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Pesquisa : G05.365.795.297 [Categoria DeCS]
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[PMID]:29173772
[Au] Autor:Tian HX; Zhang XC; Yang JJ; Guo WB; Chen ZH; Wang Z; Wu YL
[Ad] Endereço:Medical Research Center, Guangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China.
[Ti] Título:Clinical characteristics and sequence complexity of anaplastic lymphoma kinase gene fusions in Chinese lung cancer patients.
[So] Source:Lung Cancer;114:90-95, 2017 Dec.
[Is] ISSN:1872-8332
[Cp] País de publicação:Ireland
[La] Idioma:eng
[Ab] Resumo:OBJECTIVES: To investigate the clinical characteristics of anaplastic lymphoma kinase (ALK) rearrangements and sequence complexity of the ALK fusion gene in Chinese lung cancer patients. METHODS: We prospectively screened ALK rearrangements in 1474 lung cancer specimens, including 1387 cases of non-small cell lung cancer (NSCLC), 54 cases of small cell lung cancer (SCLC), and 33 cases of cancer with lung metastasis from other organs by both standard polymerase chain reaction (PCR) and rapid amplification of cDNA ends (RACE)-coupled PCR. Fifteen cases of ALK-positive RACE-coupled PCR products were transformed into Escherichia coli for molecular cloning and sequenced for complexity analysis. RESULTS: The overall frequency of ALK rearrangements was 5.1% (71/1387) in NSCLC. In 71 positive cases, the coexistence of epidermal growth factor receptor (EGFR) and ALK variations was found in 6 cases (8.5%), and the coexistence of different ALK variants was found in 2 cases (2.8%) (1 case with variants 1 and 9; the other case with variants 3 and 2) by PCR analysis. Furthermore, through sequence cloning analysis of 15 cases of non-selective ALK-positive samples, two cases with variants 1 and 3 harbored the coexistence of three subtypes (variant 1 subtypes: E13; A20, E13del63; A20 and E7E12E13; A20 and variant 3 subtypes: E6; A20, E6ins33; A20 and E3E6; A20). Variant 3a and 3b subtypes were always coexistent and had the same proportion of ALK variant 3 rearrangements. ALK rearrangement was associated with young age, female gender, never-smokers, those with adenocarcinoma, advanced stage, and EGFR mutations. No ALK fusion was detected in 54 cases of SCLC or 33 cases of cancer with lung metastasis from other organs. CONCLUSIONS: The identification of novel ALK variants, the coexistence of EGFR mutations and ALK fusions, the coexistence of ALK variants, and the coexistence of subtypes reveal the diversity and sequence complexity of ALK fusions.
[Mh] Termos MeSH primário: Grupo com Ancestrais do Continente Asiático/genética
Carcinoma Pulmonar de Células não Pequenas/genética
Fusão Gênica/genética
Neoplasias Pulmonares/genética
Receptores Proteína Tirosina Quinases/genética
Carcinoma de Pequenas Células do Pulmão/genética
[Mh] Termos MeSH secundário: Adenocarcinoma/genética
Adenocarcinoma/patologia
Adulto
Idoso
Idoso de 80 Anos ou mais
Carcinoma Pulmonar de Células não Pequenas/patologia
Feminino
Variação Genética/genética
Variação Estrutural do Genoma/genética
Seres Humanos
Neoplasias Pulmonares/patologia
Neoplasias Pulmonares/secundário
Masculino
Meia-Idade
Terapia de Alvo Molecular/métodos
Estudos Prospectivos
Receptor do Fator de Crescimento Epidérmico/genética
Carcinoma de Pequenas Células do Pulmão/patologia
Fumar/epidemiologia
Fumar/tendências
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 2.7.10.1 (EGFR protein, human); EC 2.7.10.1 (Receptor Protein-Tyrosine Kinases); EC 2.7.10.1 (Receptor, Epidermal Growth Factor); EC 2.7.10.1 (anaplastic lymphoma kinase)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180131
[Lr] Data última revisão:
180131
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171128
[St] Status:MEDLINE


  2 / 217 MEDLINE  
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[PMID]:29050564
[Au] Autor:Thorolfsdottir RB; Sveinbjornsson G; Sulem P; Helgadottir A; Gretarsdottir S; Benonisdottir S; Magnusdottir A; Davidsson OB; Rajamani S; Roden DM; Darbar D; Pedersen TR; Sabatine MS; Jonsdottir I; Arnar DO; Thorsteinsdottir U; Gudbjartsson DF; Holm H; Stefansson K
[Ad] Endereço:deCODE genetics/Amgen, Inc., Reykjavik, Iceland. Electronic address: rosath@decode.is.
