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[PMID]:29438392
[Au] Autor:Goodin DS; Khankhanian P; Gourraud PA; Vince N
[Ad] Endereço:Department of Neurology, University of California, San Francisco, CA, United States of America.
[Ti] Título:Highly conserved extended haplotypes of the major histocompatibility complex and their relationship to multiple sclerosis susceptibility.
[So] Source:PLoS One;13(2):e0190043, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:OBJECTIVE: To determine the relationship between highly-conserved extended-haplotypes (CEHs) in the major histocompatibility complex (MHC) and MS-susceptibility. BACKGROUND: Among the ~200 MS-susceptibility regions, which are known from genome-wide analyses of single nucleotide polymorphisms (SNPs), the MHC accounts for roughly a third of the currently explained variance and the strongest MS-associations are for certain Class II alleles (e.g., HLA-DRB1*15:01; HLA-DRB1*03:01; and HLA-DRB1*13:03), which frequently reside on CEHs within the MHC. DESIGN/METHODS: Autosomal SNPs (441,547) from 11,376 MS cases and 18,872 controls in the WTCCC dataset were phased. The most significant MS associated SNP haplotype was composed of 11 SNPs in the MHC Class II region surrounding the HLA-DRB1 gene. We also phased alleles at the HLA-A, HLA-C, HLA-B, HLA-DRB1, and HLA-DQB1 loci. This data was used to probe the relationship between CEHs and MS susceptibility. RESULTS: We phased a total of 59,884 extended haplotypes (HLA-A, HLA-C, HLA-B, HLA-DRB1, HLA-DQB1 and SNP haplotypes) from 29,942 individuals. Of these, 10,078 unique extended haplotypes were identified. The 10 most common CEHs accounted for 22% (13,302) of the total. By contrast, the 8,446 least common extended haplotypes also accounted for approximately 20% (12,298) of the total. This extreme frequency-disparity among extended haplotypes necessarily complicates interpretation of reported disease-associations with specific HLA alleles. In particular, the HLA motif HLA-DRB1*15:01~HLA-DQB1*06:02 is strongly associated with MS risk. Nevertheless, although this motif is almost always found on the a1 SNP haplotype, it can rarely be found on others (e.g., a27 and a36), and, in these cases, it seems to have no apparent disease-association (OR = 0.7; CI = 0.3-1.3 and OR = 0.7; CI = 0.2-2.2, respectively). Furthermore, single copy carriers of the a1 SNP-haplotype without this HLA motif still have an increased disease risk (OR = 2.2; CI = 1.2-3.8). In addition, even among the set of CEHs, which carry the Class II motif of HLA-DRB1*15:01~HLA-DQB1*06:02~a1, different CEHs have differing strengths in their MS-associations. CONCLUSIONS: The MHC in diverse human populations consists, primarily, of a very small collection of very highly-selected CEHs. Our findings suggest that the MS-association with the HLA-DRB1*15:01~HLA-DQB1*06:02 haplotype may be due primarily to the combined attributes of the CEHs on which this particular HLA-motif often resides.
[Mh] Termos MeSH primário: Predisposição Genética para Doença
Haplótipos
Complexo Principal de Histocompatibilidade/genética
Esclerose Múltipla/genética
[Mh] Termos MeSH secundário: Seres Humanos
Polimorfismo de Nucleotídeo Único
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180214
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190043


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[PMID]:29381772
[Au] Autor:Chen D; Zhou D; Guo D; Xu P; Chen B
[Ad] Endereço:Department of Hematology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, People's Republic of China.
[Ti] Título:Comparison of outcomes in hematological malignancies treated with haploidentical or HLA-identical sibling hematopoietic stem cell transplantation following myeloablative conditioning: A meta-analysis.
