analyses revealed largely overlapping genetic predispositions of the sexes (rg = 0.96). Locus annotation prioritized druggable genes such as glutamate receptors 1 and 4, and Mendelian randomization indicated RLS as a causal risk factor for diabetes. Machine learning approaches combining genetic and nongenetic information performed best in risk prediction (area under the curve (AUC) = 0.82-0.91). In summary, we identified targets for drug development and repurposing, prioritized potential causal relationships between RLS and relevant comorbidities and risk factors for follow-up and provided evidence that nonlinear interactions are likely relevant to RLS risk prediction.
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Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Síndrome das Pernas Inquietas , Síndrome das Pernas Inquietas/genética , Humanos , Fatores de Risco , Feminino , Masculino , Polimorfismo de Nucleotídeo Único , Análise da Randomização Mendeliana , Aprendizado de MáquinaRESUMO
Many genome-wide association studies have been performed on population cohorts that contain phenotype measurements at multiple time points. However, standard association methodologies only consider one time point. In this paper, we propose a mixed-model-based approach for performing association mapping which utilizes multiple phenotype measurements for each individual. We introduce an analytical approach to calculate statistical power and show that this model leads to increased power when compared to traditional approaches. Moreover, we show that by using this model we are able to differentiate the genetic, environmental, and residual error contributions to the phenotype. Using predictions of these components, we show how the proportion of the phenotype due to environment and genetics can be predicted and show that the ranking of individuals based on these predictions is very accurate. The software implementing this method may be found at http://genetics.cs.ucla.edu/longGWAS/.
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Mapeamento Cromossômico/métodos , Algoritmos , Estudos de Coortes , Simulação por Computador , Estudo de Associação Genômica Ampla , Humanos , Modelos Genéticos , Modelos Estatísticos , Fenótipo , Reprodutibilidade dos Testes , SoftwareRESUMO
MOTIVATION: The analysis of gene coexpression is at the core of many types of genetic analysis. The coexpression between two genes can be calculated by using a traditional Pearson's correlation coefficient. However, unobserved confounding effects may cause inflation of the Pearson's correlation so that uncorrelated genes appear correlated. Many general methods have been suggested, which aim to remove the effects of confounding from gene expression data. However, the residual confounding which is not accounted for by these generic correction procedures has the potential to induce correlation between genes. Therefore, a method that specifically aims to calculate gene coexpression between gene expression arrays, while accounting for confounding effects, is desirable. RESULTS: In this article, we present a statistical model for calculating gene coexpression called mixed model coexpression (MMC), which models coexpression within a mixed model framework. Confounding effects are expected to be encoded in the matrix representing the correlation between arrays, the inter-sample correlation matrix. By conditioning on the information in the inter-sample correlation matrix, MMC is able to produce gene coexpressions that are not influenced by global confounding effects and thus significantly reduce the number of spurious coexpressions observed. We applied MMC to both human and yeast datasets and show it is better able to effectively prioritize strong coexpressions when compared to a traditional Pearson's correlation and a Pearson's correlation applied to data corrected with surrogate variable analysis (SVA). AVAILABILITY: The method is implemented in the R programming language and may be found at http://genetics.cs.ucla.edu/mmc. CONTACT: nfurlott@cs.ucla.edu; eeskin@cs.ucla.edu.
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Expressão Gênica , Modelos Estatísticos , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas , Humanos , Leveduras/genéticaRESUMO
Genome-wide association studies (GWASs) examine the association between genotype and phenotype while adjusting for a set of covariates. Although the covariates may have non-linear or interactive effects, due to the challenge of specifying the model, GWAS often neglect such terms. Here we introduce DeepNull, a method that identifies and adjusts for non-linear and interactive covariate effects using a deep neural network. In analyses of simulated and real data, we demonstrate that DeepNull maintains tight control of the type I error while increasing statistical power by up to 20% in the presence of non-linear and interactive effects. Moreover, in the absence of such effects, DeepNull incurs no loss of power. When applied to 10 phenotypes from the UK Biobank (n = 370K), DeepNull discovered more hits (+6%) and loci (+7%), on average, than conventional association analyses, many of which are biologically plausible or have previously been reported. Finally, DeepNull improves upon linear modeling for phenotypic prediction (+23% on average).
