RESUMO
BACKGROUND: Identification of imprinted genes, demonstrating a consistent preference towards the paternal or maternal allelic expression, is important for the understanding of gene expression regulation during embryonic development and of the molecular basis of developmental disorders with a parent-of-origin effect. Combining allelic analysis of RNA-Seq data with phased genotypes in family trios provides a powerful method to detect parent-of-origin biases in gene expression. RESULTS: We report findings in 296 family trios from two large studies: 165 lymphoblastoid cell lines from the 1000 Genomes Project and 131 blood samples from the Genome of the Netherlands (GoNL) participants. Based on parental haplotypes, we identified > 2.8 million transcribed heterozygous SNVs phased for parental origin and developed a robust statistical framework for measuring allelic expression. We identified a total of 45 imprinted genes and one imprinted unannotated transcript, including multiple imprinted transcripts showing incomplete parental expression bias that was located adjacent to strongly imprinted genes. For example, PXDC1, a gene which lies adjacent to the paternally expressed gene FAM50B, shows a 2:1 paternal expression bias. Other imprinted genes had promoter regions that coincide with sites of parentally biased DNA methylation identified in the blood from uniparental disomy (UPD) samples, thus providing independent validation of our results. Using the stranded nature of the RNA-Seq data in lymphoblastoid cell lines, we identified multiple loci with overlapping sense/antisense transcripts, of which one is expressed paternally and the other maternally. Using a sliding window approach, we searched for imprinted expression across the entire genome, identifying a novel imprinted putative lncRNA in 13q21.2. Overall, we identified 7 transcripts showing parental bias in gene expression which were not reported in 4 other recent RNA-Seq studies of imprinting. CONCLUSIONS: Our methods and data provide a robust and high-resolution map of imprinted gene expression in the human genome.
Assuntos
Alelos , Expressão Gênica/genética , Impressão Genômica/genética , Haplótipos/genética , Análise Química do Sangue , Linhagem Celular , Humanos , Análise de Sequência de RNARESUMO
The classical twin study has been a powerful heuristic in biomedical, psychiatric and behavioural research for decades. Twin registries worldwide have collected biological material and longitudinal phenotypic data on tens of thousands of twins, providing a valuable resource for studying complex phenotypes and their underlying biology. In this Review, we consider the continuing value of twin studies in the current era of molecular genetic studies. We conclude that classical twin methods combined with novel technologies represent a powerful approach towards identifying and understanding the molecular pathways that underlie complex traits.
Assuntos
Genômica , Estudos em Gêmeos como Assunto , Epigenômica , Feminino , Doenças Genéticas Inatas/genética , Humanos , Estudos Longitudinais , Masculino , Metabolômica , Proteômica , Sistema de RegistrosRESUMO
Human aggression encompasses a wide range of behaviors and is related to many psychiatric disorders. We introduce the different classification systems of aggression and related disorders as a basis for discussing biochemical biomarkers and then present an overview of studies in humans (published between 1990 and 2015) that reported statistically significant associations of biochemical biomarkers with aggression, DSM-IV disorders involving aggression, and their subtypes. The markers are of different types, including inflammation markers, neurotransmitters, lipoproteins, and hormones from various classes. Most studies focused on only a limited portfolio of biomarkers, frequently a specific class only. When integrating the data, it is clear that compounds from several biological pathways have been found to be associated with aggressive behavior, indicating complexity and the need for a broad approach. In the second part of the paper, using examples from the aggression literature and psychiatric metabolomics studies, we argue that a better understanding of aggression would benefit from a more holistic approach such as provided by metabolomics. © 2016 Wiley Periodicals, Inc.