[Ti] Título:A Missense Variant in PLEC Increases Risk of Atrial Fibrillation.
[So] Source:J Am Coll Cardiol;70(17):2157-2168, 2017 Oct 24.
[Is] ISSN:1558-3597
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Genome-wide association studies (GWAS) have yielded variants at >30 loci that associate with atrial fibrillation (AF), including rare coding mutations in the sarcomere genes MYH6 and MYL4. OBJECTIVES: The aim of this study was to search for novel AF associations and in doing so gain insights into the mechanisms whereby variants affect AF risk, using electrocardiogram (ECG) measurements. METHODS: The authors performed a GWAS of 14,255 AF cases and 374,939 controls, using whole-genome sequence data from the Icelandic population, and tested novel signals in 2,002 non-Icelandic cases and 12,324 controls. They then tested the AF variants for effect on cardiac electrical function by using measurements in 289,297 ECGs from 62,974 individuals. RESULTS: The authors discovered 2 novel AF variants, the intergenic variant rs72700114, between the genes LINC01142 and METTL11B (risk allele frequency = 8.1%; odds ratio [OR]: 1.26; p = 3.1 × 10 ), and the missense variant p.Gly4098Ser in PLEC (frequency = 1.2%; OR: 1.55; p = 8.0 × 10 ), encoding plectin, a cytoskeletal cross-linking protein that contributes to integrity of cardiac tissue. The authors also confirmed 29 reported variants. p.Gly4098Ser in PLEC significantly affects various ECG measurements in the absence of AF. Other AF variants have diverse effects on the conduction system, ranging from none to extensive. CONCLUSIONS: The discovery of a missense variant in PLEC affecting AF combined with recent discoveries of variants in the sarcomere genes MYH6 and MYL4 points to an important role of myocardial structure in the pathogenesis of the disease. The diverse associations between AF variants and ECG measurements suggest fundamentally different categories of mechanisms contributing to the development of AF.
[Mh] Termos MeSH primário: Fibrilação Atrial/genética
Variação Estrutural do Genoma
[Mh] Termos MeSH secundário: Fibrilação Atrial/fisiopatologia
Eletrocardiografia
Estudo de Associação Genômica Ampla
Seres Humanos
Mutação de Sentido Incorreto/genética
Cadeias Leves de Miosina/genética
Plectina/genética
Risco
Sarcômeros
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Myosin Light Chains); 0 (Plectin); 0 (myosin light chain 4, human)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171117
[Lr] Data última revisão:
171117
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:171021
[St] Status:MEDLINE


  3 / 217 MEDLINE  
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[PMID]:28423598
[Au] Autor:Jaratlerdsiri W; Chan EKF; Petersen DC; Yang C; Croucher PI; Bornman MSR; Sheth P; Hayes VM
[Ad] Endereço:Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Australia.
[Ti] Título:Next generation mapping reveals novel large genomic rearrangements in prostate cancer.
[So] Source:Oncotarget;8(14):23588-23602, 2017 Apr 04.
[Is] ISSN:1949-2553
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS. In this study, we sought to determine the feasibility of using the Irys (Bionano Genomics Inc.) nanochannel NGM technology to generate whole genome maps of a primary prostate tumor and matched blood from a Gleason score 7 (4 + 3), ETS-fusion negative prostate cancer patient. With an effective mapped coverage of 35X and sequence coverage of 60X, and an estimated 43% tumor purity, we identified 85 large somatic structural rearrangements and 6,172 smaller somatic variants, respectively. The vast majority of the large SVs (89%), of which 73% are insertions, were not detectable ab initio using high-coverage short-read NGS. However, guided manual inspection of single NGS reads and de novo assembled scaffolds of NGM-derived candidate regions allowed for confirmation of 94% of these large SVs, with over a third impacting genes with oncogenic potential. From this single-patient study, the first cancer study to integrate NGS and NGM data, we hypothesise that there exists a novel spectrum of large genomic rearrangements in prostate cancer, that these large genomic rearrangements are likely early events in tumorigenesis, and they have potential to enhance taxonomy.