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Estudo de Associação Genômica Ampla/métodos , Fenótipo , Simulação por Computador , Modelos Lineares , Projetos de PesquisaRESUMO
We trained and validated risk prediction models for the three major types of skin cancer- basal cell carcinoma (BCC), squamous cell carcinoma (SCC), and melanoma-on a cross-sectional and longitudinal dataset of 210,000 consented research participants who responded to an online survey covering personal and family history of skin cancer, skin susceptibility, and UV exposure. We developed a primary disease risk score (DRS) that combined all 32 identified genetic and non-genetic risk factors. Top percentile DRS was associated with an up to 13-fold increase (odds ratio per standard deviation increase >2.5) in the risk of developing skin cancer relative to the middle DRS percentile. To derive lifetime risk trajectories for the three skin cancers, we developed a second and age independent disease score, called DRSA. Using incident cases, we demonstrated that DRSA could be used in early detection programs for identifying high risk asymptotic individuals, and predicting when they are likely to develop skin cancer. High DRSA scores were not only associated with earlier disease diagnosis (by up to 14 years), but also with more severe and recurrent forms of skin cancer.
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Carcinoma Basocelular/epidemiologia , Carcinoma de Células Escamosas/epidemiologia , Melanoma/epidemiologia , Modelos Estatísticos , Recidiva Local de Neoplasia/epidemiologia , Neoplasias Cutâneas/epidemiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Carcinoma Basocelular/etiologia , Carcinoma Basocelular/patologia , Carcinoma de Células Escamosas/etiologia , Estudos Transversais , Conjuntos de Dados como Assunto , Triagem e Testes Direto ao Consumidor/estatística & dados numéricos , Feminino , Seguimentos , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Incidência , Estudos Longitudinais , Masculino , Anamnese , Melanoma/etiologia , Melanoma/patologia , Pessoa de Meia-Idade , Recidiva Local de Neoplasia/etiologia , Recidiva Local de Neoplasia/patologia , Razão de Chances , Estudos Prospectivos , Medição de Risco/métodos , Fatores de Risco , Pele/patologia , Pele/efeitos da radiação , Neoplasias Cutâneas/etiologia , Neoplasias Cutâneas/patologia , Inquéritos e Questionários/estatística & dados numéricos , Raios Ultravioleta/efeitos adversos , População Branca/genéticaRESUMO
Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.
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BACKGROUND: Clinical genetic testing for inherited predisposition to venous thromboembolism (VTE) is common among patients and their families. However, there is incomplete consensus about which individuals should receive testing, and the relative risks and benefits. METHODS: We assessed outcomes of receiving direct-to-consumer (DTC) results for the two most common genetic risk factors for VTE, factor V Leiden in the F5 gene (FVL) and prothrombin 20210G>A in the F2 gene (PT). Two thousand three hundred fifty-four customers (1244 variant-positive and 1110 variant-negative individuals) of the personal genetics company 23andMe, Inc., who had received results online for F5 and F2 variants, participated in an online survey-based study. Participants responded to questions about perception of VTE risk, discussion of results with healthcare providers (HCPs) and recommendations received, actions taken to control risk, emotional responses to receiving risk results, and perceived value of the information. RESULTS: Most participants (90% of variant-positive individuals, 99% of variant-negative individuals) had not previously been tested for F5 and/or F2 variants. The majority of variant-positive individuals correctly perceived that they were at higher than average risk for developing VTE. These individuals reported moderate rates of discussing results with HCPs (41%); receiving prevention advice from HCPs (31%), and making behavioral changes to control risk (e.g., exercising more, 30%). A minority (36%) of variant-positive individuals worried more after receiving VTE results. Nevertheless, most participants reported that knowing their risk had been an advantage (78% variant-positive and 58% variant-negative) and were satisfied knowing their genetic probability for VTE (81% variant-positive and 67% variant-negative). CONCLUSION: Consumers reported moderate rates of behavioral change and perceived personal benefit from receiving DTC genetic results for VTE risk.
