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1.
Pestic Biochem Physiol ; 157: 80-87, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31153480

RESUMO

The European red mite Panonychus ulmi (Koch) is a major pest of apple trees worldwide and causes significant damage to apple orchards in Iran. Pyrethroid insecticides/acaricides, such as fenpropathrin and fenvalerate, are widely used to control P. ulmi, but their long-term use may lead to low efficacy. Earlier studies investigating pyrethroid resistance in closely related mites such as Tetranychus urticae revealed that pyrethroid resistance was associated with point mutations in the voltage-gated sodium channel gene (vgsc). The aim of this study was to investigate the biochemical and molecular mechanisms of fenpropathrin and fenvalerate resistance in Iranian populations of P. ulmi. Pyrethroid toxicity bioassays were carried out on different P. ulmi field populations. Marand (resistance ratio, RR = 149), Maraqeh (RR = 90) and Mianeh2 (RR = 71) populations exhibited high levels of resistance to fenpropathrin, compared to a susceptible field population (Shahin Dej). Resistance was also observed for fenvalerate with resistance ratio's ranging from 2- to 20-fold. Synergism experiments and enzyme activity assays predicted a minor role for classical detoxification enzymes. In contrast, two amino acid substitutions in the VGSC, L1024V and F1538I, that were previously shown to confer pyrethroid resistance, were detected in all three resistant P. ulmi populations and point towards target-site insensitivity as the most likely resistance mechanism. Furthermore, sequencing after cloning of vgsc fragments from single haploid males revealed the presence of multiple copies of vgsc in a highly resistant strain. The link between resistance mutations and vgsc copy number variation should be the subject of future study, as this might be used to develop molecular markers for monitoring pyrethroid resistance of P. ulmi in the field.


Assuntos
Mutação Puntual/genética , Piretrinas/farmacologia , Canais de Sódio Disparados por Voltagem/genética , Animais , Variações do Número de Cópias de DNA/genética , Duplicação Gênica/efeitos dos fármacos , Duplicação Gênica/genética , Resistência a Inseticidas/genética , Irã (Geográfico) , Ácaros , Canais de Sódio Disparados por Voltagem/metabolismo
2.
BMC Bioinformatics ; 20(1): 336, 2019 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-31208319

RESUMO

BACKGROUND: Numerical chromosomal variation is a hallmark of populations of malignant cells. Identifying the factors that promote numerical chromosomal variation is important for understanding mechanisms of carcinogenesis. However, the ability to quantify and visualize differences in chromosome number between experimentally-defined groups (e.g. control vs treated) obtained from single-cell experiments is currently limited by the lack of user-friendly software. RESULTS: Aneuvis is a web application that allows users to determine whether numerical chromosomal variation exists between experimental treatment groups. The web interface allows users to upload molecular cytogenetic or processed single cell whole-genome sequencing data in a cell-by-chromosome matrix format and automatically generates visualizations and summary statistics that reflect the degree of numeric chromosomal variability. CONCLUSIONS: Aneuvis is the first user-friendly web application to help researchers identify the genetic and environmental perturbations that promote numerical chromosomal variation. Aneuvis is freely available as a web application at https://dpique.shinyapps.io/aneuvis/ and the source code for the application is available at https://github.com/dpique/aneuvis .


Assuntos
Cromossomos/genética , Internet , Análise de Célula Única , Software , Linhagem Celular , Variações do Número de Cópias de DNA/genética , Humanos , Interface Usuário-Computador , Sequenciamento Completo do Genoma
3.
Virchows Arch ; 475(3): 383-389, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31250201

RESUMO

Gastric hyperplastic polyps are common and generally regarded as benign lesions, whereas gastric adenocarcinomas infrequently occur from gastric hyperplastic polyps. Although gastric hyperplastic polyps have received a lot of attention because of their association with malignant transformation, it remains unclear whether gastric hyperplastic polyps are neoplastic lesions that have sporadic genetic changes similar to colorectal hyperplastic polyps. We performed genome-wide analyses of two gastric adenocarcinomas with hyperplastic polyp components. The interface between "adenocarcinoma" and "hyperplastic polyp" components was fairly sharp, and the adenocarcinoma components had copy number alterations and TP53 mutations, whereas the hyperplastic polyp components had only single nucleotide polymorphisms, which were also found in adenocarcinoma components. We did not detect any somatic changes in the hyperplastic polyp components, even in genome-wide analyses, which was in contrast to the adenocarcinoma components. However, due to the small number of cases examined herein, further genetic analyses of more cases are needed.