[Mh] Termos MeSH primário: Mapeamento Cromossômico/métodos
Genoma Humano/genética
Variação Estrutural do Genoma
Genômica/métodos
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Neoplasias da Próstata/genética
[Mh] Termos MeSH secundário: Simulação por Computador
DNA de Neoplasias/genética
Estudos de Viabilidade
Deleção de Genes
Rearranjo Gênico
Seres Humanos
Mutação INDEL
Masculino
Meia-Idade
Mutagênese Insercional
Gradação de Tumores
Polimorfismo de Nucleotídeo Único
Neoplasias da Próstata/sangue
Neoplasias da Próstata/patologia
Reprodutibilidade dos Testes
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Neoplasm)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170918
[Lr] Data última revisão:
170918
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170421
[St] Status:MEDLINE
[do] DOI:10.18632/oncotarget.15802


  4 / 217 MEDLINE  
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[PMID]:28188144
[Au] Autor:Repar J; Supek F; Klanjscek T; Warnecke T; Zahradka K; Zahradka D
[Ad] Endereço:Division of Molecular Biology, Ruder Boskovic Institute, 10000 Zagreb, Croatia jelena.repar@irb.hr.
[Ti] Título:Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria.
[So] Source:Genetics;205(4):1677-1689, 2017 Apr.
[Is] ISSN:1943-2631
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A number of bacterial, archaeal, and eukaryotic species are known for their resistance to ionizing radiation. One of the challenges these species face is a potent environmental source of DNA double-strand breaks, potential drivers of genome structure evolution. Efficient and accurate DNA double-strand break repair systems have been demonstrated in several unrelated radiation-resistant species and are putative adaptations to the DNA damaging environment. Such adaptations are expected to compensate for the genome-destabilizing effect of environmental DNA damage and may be expected to result in a more conserved gene order in radiation-resistant species. However, here we show that rates of genome rearrangements, measured as loss of gene order conservation with time, are higher in radiation-resistant species in multiple, phylogenetically independent groups of bacteria. Comparison of indicators of selection for genome organization between radiation-resistant and phylogenetically matched, nonresistant species argues against tolerance to disruption of genome structure as a strategy for radiation resistance. Interestingly, an important mechanism affecting genome rearrangements in prokaryotes, the symmetrical inversions around the origin of DNA replication, shapes genome structure of both radiation-resistant and nonresistant species. In conclusion, the opposing effects of environmental DNA damage and DNA repair result in elevated rates of genome rearrangements in radiation-resistant bacteria.
[Mh] Termos MeSH primário: Deinococcus/genética
Instabilidade Genômica
Variação Estrutural do Genoma
Tolerância a Radiação/genética
[Mh] Termos MeSH secundário: Deinococcus/efeitos da radiação
Raios gama
Genoma Bacteriano
Seleção Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170922
[Lr] Data última revisão:
170922
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170212
[St] Status:MEDLINE
[do] DOI:10.1534/genetics.116.196154


  5 / 217 MEDLINE  
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[PMID]:28179367
[Au] Autor:Imprialou M; Kahles A; Steffen JG; Osborne EJ; Gan X; Lempe J; Bhomra A; Belfield E; Visscher A; Greenhalgh R; Harberd NP; Goram R; Hein J; Robert-Seilaniantz A; Jones J; Stegle O; Kover P; Tsiantis M; Nordborg M; Rätsch G; Clark RM; Mott R
[Ad] Endereço:Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, United Kingdom.
[Ti] Título:Genomic Rearrangements in Considered as Quantitative Traits.
[So] Source:Genetics;205(4):1425-1441, 2017 Apr.
