RESUMO
Numerous genetic studies have established a role for rare genomic variants in Congenital Heart Disease (CHD) at the copy number variation (CNV) and de novo variant (DNV) level. To identify novel haploinsufficient CHD disease genes, we performed an integrative analysis of CNVs and DNVs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm. We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed variation rate testing for DNVs identified in 2,489 parent-offspring trios. Our analysis revealed 21 genes which were significantly affected by rare CNVs and/or DNVs in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in small cases series or show new associations with CHD. In addition, a systems level analysis revealed affected protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes and pathways.
Assuntos
Variações do Número de Cópias de DNA/genética , Haploinsuficiência/genética , Cardiopatias Congênitas/genética , Bases de Dados Genéticas , Expressão Gênica/genética , Perfilação da Expressão Gênica/métodos , Predisposição Genética para Doença/genética , Genômica/métodos , Humanos , Canais Iônicos/genética , Proteínas de Membrana/genética , Polimorfismo de Nucleotídeo Único/genética , Transcriptoma/genéticaRESUMO
[This corrects the article DOI: 10.1371/journal.pgen.1009679.].
RESUMO
Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.
Assuntos
Variação Genética/genética , Genética Populacional/normas , Genoma Humano/genética , Genômica/normas , Análise de Sequência de DNA/normas , Adulto , Alelos , Criança , Cromossomos Humanos Y/genética , Dinamarca , Feminino , Haplótipos/genética , Humanos , Complexo Principal de Histocompatibilidade/genética , Masculino , Idade Materna , Taxa de Mutação , Idade Paterna , Mutação Puntual/genética , Padrões de ReferênciaRESUMO
MOTIVATION: Understanding the specificity of protein receptor-ligand interactions is pivotal for our comprehension of biological mechanisms and systems. Receptor protein families often have a certain level of sequence diversity that converges into fewer conserved protein structures, allowing the exertion of well-defined functions. T and B cell receptors of the immune system and protein kinases that control the dynamic behaviour and decision processes in eukaryotic cells by catalysing phosphorylation represent prime examples. Driven by the large sequence diversity, the receptors within such protein families are often found to share specificities although divergent at the sequence level. This observation has led to the notion that prediction models of such systems are most effectively handled in a receptor-specific manner. RESULTS: We show that this approach in many cases is suboptimal, and describe an alternative improved framework for generating models with pan-receptor-predictive power for receptor protein families. The framework is based on deep artificial neural networks and integrates information from individual receptors into a single pan-receptor model, leveraging information across multiple receptor-specific datasets allowing predictions of the receptor specificity for all members of a given protein family including those described by limited or no ligand data. The approach was applied to the protein kinase superfamily, leading to the method NetPhosPan. The method was extensively validated and benchmarked against state-of-the-art prediction methods and was found to have unprecedented performance in particularly for kinase domains characterized by limited or no experimental data. AVAILABILITY AND IMPLEMENTATION: The method is freely available to non-commercial users and can be downloaded at http://www.cbs.dtu.dk/services/NetPhospan-1.0. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Assuntos
Redes Neurais de Computação , Ligantes , Fosforilação , Proteínas Quinases , ProteínasRESUMO
Despite the essential role of thymic epithelial cells (TEC) in T cell development, the signals regulating TEC differentiation and homeostasis remain incompletely understood. In this study, we show a key in vivo role for the vitamin A metabolite, retinoic acid (RA), in TEC homeostasis. In the absence of RA signaling in TEC, cortical TEC (cTEC) and CD80loMHC class IIlo medullary TEC displayed subset-specific alterations in gene expression, which in cTEC included genes involved in epithelial proliferation, development, and differentiation. Mice whose TEC were unable to respond to RA showed increased cTEC proliferation, an accumulation of stem cell Ag-1hi cTEC, and, in early life, a decrease in medullary TEC numbers. These alterations resulted in reduced thymic cellularity in early life, a reduction in CD4 single-positive and CD8 single-positive numbers in both young and adult mice, and enhanced peripheral CD8+ T cell survival upon TCR stimulation. Collectively, our results identify RA as a regulator of TEC homeostasis that is essential for TEC function and normal thymopoiesis.