Assuntos
Agressão/classificação , Agressão/fisiologia , Biomarcadores , Manual Diagnóstico e Estatístico de Transtornos Mentais , Humanos , Transtornos Mentais , Metabolômica/métodos , PsiquiatriaRESUMO
BACKGROUND: The association between adiposity and cardiometabolic traits is well known from epidemiological studies. Whilst the causal relationship is clear for some of these traits, for others it is not. We aimed to determine whether adiposity is causally related to various cardiometabolic traits using the Mendelian randomization approach. METHODS AND FINDINGS: We used the adiposity-associated variant rs9939609 at the FTO locus as an instrumental variable (IV) for body mass index (BMI) in a Mendelian randomization design. Thirty-six population-based studies of individuals of European descent contributed to the analyses. Age- and sex-adjusted regression models were fitted to test for association between (i) rs9939609 and BMI (nâ =â 198,502), (ii) rs9939609 and 24 traits, and (iii) BMI and 24 traits. The causal effect of BMI on the outcome measures was quantified by IV estimators. The estimators were compared to the BMI-trait associations derived from the same individuals. In the IV analysis, we demonstrated novel evidence for a causal relationship between adiposity and incident heart failure (hazard ratio, 1.19 per BMI-unit increase; 95% CI, 1.03-1.39) and replicated earlier reports of a causal association with type 2 diabetes, metabolic syndrome, dyslipidemia, and hypertension (odds ratio for IV estimator, 1.1-1.4; all p < 0.05). For quantitative traits, our results provide novel evidence for a causal effect of adiposity on the liver enzymes alanine aminotransferase and gamma-glutamyl transferase and confirm previous reports of a causal effect of adiposity on systolic and diastolic blood pressure, fasting insulin, 2-h post-load glucose from the oral glucose tolerance test, C-reactive protein, triglycerides, and high-density lipoprotein cholesterol levels (all p < 0.05). The estimated causal effects were in agreement with traditional observational measures in all instances except for type 2 diabetes, where the causal estimate was larger than the observational estimate (pâ = â0.001). CONCLUSIONS: We provide novel evidence for a causal relationship between adiposity and heart failure as well as between adiposity and increased liver enzymes.
Assuntos
Adiposidade/genética , Doenças Cardiovasculares/genética , Doenças Cardiovasculares/metabolismo , Análise da Randomização Mendeliana , Característica Quantitativa Herdável , Dioxigenase FTO Dependente de alfa-Cetoglutarato , Índice de Massa Corporal , Estudos de Casos e Controles , Fatores de Confusão Epidemiológicos , Estudos de Associação Genética , Humanos , Metanálise como Assunto , Polimorfismo de Nucleotídeo Único/genética , Proteínas/genéticaRESUMO
Metabolomics is the comprehensive study of metabolites, which are the substrates, intermediate, and end products of cellular metabolism. The heritability of the concentrations of circulating metabolites bears relevance for evaluating their suitability as biomarkers for disease. We report aspects of familial resemblance for the concentrations in human serum of more than 100 metabolites, measured using a targeted metabolomics platform. Age- and sex-corrected monozygotic twin correlations, midparent-offspring regression coefficients, and spouse correlations in subjects from two independent cohorts (Netherlands Twin Register and Leiden Longevity Study) were estimated for each metabolite. In the Netherlands Twin Register subjects, who were largely fasting, we found significant monozygotic twin correlations for 121 out of 123 metabolites. Heritability was confirmed by midparent-offspring regression. For most detected metabolites, the correlations between spouses were considerably lower than those between twins, indicating a contribution of genetic effects to familial resemblance. Remarkably high heritability was observed for free carnitine (monozygotic twin correlation 0.66), for the amino acids serine (monozygotic twin correlation 0.77) and threonine (monozygotic twin correlation 0.64), and for phosphatidylcholine acyl-alkyl C40:3 (monozygotic twin correlation 0.77). For octenoylcarnitine, a consistent point estimate of approximately 0.50 was found for the spouse correlations in the two cohorts as well as for the monozygotic twin correlation, suggesting that familiality for this metabolite is explained by shared environment. We conclude that for the majority of metabolites targeted by the used metabolomics platform, the familial resemblance of serum concentrations is largely genetic. Our results contribute to the knowledge of the heritability of fasting serum metabolite concentrations, which is relevant for biomarker research.