Assuntos
Pólipos Adenomatosos/patologia , Pólipos Intestinais/patologia , Neoplasias Gástricas/genética , Adenocarcinoma/patologia , Idoso , Idoso de 80 Anos ou mais , Transformação Celular Neoplásica/patologia , Hibridização Genômica Comparativa/métodos , Variações do Número de Cópias de DNA/genética , Feminino , Estudo de Associação Genômica Ampla/métodos , Humanos , Hiperplasia , Polimorfismo de Nucleotídeo Único/genética , Pólipos/patologia , Neoplasias Gástricas/patologia , Proteína Supressora de Tumor p53/genética
4.
Nat Commun ; 10(1): 2595, 2019 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-31197163

RESUMO

Plasmid acquisition is an important mechanism of rapid adaptation and niche expansion in prokaryotes. Positive selection for plasmid-coded functions is a major driver of plasmid evolution, while plasmids that do not confer a selective advantage are considered costly and expected to go extinct. Yet, plasmids are ubiquitous in nature, and their persistence remains an evolutionary paradox. Here, we demonstrate that non-mobile plasmids persist over evolutionary timescales without selection for the plasmid function. Evolving a minimal plasmid encoding for antibiotics resistance in Escherichia coli, we discover that plasmid stability emerges in the absence of antibiotics and that plasmid loss is determined by transcription-replication conflicts. We further find that environmental conditions modulate these conflicts and plasmid persistence. Silencing the transcription of the resistance gene results in stable plasmids that become fixed in the population. Evolution of plasmid stability under non-selective conditions provides an evolutionary explanation for the ubiquity of plasmids in nature.


Assuntos
Adaptação Biológica/genética , Resistência Microbiana a Medicamentos/genética , Escherichia coli/genética , Plasmídeos/genética , Antibacterianos/farmacologia , Variações do Número de Cópias de DNA/genética , Evolução Molecular Direcionada/métodos , Genoma Bacteriano/genética , Plasmídeos/efeitos dos fármacos , Temperatura Ambiente
5.
Gene ; 706: 162-171, 2019 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-31085274

RESUMO

In clinical genetics, the need to discriminate between benign and pathogenic variants identified in patients with neurodevelopmental disorders is an absolute necessity. Copy number variants (CNVs) of small size can enable the identification of genes that are critical for neurologic development. However, assigning a definite association with a specific disorder is a difficult task. Among 328 trios analyzed over seven years of activity in a single laboratory, we identified 19 unrelated patients (5.8%) who carried a small (<500 kb) de novo CNV. Four patients had an additional independent de novo CNV. Nine had a variant that could be assigned as definitely pathogenic, whereas the remaining CNVs were considered as variants of unknown significance (VUS). We report clinical and molecular findings of patients harboring VUS. We reviewed the medical literature available for genes impacted by CNVs, obtained the probability of truncating loss-of-function intolerance, and compared overlapping CNVs reported in databases. The classification of small non-recurrent CNVs remains difficult but, among our findings, we provide support for a role of SND1 in the susceptibility of autism, describe a new case of the rare 17p13.1 microduplication syndrome, and report an X-linked duplication involving KIF4A and DLG3 as a likely cause of epilepsy.


Assuntos
Variações do Número de Cópias de DNA/genética , Transtornos do Neurodesenvolvimento/genética , Adulto , Transtorno Autístico/genética , Criança , Pré-Escolar , Epilepsia/genética , Feminino , Humanos , Lactente , Deficiência Intelectual/genética , Cinesina/genética , Masculino , Proteínas Nucleares/genética , Proteínas Nucleares/fisiologia , Fatores de Transcrição/genética
6.
Surg Clin North Am ; 99(3): 403-418, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31047032

RESUMO

Esophageal cancer and gastric cancer are leading causes of cancer-related mortality worldwide. In this article, the authors discuss the molecular biology of esophageal and gastric cancer with a focus on esophageal adenocarcinoma. They review data from The Cancer Genome Atlas project and advances in the molecular stratification and classification of esophageal carcinoma and gastric cancer. They also summarize advances in microRNA, molecular staging, gene expression profiling, tumor microenvironment, and detection of circulating tumor DNA. Finally, the authors summarize some of the implications of understanding the molecular basis of esophageal cancer and future directions in the management of esophageal cancer.


Assuntos
Adenocarcinoma/genética , Neoplasias Esofágicas/genética , Neoplasias Gástricas/genética , Adenocarcinoma/epidemiologia , Esôfago de Barrett/epidemiologia , Esôfago de Barrett/genética , Variações do Número de Cópias de DNA/genética , DNA de Neoplasias/genética , DNA de Neoplasias/metabolismo , Neoplasias Esofágicas/epidemiologia , Previsões , Regulação Neoplásica da Expressão Gênica , Genoma Humano , Humanos , Metástase Linfática , MicroRNAs , Mutação/genética , Estadiamento de Neoplasias , Fatores de Risco , Neoplasias Gástricas/epidemiologia , Microambiente Tumoral
7.
BMC Bioinformatics ; 20(1): 266, 2019 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-31138108