Assuntos
Células Epiteliais/imunologia , Transdução de Sinais/imunologia , Timo/imunologia , Tretinoína/imunologia , Animais , Linfócitos T CD4-Positivos/imunologia , Linfócitos T CD8-Positivos/imunologia , Diferenciação Celular/imunologia , Linhagem da Célula/imunologia , Proliferação de Células/fisiologia , Feminino , Homeostase/imunologia , Masculino , Camundongos , Camundongos Endogâmicos C57BLRESUMO
BACKGROUND: Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. METHODS: In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads. RESULTS: Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found. CONCLUSIONS: Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
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Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenoma/genética , Neoplasias/virologia , Anelloviridae/genética , Anelloviridae/isolamento & purificação , Biópsia , Conjuntos de Dados como Assunto , Feminino , Herpesviridae/genética , Herpesviridae/isolamento & purificação , Humanos , Masculino , Neoplasias/patologia , Papillomaviridae/genética , Papillomaviridae/isolamento & purificação , Parvovirus/genética , Parvovirus/isolamento & purificaçãoRESUMO
BACKGROUND: The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advances in next-generation sequencing (NGS) methodologies, have increased the need for precise computational typing methods. RESULTS: We tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific homozygosity rates as well as the allele frequencies; and we compared those to the observed values in related populations. We provide guidelines for testing the accuracy of HLA typing methods by comparing family information, which is independent of the availability of curated alleles. CONCLUSIONS: Although current computational methods for HLA typing generally provide satisfactory results, our benchmark - using data with ultra-high sequencing depth - demonstrates the incompleteness of current reference databases, and highlights the importance of providing genomic databases addressing current sequencing standards, a problem yet to be resolved before benefiting fully from personalised medicine approaches HLA phenotyping is essential.
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Benchmarking/métodos , Genômica/métodos , Técnicas de Genotipagem/métodos , Antígenos HLA/genética , Família , Teste de Histocompatibilidade , Humanos , Pais , SuéciaRESUMO
A novel human protoparvovirus related to human bufavirus and preliminarily named cutavirus has been discovered. We detected cutavirus in a sample of cutaneous malignant melanoma by using viral enrichment and high-throughput sequencing. The role of cutaviruses in cutaneous cancers remains to be investigated.
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Melanoma/etiologia , Infecções por Parvoviridae/complicações , Infecções por Parvoviridae/virologia , Parvovirus , Neoplasias Cutâneas/etiologia , DNA Viral , Genes Virais , Humanos , Melanoma/diagnóstico , Infecções por Parvoviridae/diagnóstico , Filogenia , Análise de Sequência de DNA , Neoplasias Cutâneas/diagnóstico , Melanoma Maligno CutâneoRESUMO
Most genomic alterations are tolerated while only a minor fraction disrupts molecular function sufficiently to drive disease. Protein kinases play a central biological function and the functional consequences of their variants are abundantly characterized. However, this heterogeneous information is often scattered across different sources, which makes the integrative analysis complex and laborious. wKinMut-2 constitutes a solution to facilitate the interpretation of the consequences of human protein kinase variation. Nine methods predict their pathogenicity, including a kinase-specific random forest approach. To understand the biological mechanisms causative of human diseases and cancer, information from pertinent reference knowledge bases and the literature is automatically mined, digested, and homogenized. Variants are visualized in their structural contexts and residues affecting catalytic and drug binding are identified. Known protein-protein interactions are reported. Altogether, this information is intended to assist the generation of new working hypothesis to be corroborated with ulterior experimental work. The wKinMut-2 system, along with a user manual and examples, is freely accessible at http://kinmut2.bioinfo.cnio.es, the code for local installations can be downloaded from https://github.com/Rbbt-Workflows/KinMut2.