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Atitude , Triagem e Testes Direto ao Consumidor/psicologia , Fator V/genética , Testes Genéticos/estatística & dados numéricos , Protrombina/genética , Adulto , Triagem e Testes Direto ao Consumidor/estatística & dados numéricos , Feminino , Frequência do Gene , Comportamentos Relacionados com a Saúde , Heterozigoto , Humanos , Masculino , Pacientes/psicologiaRESUMO
MOTIVATION: Motif Tool Manager is a web-based framework for comparing and combining different approaches to discover novel DNA motifs. It comes with a set of five well-known approaches to motif discovery. It provides an easy mechanism for adding new motif finding tools to the framework through a web-interface and a minimal setup of the tools on the server. Users can execute the tools through the web-based framework and compare results from such executions. The framework provides a basic mechanism for identifying the most similar motif candidates found by a majority of themotif finding tools. AVAILABILITY: http://cetus.cs.memphis.edu/motif
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Análise de Sequência de DNA/métodos , Software , Algoritmos , DNA/química , InternetRESUMO
R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely used R/qtl software package to include multiparent populations derived from more than two founder strains, such as the Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. R/qtl2 is designed to handle modern high-density genotyping data and high-dimensional molecular phenotypes, including gene expression and proteomics. R/qtl2 includes the ability to perform genome scans using a linear mixed model to account for population structure, and also includes features to impute SNPs based on founder strain genomes and to carry out association mapping. The R/qtl2 software provides all of the basic features needed for QTL mapping, including graphical displays and summary reports, and it can be extended through the creation of add-on packages. R/qtl2, which is free and open source software written in the R and C++ programming languages, comes with a test framework.
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Mapeamento Cromossômico/métodos , Estudo de Associação Genômica Ampla/métodos , Técnicas de Genotipagem/métodos , Locos de Características Quantitativas , Software , Animais , CamundongosRESUMO
In the version of the paper initially published, information on competing interests for author Benjamin M. Neale was missing. The 'Competing interests' statement should have included the sentence 'B.M.N. is on the Scientific Advisory Board of Deep Genomics'.
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In the version of the paper initially published, no competing interests were declared. The 'Competing interests' statement should have stated that B.M.N. is on the Scientific Advisory Board of Deep Genomics. The error has been corrected in the HTML and PDF versions of the article.
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Cutaneous squamous cell carcinoma (cSCC) is a common skin cancer with genetic susceptibility loci identified in recent genome-wide association studies (GWAS). Transcriptome-wide association studies (TWAS) using imputed gene expression levels can identify additional gene-level associations. Here we impute gene expression levels in 6891 cSCC cases and 54,566 controls in the Kaiser Permanente Genetic Epidemiology Research in Adult Health and Aging (GERA) cohort and 25,558 self-reported cSCC cases and 673,788 controls from 23andMe. In a discovery-validation study, we identify 19 loci containing 33 genes whose imputed expression levels are associated with cSCC at false discovery rate < 10% in the GERA cohort and validate 15 of these candidate genes at Bonferroni significance in the 23andMe dataset, including eight genes in five novel susceptibility loci and seven genes in four previously associated loci. These results suggest genetic mechanisms contributing to cSCC risk and illustrate advantages and disadvantages of TWAS as a supplement to traditional GWAS analyses.
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Carcinoma de Células Escamosas/genética , Regulação Neoplásica da Expressão Gênica , Loci Gênicos , Predisposição Genética para Doença , Neoplasias Cutâneas/genética , Bases de Dados Genéticas , Humanos , Polimorfismo de Nucleotídeo Único/genética , Reprodutibilidade dos TestesRESUMO
Over the past few years, genome-wide association studies have identified many trait-associated loci that have different effects on females and males, which increased attention to the genetic architecture differences between the sexes. The between-sex differences in genetic architectures can cause a variety of phenomena such as differences in the effect sizes at trait-associated loci, differences in the magnitudes of polygenic background effects, and differences in the phenotypic variances. However, current association testing approaches for dealing with sex, such as including sex as a covariate, cannot fully account for these phenomena and can be suboptimal in statistical power. We present a novel association mapping framework, MetaSex, that can comprehensively account for the genetic architecture differences between the sexes. Through simulations and applications to real data, we show that our framework has superior performance than previous approaches in association mapping.