RESUMO

BACKGROUND: There are over 25 tools dedicated for the detection of Copy Number Variants (CNVs) using Whole Exome Sequencing (WES) data based on read depth analysis. The tools reported consist of several steps, including: (i) calculation of read depth for each sequencing target, (ii) normalization, (iii) segmentation and (iv) actual CNV calling. The essential aspect of the entire process is the normalization stage, in which systematic errors and biases are removed and the reference sample set is used to increase the signal-to-noise ratio. Although some CNV calling tools use dedicated algorithms to obtain the optimal reference sample set, most of the advanced CNV callers do not include this feature. To our knowledge, this work is the first attempt to assess the impact of reference sample set selection on CNV detection performance. METHODS: We used WES data from the 1000 Genomes project to evaluate the impact of various methods of reference sample set selection on CNV calling performance of three chosen state-of-the-art tools: CODEX, CNVkit and exomeCopy. Two naive solutions (all samples as reference set and random selection) as well as two clustering methods (k-means and k nearest neighbours (kNN) with a variable number of clusters or group sizes) have been evaluated to discover the best performing sample selection method. RESULTS AND CONCLUSIONS: The performed experiments have shown that the appropriate selection of the reference sample set may greatly improve the CNV detection rate. In particular, we found that smart reduction of reference sample size may significantly increase the algorithms' precision while having negligible negative effect on sensitivity. We observed that a complete CNV calling process with the k-means algorithm as the selection method has significantly better time complexity than kNN-based solution.


Assuntos
Algoritmos , Variações do Número de Cópias de DNA/genética , Benchmarking , Bases de Dados Genéticas , Feminino , Humanos , Masculino , Padrões de Referência , Tamanho da Amostra
8.
BMC Bioinformatics ; 20(1): 265, 2019 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-31132991

RESUMO

BACKGROUND: In standard high throughput sequencing analysis, genetic variants are not assigned to a homologous chromosome of origin. This process, called haplotype phasing, can reveal information important for understanding the relationship between genetic variants and biological phenotypes. For example, in genes that carry multiple heterozygous missense variants, phasing resolves whether one or both gene copies are altered. Here, we present a novel approach to phasing variants that takes advantage of unique properties of paired tumor:normal sequencing data from cancer studies. RESULTS: VAF phasing uses changes in variant allele frequency (VAF) between tumor and normal samples in regions of somatic chromosomal gain or loss to phase germline variants. We apply VAF phasing to 6180 samples from the Cancer Genome Atlas (TCGA) and demonstrate that our method is highly concordant with other standard phasing methods, and can phase an average of 33% more variants than other read-backed phasing methods. Using variant annotation tools designed to score gene haplotypes, we find a suggestive association between carrying multiple missense variants in a single copy of a cancer predisposition gene and earlier age of cancer diagnosis. CONCLUSIONS: VAF phasing exploits unique properties of tumor genomes to increase the number of germline variants that can be phased over standard read-backed methods in paired tumor:normal samples. Our phase-informed association testing results call attention to the need to develop more tools for assessing the joint effect of multiple genetic variants.


Assuntos
Variação Genética , Neoplasias/genética , Análise de Sequência de DNA , Sequência de Bases , Variações do Número de Cópias de DNA/genética , Frequência do Gene/genética , Predisposição Genética para Doença , Haplótipos/genética , Humanos
9.
BMC Cancer ; 19(1): 422, 2019 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-31060523