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Biologia Computacional/métodos , Estudos de Associação Genética/métodos , Predisposição Genética para Doença , Variação Genética , Genômica/métodos , Proteínas Quinases/genética , Software , Mineração de Dados , Bases de Dados Genéticas , Fator 1 de Crescimento de Fibroblastos/química , Fator 1 de Crescimento de Fibroblastos/genética , Fator 1 de Crescimento de Fibroblastos/metabolismo , Humanos , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Proteínas Quinases/química , Proteínas Quinases/metabolismo , Proteínas Proto-Oncogênicas B-raf/química , Proteínas Proto-Oncogênicas B-raf/genética , Proteínas Proto-Oncogênicas B-raf/metabolismo , Receptor Tipo 3 de Fator de Crescimento de Fibroblastos/química , Receptor Tipo 3 de Fator de Crescimento de Fibroblastos/genética , Receptor Tipo 3 de Fator de Crescimento de Fibroblastos/metabolismo , Reprodutibilidade dos Testes , Relação Estrutura-Atividade , NavegadorRESUMO
PURPOSE OF REVIEW: Systemic lupus erythematosus (SLE) is caused by a combination of genetic and acquired immunodeficiencies and environmental factors including infections. An association with Epstein-Barr virus (EBV) has been established by numerous studies over the past decades. Here, we review recent experimental studies on EBV, and present our integrated theory of SLE development. RECENT FINDINGS: SLE patients have dysfunctional control of EBV infection resulting in frequent reactivations and disease progression. These comprise impaired functions of EBV-specific T-cells with an inverse correlation to disease activity and elevated serum levels of antibodies against lytic cycle EBV antigens. The presence of EBV proteins in renal tissue from SLE patients with nephritis suggests direct involvement of EBV in SLE development. As expected for patients with immunodeficiencies, studies reveal that SLE patients show dysfunctional responses to other viruses as well. An association with EBV infection has also been demonstrated for other autoimmune diseases, including Sjögren's syndrome, rheumatoid arthritis, and multiple sclerosis. SUMMARY: Collectively, the interplay between an impaired immune system and the cumulative effects of EBV and other viruses results in frequent reactivation of EBV and enhanced cell death, causing development of SLE and concomitant autoreactivities.
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Doenças Autoimunes/virologia , Infecções por Vírus Epstein-Barr/complicações , Lúpus Eritematoso Sistêmico/virologia , Artrite Reumatoide/imunologia , Artrite Reumatoide/virologia , Doenças Autoimunes/imunologia , Medicina Baseada em Evidências/métodos , Herpesvirus Humano 4/isolamento & purificação , Herpesvirus Humano 4/fisiologia , Humanos , Lúpus Eritematoso Sistêmico/imunologia , Síndrome de Sjogren/imunologia , Síndrome de Sjogren/virologia , Ativação Viral/imunologiaRESUMO
Propionibacterium acnesis the most abundant bacterium on human skin, particularly in sebaceous areas.P. acnesis suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence ofP. acnesDNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions ofP. acnesDNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples.P. acnesreads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show thatP. acnescan be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully whenP. acnesis detected in clinical samples. We advocate that detection ofP. acnesalways be accompanied by experiments validating the association between this bacterium and any clinical condition.