Assuntos
Gêmeos Dizigóticos , Gêmeos Monozigóticos , Doenças em Gêmeos/genética , Meio Ambiente , Humanos , Países Baixos , Gêmeos Dizigóticos/genética , Gêmeos Monozigóticos/genéticaRESUMO
Over the past 25 years, the Adult Netherlands Twin Register (ANTR) has collected a wealth of information on physical and mental health, lifestyle, and personality in adolescents and adults. This article provides an overview of the sources of information available, the main research findings, and an outlook for the future. Between 1991 and 2012, longitudinal surveys were completed by twins, their parents, siblings, spouses, and offspring. Data are available for 33,957 participants, with most individuals having completed two or more surveys. Smaller projects provided in-depth phenotyping, including measurements of the autonomic nervous system, neurocognitive function, and brain imaging. For 46% of the ANTR participants, DNA samples are available and whole genome scans have been obtained in more than 11,000 individuals. These data have resulted in numerous studies on heritability, gene x environment interactions, and causality, as well as gene finding studies. In the future, these studies will continue with collection of additional phenotypes, such as metabolomic and telomere length data, and detailed genetic information provided by DNA and RNA sequencing. Record linkage to national registers will allow the study of morbidity and mortality, thus providing insight into the development of health, lifestyle, and behavior across the lifespan.
Assuntos
Bancos de Espécimes Biológicos , Pesquisa Biomédica , Doenças em Gêmeos/genética , Interação Gene-Ambiente , Sistema de Registros , Gêmeos/genética , Adolescente , Adulto , Doenças em Gêmeos/epidemiologia , Feminino , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Estudos Longitudinais , Masculino , Países Baixos/epidemiologia , Adulto JovemRESUMO
Combination of data sets from different objects (for example, from two groups of healthy volunteers from the same population) that were measured on a common set of variables (for example, metabolites or peptides) is desirable for statistical analysis in "omics" studies because it increases power. However, this type of combination is not directly possible if nonbiological systematic differences exist among the individual data sets, or "blocks". Such differences can, for example, be due to small analytical changes that are likely to accumulate over large time intervals between blocks of measurements. In this article we present a data transformation method, that we will refer to as "quantile equating", which per variable corrects for linear and nonlinear differences in distribution among blocks of semiquantitative data obtained with the same analytical method. We demonstrate the successful application of the quantile equating method to data obtained on two typical metabolomics platforms, i.e., liquid chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy. We suggest uni- and multivariate methods to evaluate similarities and differences among data blocks before and after quantile equating. In conclusion, we have developed a method to correct for nonbiological systematic differences among semiquantitative data blocks and have demonstrated its successful application to metabolomics data sets.
Assuntos
Cromatografia Líquida de Alta Pressão/métodos , Lipídeos/sangue , Espectroscopia de Ressonância Magnética/métodos , Espectrometria de Massas/métodos , Metabolômica/métodos , Adolescente , Algoritmos , Estudos de Coortes , Feminino , Humanos , Lipídeos/química , Masculino , Análise de Componente Principal , Irmãos , Gêmeos , Adulto JovemRESUMO
Metabolomics examines the small molecules involved in cellular metabolism. Approximately 50% of total phenotypic differences in metabolite levels is due to genetic variance, but heritability estimates differ across metabolite classes. We perform a review of all genome-wide association and (exome-) sequencing studies published between November 2008 and October 2018, and identify >800 class-specific metabolite loci associated with metabolite levels. In a twin-family cohort (N = 5117), these metabolite loci are leveraged to simultaneously estimate total heritability (h2total), and the proportion of heritability captured by known metabolite loci (h2Metabolite-hits) for 309 lipids and 52 organic acids. Our study reveals significant differences in h2Metabolite-hits among different classes of lipids and organic acids. Furthermore, phosphatidylcholines with a high degree of unsaturation have higher h2Metabolite-hits estimates than phosphatidylcholines with low degrees of unsaturation. This study highlights the importance of common genetic variants for metabolite levels, and elucidates the genetic architecture of metabolite classes.