[So] Source:PLoS One;13(1):e0191955, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:PURPOSE: Haploidentical and human leukocyte antigen (HLA)-identical sibling hematopoietic stem transplantation are two main ways used in allogeneic hematopoietic stem cell transplantation (allo-HSCT). In recent years, remarkable progress has been made in haploidentical allo-HSCT (HID-SCT), and some institutions found HID-SCT had similar outcomes as HLA-identical sibling allo-HSCT (ISD-SCT). To clarify if HID-SCT has equal effects to ISD-SCT in hematologic malignancies, we performed this meta-analysis. METHODS: Relevant articles published prior to February 2017 were searched on PubMed. Two reviewers assessed the quality of the included studies and extracted data independently. Odds ratio (OR) and 95% confidence intervals (CIs) were calculated for statistical analysis. RESULTS: Seven studies including 1919 patients were included. The rate of platelet engraftment is significantly lower after HID-SCT versus ISD-SCT while there is no difference in neutrophil engraftment (OR = 2.58, 95% CI = 1.70-3.93, P < 0.00001). The risk of acute graft-versus-host disease (GVHD) is significantly higher after HID-SCT versus ISD-SCT (OR = 1.88, 95% CI = 1.42-2.49, P < 0.00001), but the relapse rate is lower in HID-SCT group (OR = 0.70, 95% CI = 0.55-0.90, P = 0.005). The incidence rates of overall survival (OS) and disease-free-survival/leukemia-free survival/relapse-free survival (DFS/LFS/RFS) after ISD-SCT are all significantly superior to HID-SCT (OR = 1.32, 95% CI = 1.08-1.62, P = 0.006; OR = 1.25, 95% CI = 1.03-1.52, P = 0.02). There is no significant difference in transplantation related mortality (TRM) rate after HID-SCT and ISD-SCT. CONCLUSION: After myeloablative conditioning, patients receiving ISD-SCT have a faster engraftment, lower acute GVHD and longer life expectancy compared to HID-SCT with GVHD prophylaxis (cyclosporine A, methotrexate, mycophenolate mofetil and antithymoglobulin; CsA + MTX + MMF + ATG). Currently, HID-SCT with GVHD prophylaxis (CsA + MTX + MMF + ATG) may not replace ISD-SCT when HLA-identical sibling donor available.
[Mh] Termos MeSH primário: Doenças Hematológicas/terapia
Condicionamento Pré-Transplante
[Mh] Termos MeSH secundário: Antígenos HLA/imunologia
Haplótipos
Transplante de Células-Tronco Hematopoéticas
Seres Humanos
Análise de Sobrevida
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE; META-ANALYSIS; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (HLA Antigens)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180131
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191955


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[PMID]:29202706
[Au] Autor:Li J; Zeng W; Zhang Y; Ko AM; Li C; Zhu H; Fu Q; Zhou H
[Ad] Endereço:College of Life Science, Jilin University, Changchun, 130023, People's Republic of China.
[Ti] Título:Ancient DNA reveals genetic connections between early Di-Qiang and Han Chinese.
[So] Source:BMC Evol Biol;17(1):239, 2017 Dec 04.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed, there is no evidence to support this view. Here we analyzed the human remains from an early Di-Qiang site (Mogou site dated ~4000 years old) and compared them to other ancient DNA across China, including an early Han-related site (Hengbei site dated ~3000 years old) to establish the underlying genetic relationship between the Di-Qiang and ancestors of Han Chinese. RESULTS: We found Mogou mtDNA haplogroups were highly diverse, comprising 14 haplogroups: A, B, C, D (D*, D4, D5), F, G, M7, M8, M10, M13, M25, N*, N9a, and Z. In contrast, Mogou males were all Y-DNA haplogroup O3a2/P201; specifically one male was further assigned to O3a2c1a/M117 using targeted unique regions on the non-recombining region of the Y-chromosome. We compared Mogou to 7 other ancient and 38 modern Chinese groups, in a total of 1793 individuals, and found that Mogou shared close genetic distances with Taojiazhai (a more recent Di-Qiang population), Hengbei, and Northern Han. We modeled their interactions using Approximate Bayesian Computation, and support was given to a potential admixture of ~13-18% between the Mogou and Northern Han around 3300-3800 years ago. CONCLUSIONS: Mogou harbors the earliest genetically identifiable Di-Qiang, ancestral to the Taojiazhai, and up to ~33% paternal and ~70% of its maternal haplogroups could be found in present-day Northern Han Chinese.