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Infecções Bacterianas/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala , Neoplasias/complicações , Propionibacterium acnes/isolamento & purificação , Humanos , Propionibacterium acnes/genéticaRESUMO
BACKGROUND: Protein kinases are involved in relevant physiological functions and a broad number of mutations in this superfamily have been reported in the literature to affect protein function and stability. Unfortunately, the exploration of the consequences on the phenotypes of each individual mutation remains a considerable challenge. RESULTS: The wKinMut web-server offers direct prediction of the potential pathogenicity of the mutations from a number of methods, including our recently developed prediction method based on the combination of information from a range of diverse sources, including physicochemical properties and functional annotations from FireDB and Swissprot and kinase-specific characteristics such as the membership to specific kinase groups, the annotation with disease-associated GO terms or the occurrence of the mutation in PFAM domains, and the relevance of the residues in determining kinase subfamily specificity from S3Det. This predictor yields interesting results that compare favourably with other methods in the field when applied to protein kinases.Together with the predictions, wKinMut offers a number of integrated services for the analysis of mutations. These include: the classification of the kinase, information about associations of the kinase with other proteins extracted from iHop, the mapping of the mutations onto PDB structures, pathogenicity records from a number of databases and the classification of mutations in large-scale cancer studies. Importantly, wKinMut is connected with the SNP2L system that extracts mentions of mutations directly from the literature, and therefore increases the possibilities of finding interesting functional information associated to the studied mutations. CONCLUSIONS: wKinMut facilitates the exploration of the information available about individual mutations by integrating prediction approaches with the automatic extraction of information from the literature (text mining) and several state-of-the-art databases.wKinMut has been used during the last year for the analysis of the consequences of mutations in the context of a number of cancer genome projects, including the recent analysis of Chronic Lymphocytic Leukemia cases and is publicly available at http://wkinmut.bioinfo.cnio.es.
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Biologia Computacional/métodos , Leucemia Linfocítica Crônica de Células B/enzimologia , Leucemia Linfocítica Crônica de Células B/genética , Mutação/genética , Proteínas Quinases/química , Bases de Dados de Proteínas/tendências , Receptores ErbB/genética , Humanos , Armazenamento e Recuperação da Informação/métodos , Leucemia Linfocítica Crônica de Células B/etiologia , Fenótipo , Valor Preditivo dos Testes , Proteínas Quinases/classificação , Proteínas Quinases/genética , Estabilidade ProteicaAssuntos
Comportamento Animal , Chlorella/virologia , Cognição , Laringe/virologia , Memória , Mariposas/virologia , Phycodnaviridae , Animais , Feminino , Humanos , MasculinoRESUMO
BACKGROUND: Most of the many mutations described in human protein kinases are tolerated without significant disruption of the corresponding structures or molecular functions, while some of them have been associated to a variety of human diseases, including cancer. In the last decade, a plethora of computational methods to predict the effect of missense single-nucleotide variants (SNVs) have been developed. Still, current high-throughput sequencing efforts and the concomitant need for massive interpretation of protein sequence variants will demand for more efficient and/or accurate computational methods in the forthcoming years. RESULTS: We present KinMut, a support vector machine (SVM) approach, to identify pathogenic mutations in the protein kinase superfamily. KinMut relays on a combination of sequence-derived features that describe mutations at different levels: (1) Gene level: membership to a specific group in Kinbase and the annotation with GO terms; (2) Domain level: annotated PFAM domains; and (3) Residue level: physicochemical features of amino acids, specificity determining positions, and functional annotations from SwissProt and FireDB. The system has been trained with the set of 3492 human kinase mutations in UniProt for which experimental validation of their pathogenic or neutral character exists. In addition, we discuss the relative importance of these independent properties and their combination for the development of a kinase-specific predictor. Finally, we compare KinMut with other state-of-the-art prediction methods. CONCLUSIONS: Family-specific features appear among the most discriminative information sources, which allow us to produce accurate results in a reliable and very simple way with minimal supervision. Our study aims to broaden the knowledge on the mechanisms by which mutations in the human kinome contribute to disease with a particular focus in cancer. The classifier as well as further documentation is available at http://kinmut.bioinfo.cnio.es/.