Assuntos
Sangue/metabolismo , Estudo de Associação Genômica Ampla , Análise Química do Sangue , Estudos de Coortes , Humanos , Metabolômica , Locos de Características Quantitativas , Gêmeos/genéticaRESUMO
X-inactivation is a well-established dosage compensation mechanism ensuring that X-chromosomal genes are expressed at comparable levels in males and females. Skewed X-inactivation is often explained by negative selection of one of the alleles. We demonstrate that imbalanced expression of the paternal and maternal X-chromosomes is common in the general population and that the random nature of the X-inactivation mechanism can be sufficient to explain the imbalance. To this end, we analyzed blood-derived RNA and whole-genome sequencing data from 79 female children and their parents from the Genome of the Netherlands project. We calculated the median ratio of the paternal over total counts at all X-chromosomal heterozygous single-nucleotide variants with coverage ≥10. We identified two individuals where the same X-chromosome was inactivated in all cells. Imbalanced expression of the two X-chromosomes (ratios ≤0.35 or ≥0.65) was observed in nearly 50% of the population. The empirically observed skewing is explained by a theoretical model where X-inactivation takes place in an embryonic stage in which eight cells give rise to the hematopoietic compartment. Genes escaping X-inactivation are expressed from both alleles and therefore demonstrate less skewing than inactivated genes. Using this characteristic, we identified three novel escapee genes (SSR4, REPS2, and SEPT6), but did not find support for many previously reported escapee genes in blood. Our collective data suggest that skewed X-inactivation is common in the general population. This may contribute to manifestation of symptoms in carriers of recessive X-linked disorders. We recommend that X-inactivation results should not be used lightly in the interpretation of X-linked variants.
Assuntos
População/genética , Inativação do Cromossomo X , Proteínas de Ligação ao Cálcio/genética , Feminino , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/genética , Masculino , Glicoproteínas de Membrana/genética , Países Baixos , Polimorfismo de Nucleotídeo Único , Receptores Citoplasmáticos e Nucleares/genética , Receptores de Peptídeos/genética , Septinas/genéticaRESUMO
Telomere shortening has been associated with multiple age-related diseases such as cardiovascular disease, diabetes, and dementia. However, the biological mechanisms responsible for these associations remain largely unknown. In order to gain insight into the metabolic processes driving the association of leukocyte telomere length (LTL) with age-related diseases, we investigated the association between LTL and serum metabolite levels in 7,853 individuals from seven independent cohorts. LTL was determined by quantitative polymerase chain reaction and the levels of 131 serum metabolites were measured with mass spectrometry in biological samples from the same blood draw. With partial correlation analysis, we identified six metabolites that were significantly associated with LTL after adjustment for multiple testing: lysophosphatidylcholine acyl C17:0 (lysoPC a C17:0, p-value = 7.1 × 10-6), methionine (p-value = 9.2 × 10-5), tyrosine (p-value = 2.1 × 10-4), phosphatidylcholine diacyl C32:1 (PC aa C32:1, p-value = 2.4 × 10-4), hydroxypropionylcarnitine (C3-OH, p-value = 2.6 × 10-4), and phosphatidylcholine acyl-alkyl C38:4 (PC ae C38:4, p-value = 9.0 × 10-4). Pathway analysis showed that the three phosphatidylcholines and methionine are involved in homocysteine metabolism and we found supporting evidence for an association of lipid metabolism with LTL. In conclusion, we found longer LTL associated with higher levels of lysoPC a C17:0 and PC ae C38:4, and with lower levels of methionine, tyrosine, PC aa C32:1, and C3-OH. These metabolites have been implicated in inflammation, oxidative stress, homocysteine metabolism, and in cardiovascular disease and diabetes, two major drivers of morbidity and mortality.