[Mh] Termos MeSH primário: Grupo com Ancestrais do Continente Asiático/genética
DNA Antigo
Grupos Étnicos/genética
[Mh] Termos MeSH secundário: Teorema de Bayes
China
Cromossomos Humanos Y/genética
Simulação por Computador
DNA Mitocondrial/genética
Genética Populacional
Geografia
Haplótipos/genética
Seres Humanos
Masculino
Modelos Genéticos
Filogenia
Polimorfismo de Nucleotídeo Único/genética
Análise de Componente Principal
Probabilidade
Fatores de Tempo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Ancient); 0 (DNA, Mitochondrial)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171206
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1082-0


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[PMID]:29187208
[Au] Autor:Segatto ALA; Reck-Kortmann M; Turchetto C; Freitas LB
[Ad] Endereço:Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, Porto Alegre, RS, 91501-970, Brazil.
[Ti] Título:Multiple markers, niche modelling, and bioregions analyses to evaluate the genetic diversity of a plant species complex.
[So] Source:BMC Evol Biol;17(1):234, 2017 Nov 29.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The classification of closely related plants is not straightforward. These morphologically similar taxa frequently maintain their inter-hybridization potential and share ancestral polymorphisms as a consequence of their recent divergence. Under the biological species concept, they may thus not be considered separate species. The Petunia integrifolia complex is especially interesting because, in addition to the features mentioned above, its taxa share a pollinator, and their geographical ranges show multiple overlaps. Here, we combined plastid genome sequences, nuclear microsatellites, AFLP markers, ecological niche modelling, and bioregions analysis to investigate the genetic variability between the different taxa of the P. integrifolia complex in a comprehensive sample covering the entire geographical range of the complex. RESULTS: Results from molecular markers did not fully align with the current taxonomic classification. Niche modelling and bioregions analyses revealed that taxa were associated with different ecological constraints, indicating that the habitat plays an important role in preserving species boundaries. For three taxa, our analyses showed a mostly conserved, non-overlapping geographical distribution over time. However, for two taxa, niche modelling found an overlapping distribution over time; these taxa were also associated with the same bioregions. CONCLUSIONS: cpDNA markers were better able to discriminate between Petunia taxa than SSRs and AFLPs. Overall, our results suggest that the P. integrifolia complex represents a continuum of individuals from distant and historically isolated populations, which share some morphological traits, but are established in four different evolutionary lineages.
[Mh] Termos MeSH primário: Ecossistema
Variação Genética
Geografia
Petunia/genética
[Mh] Termos MeSH secundário: Análise do Polimorfismo de Comprimento de Fragmentos Amplificados
DNA de Cloroplastos/genética
Marcadores Genéticos
Haplótipos/genética
Repetições de Microssatélites/genética
Filogenia
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Chloroplast); 0 (Genetic Markers)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171201
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1084-y


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[PMID]:29183283
[Au] Autor:Fraser TA; Shao R; Fountain-Jones NM; Charleston M; Martin A; Whiteley P; Holme R; Carver S; Polkinghorne A
[Ad] Endereço:School of Biological Sciences, University of Tasmania, Sandy Bay, Hobart, TAS, Australia.
[Ti] Título:Mitochondrial genome sequencing reveals potential origins of the scabies mite Sarcoptes scabiei infesting two iconic Australian marsupials.
[So] Source:BMC Evol Biol;17(1):233, 2017 Nov 28.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Debilitating skin infestations caused by the mite, Sarcoptes scabiei, have a profound impact on human and animal health globally. In Australia, this impact is evident across different segments of Australian society, with a growing recognition that it can contribute to rapid declines of native Australian marsupials. Cross-host transmission has been suggested to play a significant role in the epidemiology and origin of mite infestations in different species but a chronic lack of genetic resources has made further inferences difficult. To investigate the origins and molecular epidemiology of S. scabiei in Australian wildlife, we sequenced the mitochondrial genomes of S. scabiei from diseased wombats (Vombatus ursinus) and koalas (Phascolarctos cinereus) spanning New South Wales, Victoria and Tasmania, and compared them with the recently sequenced mitochondrial genome sequences of S. scabiei from humans. RESULTS: We found unique S. scabiei haplotypes among individual wombat and koala hosts with high sequence similarity (99.1% - 100%). Phylogenetic analysis of near full-length mitochondrial genomes revealed three clades of S. scabiei (one human and two marsupial), with no apparent geographic or host species pattern, suggestive of multiple introductions. The availability of additional mitochondrial gene sequences also enabled a re-evaluation of a range of putative molecular markers of S. scabiei, revealing that cox1 is the most informative gene for molecular epidemiological investigations. Utilising this gene target, we provide additional evidence to support cross-host transmission between different animal hosts. CONCLUSIONS: Our results suggest a history of parasite invasion through colonisation of Australia from hosts across the globe and the potential for cross-host transmission being a common feature of the epidemiology of this neglected pathogen. If this is the case, comparable patterns may exist elsewhere in the 'New World'. This work provides a basis for expanded molecular studies into mange epidemiology in humans and animals in Australia and other geographic regions.