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Proteínas Quinases/genética , Bases de Dados de Proteínas , Humanos , Mutação , Neoplasias/genética , Máquina de Vetores de SuporteRESUMO
BACKGROUND: Protein Kinases are a superfamily of proteins involved in crucial cellular processes such as cell cycle regulation and signal transduction. Accordingly, they play an important role in cancer biology. To contribute to the study of the relation between kinases and disease we compared pathogenic mutations to neutral mutations as an extension to our previous analysis of cancer somatic mutations. First, we analyzed native and mutant proteins in terms of amino acid composition. Secondly, mutations were characterized according to their potential structural effects and finally, we assessed the location of the different classes of polymorphisms with respect to kinase-relevant positions in terms of subfamily specificity, conservation, accessibility and functional sites. RESULTS: Pathogenic Protein Kinase mutations perturb essential aspects of protein function, including disruption of substrate binding and/or effector recognition at family-specific positions. Interestingly these mutations in Protein Kinases display a tendency to avoid structurally relevant positions, what represents a significant difference with respect to the average distribution of pathogenic mutations in other protein families. CONCLUSIONS: Disease-associated mutations display sound differences with respect to neutral mutations: several amino acids are specific of each mutation type, different structural properties characterize each class and the distribution of pathogenic mutations within the consensus structure of the Protein Kinase domain is substantially different to that for non-pathogenic mutations. This preferential distribution confirms previous observations about the functional and structural distribution of the controversial cancer driver and passenger somatic mutations and their use as a proxy for the study of the involvement of somatic mutations in cancer development.
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Mutação em Linhagem Germinativa , Mutação Puntual , Proteínas Quinases/genética , Humanos , Modelos Moleculares , Neoplasias/genética , Membro 2 do Grupo A da Subfamília 4 de Receptores Nucleares , Ligação Proteica , Proteínas Quinases/química , Proteínas Quinases/metabolismo , Estrutura Terciária de Proteína , Transdução de SinaisRESUMO
Cancer genome projects are now being expanded in an attempt to provide complete landscapes of the mutations that exist in tumours. Although the importance of cataloguing genome variations is well recognized, there are obvious difficulties in bridging the gaps between high-throughput resequencing information and the molecular mechanisms of cancer evolution. Here, we describe the current status of the high-throughput genomic technologies, and the current limitations of the associated computational analysis and experimental validation of cancer genetic variants. We emphasize how the current cancer-evolution models will be influenced by the high-throughput approaches, in particular through efforts devoted to monitoring tumour progression, and how, in turn, the integration of data and models will be translated into mechanistic knowledge and clinical applications.
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Biologia Computacional/métodos , Genômica/métodos , Neoplasias/genética , Humanos , Modelos Biológicos , Neoplasias/patologiaRESUMO
BACKGROUND: Assessment of semen quality is a key pillar in the evaluation of men from infertile couples. Usually, semen parameters are interpreted individually because the interactions between parameters are difficult to account for. OBJECTIVES: To determine how combinations of classical semen parameters and female partner age were associated with waiting time to pregnancy (TTP). MATERIALS AND METHODS: Semen results of 500 fertile men, information of TTP, and partner age were used for regressions and to detect breaking points. For a modified Association Rule Mining algorithm, semen parameters were categorized as High, Medium, and Low. RESULTS: Men ≤32.1 years and women ≤32.9 years had shorter TTP than older. Decreasing TTP was associated with increasing level of individual semen parameters up to threshold values: sperm concentration 46 mill/mL, total sperm count 179 mill, progressive motility 63%, and normal morphology 11.5%. Using association mining, approximately 100 combinations of semen parameters and partner age were associated with TTP. TTP ≤ 1 month often co-occurred with high percentages of progressive motility (≥62%) and morphologically normal spermatozoa (≥10.5%). Furthermore, TTP ≤ 1 did not tend to appear with lower percentages of these two semen parameters or high partner age (≥32 years). However, high percentages of motile or normal spermatozoa could not compensate for sperm concentration ≤42 mill/mL or total sperm count ≤158 mill. The prolonging effect of high partner age could not be compensated for by the man's semen quality. DISCUSSION AND CONCLUSION: Using association mining, we observed that TTP was best predicted when combinations of semen parameters were accounted for. Sperm counts, motility, and morphology were all important, and no single semen parameter was inferior. Additionally, female age above 32 years had a negative impact on TTP that could not be compensated for by high semen parameters of the man.