Assuntos
Homocisteína/metabolismo , Leucócitos/ultraestrutura , Metabolismo dos Lipídeos , Metabolômica/métodos , Telômero , Adulto , Idoso , Estudos de Coortes , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Encurtamento do TelômeroRESUMO
Differences in genetic background and/or environmental exposure among individuals are expected to give rise to differences in measurable characteristics, or phenotypes. Consequently, genetic resemblance and similarities in environment should manifest as similarities in phenotypes. The metabolome reflects many of the system properties, and is therefore an important part of the phenotype. Nevertheless, it has not yet been examined to what extent individuals sharing part of their genome and/or environment indeed have similar metabolomes. Here we present the results of hierarchical clustering of blood plasma lipid profile data obtained by liquid chromatography-mass spectrometry from 23 healthy, 18-year-old twin pairs, of which 21 pairs were monozygotic, and 8 of their siblings. For 13 monozygotic twin pairs, within-pair similarities in relative concentrations of the detected lipids were indeed larger than the similarities with any other study participant. We demonstrate such high coclustering to be unexpected on basis of chance. The similarities between dizygotic twins and between nontwin siblings, as well as between nonfamilial participants, were less pronounced. In a number of twin pairs, within-pair dissimilarity of lipid profiles positively correlated with increased blood plasma concentrations of C-reactive protein in one twin. In conclusion, this study demonstrates that in healthy individuals, the individual genetic background contributes to the blood plasma lipid profile. Furthermore, lipid profiling may prove useful in monitoring health status, for example, in the context of personalized medicine.
Assuntos
Lipídeos/sangue , Gêmeos Monozigóticos/sangue , Gêmeos Monozigóticos/genética , Adolescente , Proteína C-Reativa/metabolismo , Cromatografia Líquida , Feminino , Humanos , Masculino , Espectrometria de Massas por Ionização por ElectrosprayRESUMO
Electrocardiograms (ECGs) made with Mason-Likar electrode configuration (ML-ECGs) show well-known differences from standard 12-lead ECGs (Std-ECGs). We recorded, simultaneously, Std-ECGs and ML-ECGs in 180 subjects. Using these ECGs, 8 x 8 individual and general conversion matrices were created by linear regression, and standard ECGs were reconstructed from ML-ECGs using these matrices. The performance of the matrices was assessed by the root mean square differences between the original Std-ECGs and the reconstructed standard ECGs, by the differences in major ECG parameters, and by comparison of computer-generated diagnostic statements. As a result, we conclude that, based on the root mean square differences, reconstructions with 8 x 8 individual matrices perform significantly better than reconstructions with the group matrix and perform equally well with respect to the calculation of major electrocardiographic parameters, which gives an improved reliability of the QRS frontal axis and the maximal QRS and T amplitudes. Both types of matrices were able to reverse the underdiagnosis of inferior myocardial infarctions and the erroneous statements about the QRS frontal axis that arose in the ECGs that were made by using the Mason-Likar electrode positions.