RESUMO

BACKGROUND: Ovarian carcinomas presenting homologous recombination deficiency (HRD), which is observed in about 50% of cases, are more sensitive to platinum and PARP inhibitor therapies. Although platinum resistant disease has a low chance to be responsive to platinum-based chemotherapy, a set of patients is retreated with platinum and some of them are responsive. In this study, we evaluated copy number alterations, HR gene mutations and HR deficiency scores in ovarian cancer patients with prolonged platinum sensitivity. METHODS: In this retrospective study (2005 to 2014), we selected 31 patients with platinum resistant ovarian cancer retreated with platinum therapy. Copy number alterations and HR scores were evaluated using the OncoScan® FFPE platform in 15 cases. The mutational profile of 24 genes was investigated by targeted-NGS. RESULTS: The median values of the four HRD scores were higher in responders (LOH = 15, LST = 28, tAI = 33, CS = 84) compared with non-responders (LOH = 7.5, LST = 17.5, tAI = 23, CS = 47). Patients with high LOH, LST, tAI and CS scores had better response rates, although these differences were not statistically significant. Response rate to platinum retreatment was 22% in patients with CCNE1 gains and 83.5% in patients with no CCNE1 gains (p = 0.041). Furthermore, response rate was 54.5% in patients with RB1 loss and 25% in patients without RB1 loss (p = 0.569). Patients with CCNE1 gains showed a worse progression free survival (PFS = 11.1 months vs 3.7 months; p = 0.008) and a shorter overall survival (OS = 39.3 months vs 7.1 months; p = 0.007) in comparison with patients with no CCNE1 gains. Patients with RB1 loss had better PFS (9.0 months vs 2.6 months; p = 0.093) and OS (27.4 months vs 3.6 months; p = 0.025) compared with cases with no RB1 loss. Four tumor samples were BRCA mutated and tumor mutations were not associated with response to treatment. CONCLUSIONS: HR deficiency was found in 60% of our cases and HRD medium values were higher in responders than in non-responders. Despite the small number of patients tested, CCNE1 gain and RB1 loss discriminate patients with tumors extremely sensitive to platinum retreatment.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/farmacologia , Ciclina E/genética , Resistencia a Medicamentos Antineoplásicos/genética , Proteínas Oncogênicas/genética , Neoplasias Ovarianas/genética , Compostos de Platina/farmacologia , Proteínas de Ligação a Retinoblastoma/genética , Ubiquitina-Proteína Ligases/genética , Idoso , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Brasil/epidemiologia , Pré-Escolar , Variações do Número de Cópias de DNA/genética , Análise Mutacional de DNA , Feminino , Recombinação Homóloga/genética , Humanos , Pessoa de Meia-Idade , Neoplasias Ovarianas/tratamento farmacológico , Neoplasias Ovarianas/mortalidade , Compostos de Platina/uso terapêutico , Intervalo Livre de Progressão , Retratamento , Estudos Retrospectivos , Análise de Sobrevida
10.
Scand J Immunol ; 90(2): e12776, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31069824

RESUMO

The number of the X chromosome-linked genes has been previously suggested to influence immune responses and the development of autoimmune diseases. In the present study, we aimed at evaluating the level of expression of CD40L (an X-linked gene involved in adaptive immunity) and TLR7 (an X-linked gene involved in innate immunity) in a variety of different karyotypes. Those included males, females and patients with X chromosome aneuploidy. Healthy females (46, XX; n = 10) and healthy males (46, XY; n = 10) were compared to females with Turner syndrome (TS) (45, X; n = 11) and males with Klinefelter syndrome (KS) (47, XXY; n = 5). Stimulation of peripheral blood mononuclear cells (PBMCs) with PMA and ionomycin resulted in higher percentage of CD3 + CD40L+ T cells (P < 0.001) and higher level expression of CD40L in T cell (P < 0.001) in female and KS patients compared with male and TS patients. TLR7-mediated IFN-alpha production by HLADR + CD3- CD19- cells was significantly upregulated in healthy women compared with healthy males, TS and KS patients (P < 0.001). TLR7 agonist-stimulated PBMCs from healthy females and KS patients expressed significantly higher levels of TLR7 mRNA than those from male and TS patients (P < 0.05). The increased expression of the X-linked genes TLR7 and CD40L in healthy females and KS patients suggests that the presence of two X chromosomes plays a major role in enhancing both innate and adaptive immune responses. These results may contribute to the explanation of sex-based differences in immune biology and the sex bias in predisposition to autoimmune diseases.


Assuntos
Imunidade Adaptativa/genética , Ligante de CD40/biossíntese , Ligante de CD40/genética , Cromossomos Humanos X/genética , Dosagem de Genes/genética , Imunidade Inata/genética , Receptor 7 Toll-Like/biossíntese , Receptor 7 Toll-Like/genética , Imunidade Adaptativa/imunologia , Antígenos CD19/biossíntese , Complexo CD3/biossíntese , Células Cultivadas , Variações do Número de Cópias de DNA/genética , Feminino , Humanos , Imunidade Inata/imunologia , Interferon-alfa/biossíntese , Ionomicina/farmacologia , Síndrome de Klinefelter/genética , Leucócitos Mononucleares/metabolismo , Ativação Linfocitária/efeitos dos fármacos , Ativação Linfocitária/imunologia , Masculino , Ácidos Polimetacrílicos/farmacologia , RNA Mensageiro/biossíntese , Linfócitos T/efeitos dos fármacos , Linfócitos T/imunologia , Síndrome de Turner/genética
11.
Zhonghua Fu Chan Ke Za Zhi ; 54(4): 221-225, 2019 Apr 25.
Artigo em Chinês | MEDLINE | ID: mdl-31006186

RESUMO

Objective: To investigate pathogenic genes related to the phenotype of fetus with severely short limbs in the first and second trimester by whole exome sequencing (WES). Methods: Thirteen fetuses with severely short limbs detected by ultrasonography in the first and second trimester admitted in Chinese PLA General Hospital from September 2016 to June 2018 were collected. All cases were performed induced abortion, 6 of which were carried out karyotype analysis of amniotic fluid at the same time. WES and copy number variations (CNV) were performed on specimens from fetal tissues after labor induction. The suspected pathogenic mutations were validated by Sanger sequencing reactions. Results: No abnormal karyotypes or pathological CNV were found. In 10 fetuses, pathogenic or possibly pathogenic mutations were detected in the following genes: COL2A1, FGFR3, COL1A1, COL1A2, DYNC2LI1 and TRIP11, all of which were essential to skeletal development. The diagnostic yield of WES in the fetuses with severe short limbs was 10/13. Conclusions: In the first and second trimester, most of the fetuses with extremely short limbs suffer from monogenic diseases. WES is likely to be a valuable diagnostic testing option for the fetuses with severe short limbs.