[Mh] Termos MeSH primário: Genoma Mitocondrial
Marsupiais/parasitologia
Sarcoptes scabiei/genética
Escabiose/parasitologia
Análise de Sequência de DNA
[Mh] Termos MeSH secundário: Animais
Animais Selvagens/genética
Austrália/epidemiologia
Composição de Bases/genética
Sequência de Bases
Complexo IV da Cadeia de Transporte de Elétrons/genética
Genes Mitocondriais
Tamanho do Genoma
Haplótipos/genética
Seres Humanos
Anotação de Sequência Molecular
Filogenia
Escabiose/epidemiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 1.9.3.1 (Electron Transport Complex IV)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171130
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1086-9


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[PMID]:29188670
[Au] Autor:Sun DP; Min YL; Lian CZ; Yu WD
[Ad] Endereço:Nanjing Public Security Bureau, Nanjing 210012, China.
[Ti] Título:[Genetic Polymorphisms of 24 Y-STR Loci in Nanjing Han Population].
[So] Source:Fa Yi Xue Za Zhi;32(4):269-272, 2016 Aug.
[Is] ISSN:1004-5619
[Cp] País de publicação:China
[La] Idioma:chi
[Ab] Resumo:OBJECTIVES: To investigate the genetic polymorphism of and other 23 Y-STR loci and to explore its application value in forensic science. METHODS: Y-STRs loci of 580 unrelated Han males in Nanjing were amplified using AGCU Y-PLUS PCR (24) kit. The genetic parameters of 24 Y-STR loci such as gene frequency were calculated by software, and compared with the data of Hubei, Liao- ning, Guangdong, Beijing and Chengdu Han population. RESULTS: Total 580 haplotypes were detected among 24 Y-STR loci in 580 unrelated Han males in Nanjing. The genetic diversity (GD) of each locus was from 0.294 6 to 0.939 8, and the haplotypes diversity (HD) was 0.983 7. There was a significant difference between the GD of 6 areas. CONCLUSIONS: The 24 Y-STR loci such as in Nanjing Han population have an application value in forensic science. They can also be used for cases testing and pedigree investigation.
[Mh] Termos MeSH primário: Grupo com Ancestrais do Continente Asiático/genética
Cromossomos Humanos Y/genética
Polimorfismo Genético
[Mh] Termos MeSH secundário: Pequim
China
Ciências Forenses
Frequência do Gene
Haplótipos
Seres Humanos
Masculino
Linhagem
Reação em Cadeia da Polimerase
Software
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171201
[St] Status:MEDLINE
[do] DOI:10.3969/j.issn.1004-5619.2016.04.009


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[PMID]:29188666
[Au] Autor:He WZ; Ma XY; Xian JJ; Yuan TL; Li SY; Li SL; Liu HB; Li Q
[Ad] Endereço:Key Laboratory for Major Obstetric Diseases of Guangdong Province, Forensic Identification Institute of the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China.
[Ti] Título:[Genetic Polymorphisms of SNP Located in the 5' Region of VEGF Gene in Han Population in Guangdong].
[So] Source:Fa Yi Xue Za Zhi;32(4):257-260, 2016 Aug.