Assuntos
Algoritmos , Mapeamento Potencial de Superfície Corporal/métodos , Diagnóstico por Computador/métodos , Eletrocardiografia/métodos , Adulto , Idoso , Mapeamento Potencial de Superfície Corporal/instrumentação , Mapeamento Potencial de Superfície Corporal/normas , Eletrocardiografia/instrumentação , Eletrocardiografia/normas , Eletrodos/normas , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Reprodutibilidade dos Testes , Sensibilidade e EspecificidadeRESUMO
BACKGROUND AND PURPOSE: Normal limits of the spatial QRS-T angle and spatial ventricular gradient (SVG) are only available from Frank vectorcardiograms (VCGs) of male subjects. We determined normal limits for these variables derived from standard 12-lead electrocardiograms (ECGs) of 660 male and female students aged 18 to 29 years. METHODS: A computer algorithm was used that constructed approximated VCG leads by inverse Dower matrix transformation of the 12-lead ECG and subsequently calculated the spatial QRS-T angle, SVG magnitude, and orientation. RESULTS: In female subjects, the QRS-T angle was more acute (females, 66 degrees +/- 23 degrees; normal, 20 degrees-116 degrees; males, 80 degrees +/- 24 degrees; normal, 30 degrees-130 degrees; P < .001), and the SVG magnitude was smaller (females, 81 +/- 23 mV x ms; normal, 39-143 mV x ms; males, 110 +/- 29 mV x ms; normal, 59-187 mV x ms; P < .001) than in male subjects. The male SVG magnitude in our study was larger than that computed in Frank VCGs (79 +/- 28 mV.ms; P < .001). CONCLUSIONS: The spatial QRS-T angle and SVG depend strongly on sex. Furthermore, normal limits of SVG derived from Frank VCGs differ markedly from those derived from VCGs synthesized from the standard ECG. As nowadays, VCGs are usually synthesized from the 12-lead ECG; normal limits derived from the standard ECG should preferably be used.
Assuntos
Diagnóstico por Computador/métodos , Diagnóstico por Computador/estatística & dados numéricos , Eletrocardiografia/métodos , Eletrocardiografia/estatística & dados numéricos , Frequência Cardíaca/fisiologia , Adulto , Feminino , Humanos , Masculino , Países Baixos/epidemiologia , Valores de Referência , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Fatores Sexuais , Adulto JovemRESUMO
Systemic sclerosis is an autoimmune disease characterized by fibrosis of skin and multiple organs of which the pathogenesis is poorly understood. We studied differentially expressed coding and non-coding genes in relation to systemic sclerosis pathogenesis with a specific focus on antisense non-coding RNAs. Skin biopsy-derived RNAs from 14 early systemic sclerosis patients and six healthy individuals were sequenced with ion-torrent and analyzed using DEseq2. Overall, 4,901 genes with a fold change >1.5 and a false discovery rate <5% were detected in patients versus controls. Upregulated genes clustered in immunologic, cell adhesion, and keratin-related processes. Interestingly, 676 deregulated non-coding genes were detected, 257 of which were classified as antisense genes. Sense genes expressed opposite of these antisense genes were also deregulated in 42% of the observed sense-antisense gene pairs. The majority of the antisense genes had a similar effect sizes in an independent North American dataset with three genes (CTBP1-AS2, OTUD6B-AS1, and AGAP2-AS1) exceeding the study-wide Bonferroni-corrected P-value (PBonf < 0.0023, Pcombined = 1.1 × 10-9, 1.4 × 10-8, 1.7 × 10-6, respectively). In this study, we highlight that together with coding genes, (antisense) long non-coding RNAs are deregulated in skin tissue of systemic sclerosis patients suggesting a novel class of genes involved in pathogenesis of systemic sclerosis.