Assuntos
Anormalidades Congênitas/genética , Dineínas do Citoplasma , Variações do Número de Cópias de DNA , Desenvolvimento Fetal/genética , Feto/anormalidades , Sequenciamento Completo do Exoma/métodos , Anormalidades Congênitas/diagnóstico , Variações do Número de Cópias de DNA/genética , Feminino , Feto/diagnóstico por imagem , Humanos , Cariotipagem , Gravidez , Primeiro Trimestre da Gravidez , Segundo Trimestre da Gravidez , Ultrassonografia Pré-Natal
12.
BMC Cancer ; 19(1): 396, 2019 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-31029168

RESUMO

BACKGROUND: With the introduction of Olaparib treatment for BRCA-deficient recurrent ovarian cancer, testing for somatic and/or germline mutations in BRCA1/2 genes in tumor tissues became essential for treatment decisions. In most cases only formalin-fixed paraffin-embedded (FFPE) samples, containing fragmented and chemically modified DNA of minor quality, are available. Thus, multiplex PCR-based sequencing is most commonly applied in routine molecular testing, which is predominantly focused on the identification of known hot spot mutations in oncogenes. METHODS: We compared the overall performance of an adjusted targeted capture-based enrichment protocol and a multiplex PCR-based approach for calling of pathogenic SNVs and InDels using DNA extracted from 13 FFPE tissue samples. We further applied both strategies to seven blood samples and five matched FFPE tumor tissues of patients with known germline exon-spanning deletions and gene-wide duplications in BRCA1/2 to evaluate CNV detection based solely on panel NGS data. Finally, we analyzed DNA from FFPE tissues of 11 index patients from families suspected of having hereditary breast and ovarian cancer, of whom no blood samples were available for testing, in order to identify underlying pathogenic germline BRCA1/2 mutations. RESULTS: The multiplex PCR-based protocol produced inhomogeneous coverage among targets of each sample and between samples as well as sporadic amplicon drop out, leading to insufficiently or non-covered nucleotides, which subsequently hindered variant detection. This protocol further led to detection of PCR-artifacts that could easily have been misinterpreted as pathogenic mutations. No such limitations were observed by application of an adjusted targeted capture-based protocol, which allowed for CNV calling with 86% sensitivity and 100% specificity. All pathogenic CNVs were confirmed in the five matched FFPE tumor samples from patients carrying known pathogenic germline mutations and we additionally identified somatic loss of the second allele in BRCA1/2. Furthermore we detected pathogenic BRCA1/2 variants in four the eleven FFPE samples from patients of whom no blood was available for analysis. CONCLUSIONS: We demonstrate that an adjusted targeted capture-based enrichment protocol is superior to commonly applied multiplex PCR-based protocols for reliable BRCA1/2 variant detection, including CNV-detection, using FFPE tumor samples.


Assuntos
Proteína BRCA1/genética , Proteína BRCA2/genética , Neoplasias da Mama/genética , Mutação em Linhagem Germinativa , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Neoplasias Ovarianas/genética , Neoplasias da Mama/sangue , Neoplasias da Mama/diagnóstico , Variações do Número de Cópias de DNA/genética , Feminino , Formaldeído/química , Humanos , Mutação INDEL , Masculino , Reação em Cadeia da Polimerase Multiplex/métodos , Neoplasias Ovarianas/sangue , Neoplasias Ovarianas/diagnóstico , Inclusão em Parafina , Linhagem , Reprodutibilidade dos Testes , Fixação de Tecidos
13.
J Biotechnol ; 298: 76-81, 2019 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-31002856