[Is] ISSN:1943-2631
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between a structural variant trait at one locus, and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3×) population sequence data from 488 recombinant inbred genomes, we identified 6502 segregating structural variants. Remarkably, 25% of these were transpositions. While many structural variants cannot be delineated precisely, we validated 83% of 44 predicted transposition breakpoints by polymerase chain reaction. We show that specific structural variants may be causative for quantitative trait loci for germination and resistance to infection by the fungus , isolate Nc14. Further we show that the phenotypic heritability attributable to read-mapping anomalies differs from, and, in the case of time to germination and bolting, exceeds that due to standard genetic variation. Genes within structural variants are also more likely to be silenced or dysregulated. This approach complements the prevalent strategy of structural variant discovery in fewer individuals sequenced at high coverage. It is generally applicable to large populations sequenced at low-coverage, and is particularly suited to mapping transpositions.
[Mh] Termos MeSH primário: Arabidopsis/genética
Variação Estrutural do Genoma
Característica Quantitativa Herdável
[Mh] Termos MeSH secundário: Arabidopsis/crescimento & desenvolvimento
Arabidopsis/imunologia
Fenótipo
Imunidade Vegetal/genética
Locos de Características Quantitativas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170922
[Lr] Data última revisão:
170922
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170210
[St] Status:MEDLINE
[do] DOI:10.1534/genetics.116.192823


  6 / 217 MEDLINE  
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[PMID]:28096516
[Au] Autor:Berg JS; Agrawal PB; Bailey DB; Beggs AH; Brenner SE; Brower AM; Cakici JA; Ceyhan-Birsoy O; Chan K; Chen F; Currier RJ; Dukhovny D; Green RC; Harris-Wai J; Holm IA; Iglesias B; Joseph G; Kingsmore SF; Koenig BA; Kwok PY; Lantos J; Leeder SJ; Lewis MA; McGuire AL; Milko LV; Mooney SD; Parad RB; Pereira S; Petrikin J; Powell BC; Powell CM; Puck JM; Rehm HL; Risch N; Roche M; Shieh JT; Veeraraghavan N; Watson MS; Willig L; Yu TW; Urv T; Wise AL
[Ad] Endereço:Departments of Genetics and jonathan_berg@med.unc.edu.
[Ti] Título:Newborn Sequencing in Genomic Medicine and Public Health.
[So] Source:Pediatrics;139(2), 2017 Feb.
[Is] ISSN:1098-4275
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The rapid development of genomic sequencing technologies has decreased the cost of genetic analysis to the extent that it seems plausible that genome-scale sequencing could have widespread availability in pediatric care. Genomic sequencing provides a powerful diagnostic modality for patients who manifest symptoms of monogenic disease and an opportunity to detect health conditions before their development. However, many technical, clinical, ethical, and societal challenges should be addressed before such technology is widely deployed in pediatric practice. This article provides an overview of the Newborn Sequencing in Genomic Medicine and Public Health Consortium, which is investigating the application of genome-scale sequencing in newborns for both diagnosis and screening.
[Mh] Termos MeSH primário: Testes Genéticos
Triagem Neonatal
Saúde Pública
Análise de Sequência de DNA
[Mh] Termos MeSH secundário: Exoma/genética
Triagem de Portadores Genéticos
Pesquisa em Genética
Estudo de Associação Genômica Ampla
Variação Estrutural do Genoma/genética
Seres Humanos
Recém-Nascido
Unidades de Terapia Intensiva Neonatal
Valor Preditivo dos Testes
Estudos Prospectivos
Estados Unidos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RANDOMIZED CONTROLLED TRIAL
[Em] Mês de entrada:1706
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:170119
[St] Status:MEDLINE


  7 / 217 MEDLINE  
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[PMID]:28031184
[Au] Autor:Ganel L; Abel HJ; Hall IM; FinMetSeq Consortium
[Ad] Endereço:McDonnell Genome Institute.
[Ti] Título:SVScore: an impact prediction tool for structural variation.