Assuntos
RNA Longo não Codificante/genética , Escleroderma Sistêmico/genética , Pele/metabolismo , Regulação para Cima , Células Cultivadas , Humanos , RNA Longo não Codificante/biossíntese , Escleroderma Sistêmico/metabolismo , Escleroderma Sistêmico/patologia , Pele/patologia , Fatores de Transcrição , Ativação TranscricionalRESUMO
BACKGROUND AND AIM: Previous studies have shown a relationship between schizophrenia and cannabis use. As both traits are substantially heritable, a shared genetic liability could explain the association. We use two recently developed genomics methods to investigate the genetic overlap between schizophrenia and cannabis use. METHODS: Firstly, polygenic risk scores for schizophrenia were created based on summary statistics from the largest schizophrenia genome-wide association (GWA) meta-analysis to date. We analysed the association between these schizophrenia polygenic scores and multiple cannabis use phenotypes (lifetime use, regular use, age at initiation, and quantity and frequency of use) in a sample of 6,931 individuals. Secondly, we applied LD-score regression to the GWA summary statistics of schizophrenia and lifetime cannabis use to calculate the genome-wide genetic correlation. RESULTS: Polygenic risk scores for schizophrenia were significantly (α<0.05) associated with five of the eight cannabis use phenotypes, including lifetime use, regular use, and quantity of use, with risk scores explaining up to 0.5% of the variance. Associations were not significant for age at initiation of use and two measures of frequency of use analyzed in lifetime users only, potentially because of reduced power due to a smaller sample size. The LD-score regression revealed a significant genetic correlation of rg=0.22 (SE=0.07, p=0.003) between schizophrenia and lifetime cannabis use. CONCLUSIONS: Common genetic variants underlying schizophrenia and lifetime cannabis use are partly overlapping. Individuals with a stronger genetic predisposition to schizophrenia are more likely to initiate cannabis use, use cannabis more regularly, and consume more cannabis over their lifetime.
Assuntos
Fumar Maconha/epidemiologia , Fumar Maconha/genética , Herança Multifatorial/genética , Esquizofrenia/epidemiologia , Esquizofrenia/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Doenças em Gêmeos/epidemiologia , Doenças em Gêmeos/genética , Feminino , Predisposição Genética para Doença/epidemiologia , Predisposição Genética para Doença/genética , Estudo de Associação Genômica Ampla/métodos , Humanos , Masculino , Pessoa de Meia-Idade , Países Baixos/epidemiologia , Fenótipo , Sistema de Registros , Adulto JovemRESUMO
An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10-8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10-8), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development.
Assuntos
Estudo de Associação Genômica Ampla , Projeto HapMap , HumanosRESUMO
The ventricular gradient, a notion conceived by Wilson et al during the 1930s, has contributed considerably to a better understanding of the ECG manifestations of the cardiac repolarization process. The power of the ventricular gradient is its ability to assess the primary factors that contribute to the T wave (i.e., heterogeneity of action potential morphology throughout the ventricles) in the presence of secondary factors contributing to the T wave (i.e., heterogeneity in ventricular depolarization instants). Where T-wave morphology is an ECG expression of heterogeneity of the repolarization, the ventricular gradient discriminates between primary or secondary causes of such heterogeneity. Besides the spatial ventricular gradient (Burger's three-dimensional elaboration of Wilson's two-dimensional concept), body surface mapping of local components of the ventricular gradient has emerged as a technique for assessing local ventricular action potential duration heterogeneity. The latter is believed to contribute to localization of arrhythmogenic areas in the heart. The spatial ventricular gradient, which can be computed on the basis of a regular routine ECG and does not require body surface mapping, aims to assess the overall heterogeneity of ventricular action potential morphology. This review addresses the nature and diagnostic potential of the spatial ventricular gradient. The main focus is the role of the spatial ventricular gradient in ECG assessment of dispersion of repolarization, a key factor in arrhythmogeneity.
Assuntos
Eletrocardiografia/história , Sistema de Condução Cardíaco/fisiologia , História do Século XX , Humanos , Função VentricularRESUMO
Genome-wide association studies have identified numerous loci linked with complex diseases, for which the molecular mechanisms remain largely unclear. Comprehensive molecular profiling of circulating metabolites captures highly heritable traits, which can help to uncover metabolic pathophysiology underlying established disease variants. We conduct an extended genome-wide association study of genetic influences on 123 circulating metabolic traits quantified by nuclear magnetic resonance metabolomics from up to 24,925 individuals and identify eight novel loci for amino acids, pyruvate and fatty acids. The LPA locus link with cardiovascular risk exemplifies how detailed metabolic profiling may inform underlying aetiology via extensive associations with very-low-density lipoprotein and triglyceride metabolism. Genetic fine mapping and Mendelian randomization uncover wide-spread causal effects of lipoprotein(a) on overall lipoprotein metabolism and we assess potential pleiotropic consequences of genetically elevated lipoprotein(a) on diverse morbidities via electronic health-care records. Our findings strengthen the argument for safe LPA-targeted intervention to reduce cardiovascular risk.