RESUMO

Ovarian tumor is one of the leading causes of cancer among women. Patients are diagnosed at an advanced stage, usually. There is a need for new specific and sensitive biomarkers. Mitochondrial DNA copy number change was observed in various cancers. Our aim was to detect mitochondrial DNA copy number in whole blood (wb-mtDNA) and in plasma (cell-free and exosome encapsulated mtDNA) in patients with serous epithelial ovarian tumor. DNA was isolated from EDTA blood and plasma obtained from 24 patients and 24 healthy controls. Exosomes were isolated from cell-free plasma, and exosome encapsulated DNA (exoDNA) was extracted. Quantitative-real-time PCR was performed with Human Mitochondrial DNA (mtDNA) Monitoring Primer Set. Kruskall­Wallis and Mann­Whitney U test were used for data analysis. Wb-mtDNA copy number was significantly different among healthy controls and patients in multiple comparison (p = 0.0090 considering FIGO stage independently, and p = 0.0048 considering early- and late-stage cancers). There was a significant decrease among early-stage, all advanced stage and all cancer patients (FIGO I: 32.5 ± 8.3, p = 0.0061; FIGO III + IV: 37.2 ± 13.7 p = 0.0139; FIGO I + III + IV: 35.6 ± 12.2, p = 0.0017) or FIGO III patients alone (32.8 ± 5.6, p = 0.00089) compared to healthy controls. We found significant increase in copy number in exosomal mtDNA in cancer patients (236.0 ± 499.0, p = 0.0155), advanced-stage cancer patients (333.0 ± 575.0, p = 0.0095), of FIGO III (362.0 ± 609.2, p = 0.0494), and FIGO IV (304.0 ± 585.0, p = 0.0393) patients alone but not in samples of FIGO I patients (10.0 ± 3.5, p = 0.3907). In multiple comparison the increase was significant considering early- and late-stage cancers (p = 0.0253). Cell-free mtDNA copy numbers were not increased significantly. We found the highest copy number of mtDNA in exosomes, followed by plasma and peripheral blood in late-stage cancer patients. We observed significant difference in wb-mtDNA copy number between healthy controls and both early- and late-stage cancer patients.


Assuntos
Carcinoma Epitelial do Ovário/sangue , Ácidos Nucleicos Livres/sangue , DNA Mitocondrial/sangue , Mitocôndrias/genética , Idoso , Carcinoma Epitelial do Ovário/genética , Carcinoma Epitelial do Ovário/patologia , Variações do Número de Cópias de DNA/genética , Exossomos/genética , Exossomos/metabolismo , Feminino , Humanos , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase em Tempo Real
14.
J Appl Genet ; 60(2): 199-207, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30997664

RESUMO

Sonic Hedgehog (Shh) regulates many key developmental processes during vertebrate limb development, fat formation, and skeletal tissue regeneration. Current whole genome sequencing data have identified a copy number variation mapping to bovine Sonic Hedgehog gene (SHH-CNV). The object of this study was to characterize the SHH-CNV distributions in 648 individuals from 11 Chinese cattle populations and further to investigate the associations of the copy number changes with gene expression and cattle growth traits. The SHH-CNV showed a high variance within Chinese indigenous yellow cattle. Compared to yak and dairy cattle, the beef cattle like Luxi and Xianan breed had significantly higher median copy numbers, suggesting the diversity of SHH-CNV in beef cattle selections. The negative correlation of SHH-CNV with SHH transcriptional level in adult adipose tissue (P < 0.01) indicated the dosage effects of SHH-CNV related to bovine fat formation. Association analysis of SHH-CNV and body size traits was conducted in five breeds. The results revealed that the copy number gain type of SHH-CNV exhibited significantly better chest depth in 24 months old Qinchuan cattle, and better body weight, body length, and chest girth in 18 months old Nanyang cattle, whereas the normal copy number had superior chest girth and body weight in adult Jinnan cattle (P < 0.05 or P < 0.01). In summary, this research uncovered meaningful effects of SHH-CNV on gene expression and cattle phenotypic traits, indicating its potential applications for genetic improvement of beef cattle.


Assuntos
Cruzamento , Variações do Número de Cópias de DNA/genética , Proteínas Hedgehog/genética , Locos de Características Quantitativas/genética , Animais , Composição Corporal/genética , Tamanho Corporal , Peso Corporal/genética , Bovinos , China , Regulação da Expressão Gênica/genética , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Carne Vermelha
15.
Int J Mol Sci ; 20(5)2019 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-30836598

RESUMO

Chromosome 16 is one of the most gene-rich chromosomes of our genome, and 10% of its sequence consists of segmental duplications, which give instability and predisposition to rearrangement by the recurrent mechanism of non-allelic homologous recombination. Microarray technologies have allowed for the analysis of copy number variations (CNVs) that can contribute to the risk of developing complex diseases. By array comparative genomic hybridization (CGH) screening of 1476 patients, we detected 27 cases with CNVs on chromosome 16. We identified four smallest regions of overlapping (SROs): one at 16p13.11 was found in seven patients; one at 16p12.2 was found in four patients; two close SROs at 16p11.2 were found in twelve patients; finally, six patients were found with atypical rearrangements. Although phenotypic variability was observed, we identified a male bias for Childhood Apraxia of Speech associated to 16p11.2 microdeletions. We also reported an elevated frequency of second-site genomic alterations, supporting the model of the second hit to explain the clinical variability associated with CNV syndromes. Our goal was to contribute to the building of a chromosome 16 disease-map based on disease susceptibility regions. The role of the CNVs of chromosome 16 was increasingly made clear in the determination of developmental delay. We also found that in some cases a second-site CNV could explain the phenotypic heterogeneity by a simple additive effect or a pejorative synergistic effect.