[So] Source:Bioinformatics;33(7):1083-1085, 2017 Apr 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Summary: Here we present SVScore, a tool for in silico structural variation (SV) impact prediction. SVScore aggregates per-base single nucleotide polymorphism (SNP) pathogenicity scores across relevant genomic intervals for each SV in a manner that considers variant type, gene features and positional uncertainty. We show that the allele frequency spectrum of high-scoring SVs is strongly skewed toward lower frequencies, suggesting that they are under purifying selection, and that SVScore identifies deleterious variants more effectively than alternative methods. Notably, our results also suggest that duplications are under surprisingly strong selection relative to deletions, and that there are a similar number of strongly pathogenic SVs and SNPs in the human population. Availability and Implementation: SVScore is implemented in Perl and available freely at {{ http://www.github.com/lganel/SVScore }} for use under the MIT license. Contact: ihall@wustl.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Variação Estrutural do Genoma
Software
[Mh] Termos MeSH secundário: Frequência do Gene
Genômica/métodos
Seres Humanos
Polimorfismo de Nucleotídeo Único
Deleção de Sequência
[Pt] Tipo de publicação:EVALUATION STUDIES; JOURNAL ARTICLE
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170614
[Lr] Data última revisão:
170614
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161230
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btw789


  8 / 217 MEDLINE  
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[PMID]:27730700
[Au] Autor:Cox SN; Pesce F; El-Sayed Moustafa JS; Sallustio F; Serino G; Kkoufou C; Giampetruzzi A; Ancona N; Falchi M; Schena FP; European IgAN Consortium
[Ad] Endereço:Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy.
[Ti] Título:Multiple rare genetic variants co-segregating with familial IgA nephropathy all act within a single immune-related network.
[So] Source:J Intern Med;281(2):189-205, 2017 Feb.
[Is] ISSN:1365-2796
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: IgA nephropathy (IgAN) is a common complex disease with a strong genetic involvement. We aimed to identify novel, rare, highly penetrant risk variants combining family-based linkage analysis with whole-exome sequencing (WES). METHODS: Linkage analysis of 16 kindreds of South Italian ancestry was performed using an 'affected-only' strategy. Eight most informative trios composed of two familial cases and an intrafamilial control were selected for WES. High-priority variants in linked regions were identified and validated using Sanger sequencing. Custom TaqMan assays were designed and carried out in the 16 kindreds and an independent cohort of 240 IgAN patients and 113 control subjects. RESULTS: We found suggestive linkage signals in 12 loci. After sequential filtering and validation of WES data, we identified 24 private or extremely rare (MAF <0.0003) linked variants segregating with IgAN status. These were present within coding or regulatory regions of 23 genes that merged into a common functional network. The genes were interconnected by AKT, CTNNB1, NFKB, MYC and UBC, key modulators of WNT/ß-catenin and PI3K/Akt pathways, which are implicated in IgAN pathogenesis. Overlaying publicly available expression data, genes/proteins with expression notably altered in IgAN were included in this immune-related network. In particular, the network included the glucocorticoid receptor gene, NR3C1, which is the target of corticosteroid therapy routinely used in the treatment of IgAN. CONCLUSION: Our findings suggest that disease susceptibility could be influenced by multiple rare variants acting in a common network that could provide the starting point for the identification of potential drug targets for personalized therapy.
[Mh] Termos MeSH primário: Exoma
Genoma Humano
Variação Estrutural do Genoma
Glomerulonefrite por IGA/genética
[Mh] Termos MeSH secundário: Ligação Genética
Predisposição Genética para Doença
Glomerulonefrite por IGA/imunologia
Seres Humanos
Linhagem
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170621
[Lr] Data última revisão:
170621
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161013
[St] Status:MEDLINE
[do] DOI:10.1111/joim.12565


  9 / 217 MEDLINE  
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[PMID]:27540267
[Au] Autor:Hilker R; Stadermann KB; Schwengers O; Anisiforov E; Jaenicke S; Weisshaar B; Zimmermann T; Goesmann A
[Ad] Endereço:Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany.