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Idade Materna , Gravidez/fisiologia , Sêmen/fisiologia , Adulto , Algoritmos , Feminino , Fertilidade , Fertilização , Humanos , Masculino , Pessoa de Meia-Idade , Análise do Sêmen , Fatores de Tempo , Adulto JovemRESUMO
AIM: It is debated whether the inhibition of glucagon secretion by glucose results from direct effects of glucose on the α-cell (intrinsic regulation) or by paracrine effects exerted by beta- or delta-cell products. METHODS: To study this in a more physiological model than isolated islets, we perfused isolated rat pancreases and measured glucagon, insulin and somatostatin secretion in response to graded increases in perfusate glucose concentration (from 3.5 to 4, 5, 6, 7, 8, 10, 12 mmol/L) as well as glucagon responses to blockage/activation of insulin/GABA/somatostatin signalling with or without addition of glucose. RESULTS: Glucagon secretion was reduced by about 50% (compared to baseline secretion at 3.5 mmol/L) within minutes after increasing glucose from 4 to 5 mmol/L (P < .01, n = 13). Insulin secretion was increased minimally, but significantly, compared to baseline (3.5 mmol/L) at 4 mmol/L, whereas somatostatin secretion was not significantly increased from baseline until 7 mmol/L. Hereafter secretion of both increased gradually up to 12 mmol/L glucose. Neither recombinant insulin (1 µmol/L), GABA (300 µmol/L) or the insulin-receptor antagonist S961 (at 1 µmol/L) affected basal (3.5 mmol/L) or glucose-induced (5.0 mmol/L) attenuation of glucagon secretion (n = 7-8). Somatostatin-14 attenuated glucagon secretion by ~ 95%, and blockage of somatostatin-receptor (SSTR)-2 or combined blockage of SSTR-2, -3 and -5 by specific antagonists increased glucagon output (at 3.5 mmol/L glucose) and prevented glucose-induced (from 3.5 to 5.0 mmol/L) suppression of secretion. CONCLUSION: Somatostatin is a powerful and tonic inhibitor of glucagon secretion from the rat pancreas and is required for glucose to inhibit glucagon secretion.
Assuntos
Glucagon/sangue , Glucose/administração & dosagem , Pâncreas/fisiologia , Somatostatina/fisiologia , Animais , Insulina/sangue , Perfusão , RatosRESUMO
BACKGROUND: Individuals respond differently to dietary intake leading to different associations between diet and traits. Most studies have investigated large cohorts without subgrouping them. OBJECTIVE: The purpose was to identify non-uniform associations between diets and anthropometric traits that appeared to be in conflict with one another across subgroups. DESIGN: We used a cohort comprising 43,790 women and men, the Danish Diet, Cancer and Health study, which includes a baseline examination at age 50-64 years and a follow-up about 5 years later. The baseline examination involved anthropometrics, body fat percentage, a food frequency questionnaire and information on lifestyle. From the questionnaire data we computed association rules between the intake of food groups and changes in waist circumference and body weight. Using association rule mining on subgroups and gender-specific cohorts, we identified non-uniform associations. The two gender-specific cohorts were stratified into subgroups using a non-linear, self-organizing map based method. RESULTS: We found 22 and 7 cases of conflicting rules in 8 participant subgroups for different anthropometric traits in women and men, respectively. For example, in a subgroup of women moderate waist loss was associated with a dietary pattern characterized by low intake in both cabbages and wine, in conflict with the association trends of both dietary factors in the female cohort. The finding of more conflicting rules in women suggests that inter-individual differences in response to dietary intake are stronger in women than in men. CONCLUSIONS: This combined stratification and association discovery approach revealed epidemiological relationships between dietary factors and changes in anthropometric traits in subgroups that take food group interactions into account. Conflicting rules adds an additional layer of complexity that should be integrated into the study of these relationships, for example in relation to genotypes.