Assuntos
Anormalidades Múltiplas/genética , Cromossomos Humanos Par 16/genética , Hibridização Genômica Comparativa , Deficiências do Desenvolvimento/genética , Anormalidades Múltiplas/classificação , Anormalidades Múltiplas/fisiopatologia , Adolescente , Adulto , Criança , Pré-Escolar , Aberrações Cromossômicas , Deleção Cromossômica , Variações do Número de Cópias de DNA/genética , Deficiências do Desenvolvimento/classificação , Deficiências do Desenvolvimento/fisiopatologia , Feminino , Recombinação Homóloga/genética , Humanos , Lactente , Recém-Nascido , Cariótipo , Masculino , Fenótipo , Duplicações Segmentares Genômicas/genética , Adulto Jovem
16.
Pediatr Cardiol ; 40(4): 762-767, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30868185

RESUMO

Congenital heart defect (CHD) is one of the most common birth defects in China, while pulmonary atresia with intact ventricular septum (PA-IVS) is the life-threatening form of CHD. Numerous previous studies revealed that rare copy number variants (CNVs) play important roles in CHD, but little is known about the prevalence and role of rare CNVs in PA-IVS. In this study, we conducted a genome-wide scanning of rare CNVs in an unselected cohort consisted of 54 Chinese patients with PA-IVS and 20 patients with pulmonary atresia with ventricular septal defect (PA-VSD). CNVs were identified in 6/20 PA-VSD patients (30%), and three of these CNVs (15%) were considered potentially pathogenic. Two pathogenic CNVs occurred at a known CHD locus (22q11.2) and one likely pathogenic deletion located at 13q12.12. However, no rare CNVs were detected in patients with PA-IVS. Potentially pathogenic CNVs were more enriched in PA-VSD patients than in PA-IVS patients (p = 0.018). No rare CNVs were detected in patients with PA-IVS in our study. PA/IVS might be different from PA/VSD in terms of genetics as well as anatomy.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Variações do Número de Cópias de DNA/genética , Cardiopatias Congênitas/genética , Comunicação Interventricular/genética , Atresia Pulmonar/genética , Criança , Pré-Escolar , China , Feminino , Estudo de Associação Genômica Ampla/métodos , Cardiopatias Congênitas/etnologia , Humanos , Lactente , Recém-Nascido , Masculino , Fenótipo , Prevalência , Atresia Pulmonar/etnologia
17.
Clin Chim Acta ; 494: 138-142, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30898509

RESUMO

Haptoglobin (Hp) is a major plasma acute-phase glycoprotein, which binds free haemoglobin to neutralize its toxicity. The HP gene exists as two copy number variants (CNV), Hp1 and HP2, which differ in two ways: serum Hp level and functional differences in Hp protein products. Both mechanisms may underlie the HP CNV's influence on susceptibility and/or outcome in several diseases. A single nucleotide polymorphism rs2000999 has also been associated with serum Hp level. In a meta-analysis of three studies from England, France and Japan, with a combined sample size of 1210 participants, we show that rs2000999's effect on circulating Hp level is independent from that of the HP CNV. The combined use of rs2000999 and the HP CNV can be an important genetic epidemiological tool to discriminate between the two potential mechanisms underlying differences between HP1 and HP2 alleles.


Assuntos
Alelos , Haptoglobinas/análise , Adolescente , Adulto , Análise Química do Sangue , Variações do Número de Cópias de DNA/genética , Feminino , França , Genótipo , Humanos , Japão , Masculino , Epidemiologia Molecular , Polimorfismo de Nucleotídeo Único/genética , Reino Unido
18.
Nat Med ; 25(3): 389-402, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30842677

RESUMO

Despite impressive durable responses, immune checkpoint inhibitors do not provide a long-term benefit to the majority of patients with cancer. Understanding genomic correlates of response and resistance to checkpoint blockade may enhance benefits for patients with cancer by elucidating biomarkers for patient stratification and resistance mechanisms for therapeutic targeting. Here we review emerging genomic markers of checkpoint blockade response, including those related to neoantigens, antigen presentation, DNA repair, and oncogenic pathways. Compelling evidence also points to a role for T cell functionality, checkpoint regulators, chromatin modifiers, and copy-number alterations in mediating selective response to immune checkpoint blockade. Ultimately, efforts to contextualize genomic correlates of response into the larger understanding of tumor immune biology will build a foundation for the development of novel biomarkers and therapies to overcome resistance to checkpoint blockade.