Assuntos
Doenças Cardiovasculares/genética , Lipoproteína(a)/genética , Metabolômica/métodos , Adulto , Idoso , Doenças Cardiovasculares/metabolismo , Mapeamento Cromossômico , Feminino , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Lipoproteínas VLDL/metabolismo , Espectroscopia de Ressonância Magnética , Masculino , Análise da Randomização Mendeliana , Pessoa de Meia-Idade , Triglicerídeos/metabolismo , Adulto JovemRESUMO
BACKGROUND: Proarrhythmic effects of cardiac resynchronization therapy (CRT) as a result of increased transmural dispersion of repolarization (TDR) induced by left ventricular (LV) epicardial pacing in a subset of vulnerable patients have been reported. The possibility of identifying these patients by ECG repolarization indices has been suggested. OBJECTIVES: The purpose of this study was to test whether repolarization indices on the ECG can be used to measure dispersion of repolarization during pacing. METHODS: CRT devices of 28 heart failure patients were switched among biventricular, LV, and right ventricular (RV) pacing. ECG indices proposed to measure dispersion of repolarization were calculated. The effects of CRT on repolarization were simulated in ECGSIM, a mathematical model of electrocardiogram genesis. TDR was calculated as the difference in repolarization time between the epicardial and endocardial nodes of the heart model. PATIENTS: The interval from the apex to the end of the T wave was shorter during biventricular pacing (102 +/- 18 ms) and LV pacing (106 +/- 21 ms) than during RV pacing (117 +/- 22 ms, P < or =.005). T-wave amplitude and area were low during biventricular pacing (287 +/- 125 microV and 56 +/- 22 microV.s, respectively, P = .0006 vs RV pacing). T-wave complexity was high during biventricular pacing (0.42 +/- 0.26, P = .004 vs RV pacing). Simulations: Repolarization patterns were highly similar to the preceding depolarization patterns. The repolarization patterns of different pacing modes explained the observed magnitudes of the ECG repolarization indices. Average and local TDR were not different between pacing modes. CONCLUSION: In patients treated with CRT, ECG repolarization indices are related to pacing-induced activation sequences rather than transmural dispersion. TDR during biventricular and LV pacing is not larger than TDR during conventional RV endocardial pacing.
Assuntos
Estimulação Cardíaca Artificial , Insuficiência Cardíaca/terapia , Disfunção Ventricular/terapia , Idoso , Mapeamento Potencial de Superfície Corporal , Simulação por Computador , Eletrocardiografia , Feminino , Humanos , Masculino , Modelos Cardiovasculares , Marca-Passo ArtificialRESUMO
Metabolites are small molecules involved in cellular metabolism, which can be detected in biological samples using metabolomic techniques. Here we present the results of genome-wide association and meta-analyses for variation in the blood serum levels of 129 metabolites as measured by the Biocrates metabolomic platform. In a discovery sample of 7,478 individuals of European descent, we find 4,068 genome- and metabolome-wide significant (Z-test, P < 1.09 × 10(-9)) associations between single-nucleotide polymorphisms (SNPs) and metabolites, involving 59 independent SNPs and 85 metabolites. Five of the fifty-nine independent SNPs are new for serum metabolite levels, and were followed-up for replication in an independent sample (N = 1,182). The novel SNPs are located in or near genes encoding metabolite transporter proteins or enzymes (SLC22A16, ARG1, AGPS and ACSL1) that have demonstrated biomedical or pharmaceutical importance. The further characterization of genetic influences on metabolic phenotypes is important for progress in biological and medical research.