[Is] ISSN:1004-5619
[Cp] País de publicação:China
[La] Idioma:chi
[Ab] Resumo:OBJECTIVES: To investigate the genetic polymorphism of SNP located in the 5' region of the vascular endothelial growth factor (VEGF) gene in Han population in Guangdong and provide basic data for forensic application and population genetics research. METHODS: The genetic polymorphisms of 4 SNP loci (rs699947, rs1570360, rs833061, rs2010963) within 5' region of VEGF gene of 184 unrelated individuals in Han population in Guangdong were analyzed by DNA micro sequencing technology SNaPshot. The statistical analysis was carried out by PowerMarker v3.25 software. RESULTS: The genotype distributions of the 4 SNP loci within 5' region of VEGF gene of 184 unrelated individuals in Han population in Guangdong were in accordance with Hardy-Weinberg equilibrium ( >0.05) and 3 kinds of genotypes were detected from each loci. There was high linkage disequilibrium between the rs833061 and rs699947 SNP loci. Six haplotypes were observed, while the frequency of C-G-T-C, C-G-T-G, A-A-C-G and A-G-C-G were more than 10%, which were the main haplotypes. The discrimination probabilities (DP) of rs699947, rs833061, and rs2010963 loci were between 0.583 and 0.634, with the power of exclusion (PE) between 0.133 and 0.144. The DP and PE of haplotypes of 4 SNP were 0.868 and 0.438, respectively. CONCLUSIONS: There are great polymorphisms in the 5' region of VEGF gene in Han population in Guangdong, which could be used as genetic indexes for individual identification and paternity testing, as well as association analysis of the related diseases.
[Mh] Termos MeSH primário: Grupo com Ancestrais do Continente Asiático/genética
Polimorfismo de Nucleotídeo Único
Fator A de Crescimento do Endotélio Vascular/genética
[Mh] Termos MeSH secundário: China
Genética Populacional
Genótipo
Haplótipos
Seres Humanos
Desequilíbrio de Ligação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (VEGFA protein, human); 0 (Vascular Endothelial Growth Factor A)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171201
[St] Status:MEDLINE
[do] DOI:10.3969/j.issn.1004-5619.2016.04.005


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[PMID]:28457509
[Au] Autor:Fracasso NCA; de Andrade ES; Wiezel CEV; Andrade CCF; Zanão LR; da Silva MS; Marano LA; Donadi EA; C Castelli E; Simões AL; Mendes-Junior CT
[Ad] Endereço:Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900, Ribeirão Preto-SP, Brazil. Electronic address: nadiadeaguiar@gmail.com.
[Ti] Título:Haplotypes from the SLC45A2 gene are associated with the presence of freckles and eye, hair and skin pigmentation in Brazil.
[So] Source:Leg Med (Tokyo);25:43-51, 2017 Mar.
[Is] ISSN:1873-4162
[Cp] País de publicação:Ireland
[La] Idioma:eng
[Ab] Resumo:The Solute Carrier Family 45, Member 2 (SLC45A2) gene encodes the Membrane-Associated Transporter Protein (MATP), which mediates melanin synthesis by tyrosinase trafficking and proton transportation to melanosomes. At least two SLC45A2 coding SNPs [E272K (rs26722) and L374F (rs16891982)] were reported influencing normal variation of human pigmentation. Here we aimed at evaluating the influence of haplotypes of 12 SNPs within SLC45A2 in the determination of eye, hair and skin pigmentation in a highly admixed population sample and comparing their frequencies with the ones found in data retrieved from the 1000 Genomes Project. To achieve this goal, 12 SLC45A2 SNPs were evaluated in 288 unrelated individuals from the Ribeirão Preto city area, Southeastern Brazil. SNPs were genotyped by PCR-RFLP or Allele-specific PCR, followed by polyacrylamide gel electrophoresis. Haplotypes of each individual were inferred by two independent computational methods, PHASE and Partition-Ligation-Expectation-Maximization (PL-EM) algorithms, and 34 different haplotypes were identified. The hp9 haplotype was the most frequent (58.3%) and was associated with the presence of blond/red hair, pale skin, blue eyes and freckles. All haplotypes significantly associated with dark or light pigmentation features harbor the 374L and 374F alleles, respectively. These results emphasize the role played by haplotypes at SLC45A2 in the determination of pigmentation aspects of human populations and reinforce the relevance of SNP L374F in human pigmentation.