Assuntos
Apresentação do Antígeno/genética , Antígenos de Neoplasias/genética , Antineoplásicos Imunológicos/uso terapêutico , Reparo do DNA/genética , Genoma/genética , Neoplasias/tratamento farmacológico , Linfócitos T/imunologia , Apresentação do Antígeno/imunologia , Antígenos de Neoplasias/imunologia , Antígeno B7-H1/imunologia , Antígeno CTLA-4/antagonistas & inibidores , Antígeno CTLA-4/imunologia , Carcinogênese/genética , Montagem e Desmontagem da Cromatina/genética , Variações do Número de Cópias de DNA/genética , Resistencia a Medicamentos Antineoplásicos/genética , Humanos , Mutação , Neoplasias/genética , Neoplasias/imunologia , Receptor de Morte Celular Programada 1/antagonistas & inibidores , Receptor de Morte Celular Programada 1/imunologia , Transdução de Sinais
19.
Int J Mol Sci ; 20(5)2019 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-30871102

RESUMO

A collection of intracranial astrocytomas of different malignancy grades was analyzed for copy number aberrations (CNA) in order to identify regions that are driving cancer pathogenesis. Astrocytomas were analyzed by Array Comparative Genomic Hybridization (aCGH) and bioinformatics utilizing a Bioconductor package, Genomic Identification of Significant Targets in Cancer (GISTIC) 2.0.23 and DAVID software. Altogether, 1438 CNA were found of which losses prevailed. On our total sample, significant deletions affected 14 chromosomal regions, out of which deletions at 17p13.2, 9p21.3, 13q12.11, 22q12.3 remained significant even at 0.05 q-value. When divided into malignancy groups, the regions identified as significantly deleted in high grades were: 9p21.3; 17p13.2; 10q24.2; 14q21.3; 1p36.11 and 13q12.11, while amplified were: 3q28; 12q13.3 and 21q22.3. Low grades comprised significant deletions at 3p14.3; 11p15.4; 15q15.1; 16q22.1; 20q11.22 and 22q12.3 indicating their involvement in early stages of tumorigenesis. Significantly enriched pathways were: PI3K-Akt, Cytokine-cytokine receptor, the nucleotide-binding oligomerization domain (NOD)⁻like receptor, Jak-STAT, retinoic acid-inducible gene (RIG)-I-like receptor and Toll-like receptor pathways. HPV and herpex simplex infection and inflammation pathways were also represented. The present study brings new data to astrocytoma research amplifying the wide spectrum of changes that could help us identify the regions critical for tumorigenesis.


Assuntos
Astrocitoma/genética , Astrocitoma/patologia , Variações do Número de Cópias de DNA/genética , Adulto , Idoso , Carcinogênese/genética , Carcinogênese/patologia , Aberrações Cromossômicas , Hibridização Genômica Comparativa/métodos , Feminino , Genômica/métodos , Humanos , Masculino , Pessoa de Meia-Idade , Fosfatidilinositol 3-Quinases/genética , Proteínas Proto-Oncogênicas c-akt/genética , Transdução de Sinais/genética , Adulto Jovem
20.
Biomed Res Int ; 2019: 7235914, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30834272

RESUMO

Leukodystrophies (LDs) are heterogeneous genetic disorders characterized by abnormal white matter in the central nervous system. Some of the LDs are progressive and often fatal. In general, LD is primarily diagnosed based on the neuroimaging; however, definitive diagnosis of the LD type is done using genetic testing such as next-generation sequencing. The aim of this study is to identify the genetic causes of LD in two independent Jordanian cases that exhibit MRI findings confirming LD with no definitive diagnosis using whole exome sequencing (WES). The most likely causative variants were identified. In one case, the homozygous pathogenic variant NM_000049.2:c.914C>A;p.Ala305Glu, which is previously reported in ClinVar, in the gene ASPA was identified causing Canavan disease. In the second case, the homozygous novel variant NM_000487.5:c.256C>G;p.Arg86Gly in the gene ARSA was identified causing metachromatic leukodystrophy. The two variants segregate in their families. The phenotypes of the two studied cases overlap with assigned diseases. The present study raises the importance of using WES to identify the precise neurodevelopmental diseases in Jordan.


Assuntos
Amidoidrolases/genética , Cerebrosídeo Sulfatase/genética , Leucodistrofia Metacromática/genética , Sequenciamento Completo do Exoma , Adulto , Variações do Número de Cópias de DNA/genética , Exoma/genética , Feminino , Predisposição Genética para Doença , Homozigoto , Humanos , Lactente , Jordânia , Leucodistrofia Metacromática/diagnóstico , Leucodistrofia Metacromática/diagnóstico por imagem , Leucodistrofia Metacromática/patologia , Masculino , Mutação , Linhagem , Fenótipo , Substância Branca/patologia
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