[Ti] Título:ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
[So] Source:Bioinformatics;32(24):3702-3708, 2016 Dec 15.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:MOTIVATION: The vast amount of already available and currently generated read mapping data requires comprehensive visualization, and should benefit from bioinformatics tools offering a wide spectrum of analysis functionality from just one source. Appropriate handling of multiple mapped reads during mapping analyses remains an issue that demands improvement. RESULTS: The capabilities of the read mapping analysis and visualization tool ReadXplorer were vastly enhanced. Here, we present an even finer granulated read mapping classification, improving the level of detail for analyses and visualizations. The spectrum of automatic analysis functions has been broadened to include genome rearrangement detection as well as correlation analysis between two mapping data sets. Existing functions were refined and enhanced, namely the computation of differentially expressed genes, the read count and normalization analysis and the transcription start site detection. Additionally, ReadXplorer 2 features a highly improved support for large eukaryotic data sets and a command line version, enabling its integration into workflows. Finally, the new version is now able to display any kind of tabular results from other bioinformatics tools. AVAILABILITY AND IMPLEMENTATION: http://www.readxplorer.org CONTACT: readxplorer@computational.bio.uni-giessen.deSupplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Variação Estrutural do Genoma
Análise de Sequência de RNA/métodos
Software
Sítio de Iniciação de Transcrição
[Mh] Termos MeSH secundário: Arabidopsis/genética
Expressão Gênica
Genoma
RNA de Plantas/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Plant)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170816
[Lr] Data última revisão:
170816
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160820
[St] Status:MEDLINE


  10 / 217 MEDLINE  
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[PMID]:27521814
[Au] Autor:Kiran K; Rawal HC; Dubey H; Jaswal R; Devanna BN; Gupta DK; Bhardwaj SC; Prasad P; Pal D; Chhuneja P; Balasubramanian P; Kumar J; Swami M; Solanke AU; Gaikwad K; Singh NK; Sharma TR
[Ad] Endereço:ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
[Ti] Título:Draft Genome of the Wheat Rust Pathogen (Puccinia triticina) Unravels Genome-Wide Structural Variations during Evolution.
[So] Source:Genome Biol Evol;8(9):2702-21, 2016 Sep 11.
[Is] ISSN:1759-6653
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Leaf rust is one of the most important diseases of wheat and is caused by Puccinia triticina, a highly variable rust pathogen prevalent worldwide. Decoding the genome of this pathogen will help in unraveling the molecular basis of its evolution and in the identification of genes responsible for its various biological functions. We generated high quality draft genome sequences (approximately 100- 106 Mb) of two races of P. triticina; the variable and virulent Race77 and the old, avirulent Race106. The genomes of races 77 and 106 had 33X and 27X coverage, respectively. We predicted 27678 and 26384 genes, with average lengths of 1,129 and 1,086 bases in races 77 and 106, respectively and found that the genomes consisted of 37.49% and 39.99% repetitive sequences. Genome wide comparative analysis revealed that Race77 differs substantially from Race106 with regard to segmental duplication (SD), repeat element, and SNP/InDel characteristics. Comparative analyses showed that Race 77 is a recent, highly variable and adapted Race compared with Race106. Further sequence analyses of 13 additional pathotypes of Race77 clearly differentiated the recent, active and virulent, from the older pathotypes. Average densities of 2.4 SNPs and 0.32 InDels per kb were obtained for all P. triticina pathotypes. Secretome analysis demonstrated that Race77 has more virulence factors than Race 106, which may be responsible for the greater degree of adaptation of this pathogen. We also found that genes under greater selection pressure were conserved in the genomes of both races, and may affect functions crucial for the higher levels of virulence factors in Race77. This study provides insights into the genome structure, genome organization, molecular basis of variation, and pathogenicity of P. triticina The genome sequence data generated in this study have been submitted to public domain databases and will be an important resource for comparative genomics studies of the more than 4000 existing Puccinia species.
[Mh] Termos MeSH primário: Basidiomycota/genética
Evolução Molecular
Genoma Fúngico
Variação Estrutural do Genoma
[Mh] Termos MeSH secundário: Basidiomycota/patogenicidade
Proteínas Fúngicas/genética
Mutação INDEL
Polimorfismo de Nucleotídeo Único
Fatores de Virulência/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Fungal Proteins); 0 (Virulence Factors)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171102
[Lr] Data última revisão:
171102
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160814
[St] Status:MEDLINE
[do] DOI:10.1093/gbe/evw197



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