[Mh] Termos MeSH primário: Cor de Olho/genética
Cor de Cabelo/genética
Haplótipos/genética
Melanose/genética
Pigmentação da Pele/genética
[Mh] Termos MeSH secundário: Alelos
Brasil
Frequência do Gene
Projeto Genoma Humano
Seres Humanos
Polimorfismo de Fragmento de Restrição
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE


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[PMID]:29295990
[Au] Autor:Bell CG; Gao F; Yuan W; Roos L; Acton RJ; Xia Y; Bell J; Ward K; Mangino M; Hysi PG; Wang J; Spector TD
[Ad] Endereço:Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK. cgb@mrc.soton.ac.uk.
[Ti] Título:Obligatory and facilitative allelic variation in the DNA methylome within common disease-associated loci.
[So] Source:Nat Commun;9(1):8, 2018 01 02.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Integrating epigenetic data with genome-wide association study (GWAS) results can reveal disease mechanisms. The genome sequence itself also shapes the epigenome, with CpG density and transcription factor binding sites (TFBSs) strongly encoding the DNA methylome. Therefore, genetic polymorphism impacts on the observed epigenome. Furthermore, large genetic variants alter epigenetic signal dosage. Here, we identify DNA methylation variability between GWAS-SNP risk and non-risk haplotypes. In three subsets comprising 3128 MeDIP-seq peripheral-blood DNA methylomes, we find 7173 consistent and functionally enriched Differentially Methylated Regions. 36.8% can be attributed to common non-SNP genetic variants. CpG-SNPs, as well as facilitative TFBS-motifs, are also enriched. Highlighting their functional potential, CpG-SNPs strongly associate with allele-specific DNase-I hypersensitivity sites. Our results demonstrate strong DNA methylation allelic differences driven by obligatory or facilitative genetic effects, with potential direct or regional disease-related repercussions. These allelic variations require disentangling from pure tissue-specific modifications, may influence array studies, and imply underestimated population variability in current reference epigenomes.
[Mh] Termos MeSH primário: Metilação de DNA
Doença/genética
Variação Genética
Estudo de Associação Genômica Ampla/métodos
[Mh] Termos MeSH secundário: Alelos
Ilhas de CpG/genética
Epigênese Genética
Predisposição Genética para Doença/genética
Genoma Humano/genética
Haplótipos
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Seres Humanos
Polimorfismo de Nucleotídeo Único
Fatores de Risco
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180104
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-01586-1


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[PMID]:28455625
[Au] Autor:Balanovsky O
[Ad] Endereço:Vavilov Institute of General Genetics, Moscow, Russia. balanovsky@inbox.ru.
[Ti] Título:Toward a consensus on SNP and STR mutation rates on the human Y-chromosome.
[So] Source:Hum Genet;136(5):575-590, 2017 05.
[Is] ISSN:1432-1203
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate. The current estimate of the "envelope rate" is 0.75-0.89 substitutions per billion base pairs per year. The available Y-SNP mutation rates can be applied to high-coverage data from the entire X-degenerate region, but other datasets may demand recalibrated rates. While a consensus on Y-SNP rates is approaching, the debate on Y-STR rates has continued for two decades, because multiple genealogical rates were consistent with each other but three times faster than the single evolutionary estimate. Applying Y-SNP and Y-STR rates to the same haplogroups recently helped to clarify the issue. Genealogical and evolutionary STR rates typically provide lower and upper bounds of the "true" (SNP-based) age. The genealogical rate often-but not always-works well for haplogroups less than 7000 years old. The evolutionary rate, although calibrated using recent events, inflates ages of young haplogroups and deflates the age of the entire Y-chromosomal tree, but often provides reasonable estimates for intermediate ages (old haplogroups). Future rate estimates and accumulating case studies should further clarify the Y-SNP rates.
[Mh] Termos MeSH primário: Cromossomos Humanos Y/genética
Repetições de Microssatélites
Taxa de Mutação
Mutação
Polimorfismo de Nucleotídeo Único
[Mh] Termos MeSH secundário: Genética Populacional
Haplótipos
Seres Humanos
Masculino
Linhagem
Filogenia
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1707
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170430
[St] Status:MEDLINE
[do] DOI:10.1007/s00439-017-1805-8



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