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1.
World J Urol ; 2019 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-31254099

RESUMO

PURPOSE: Urinary tract infections are amongst the most frequent nosocomial infections followed by surgical site infections (SSI). Antibiotic prophylaxis is only one way to reduce the risk of post-operative infection. Our aim was to establish a review of the literature on measures to reduce post-operative infections outside antibiotic prophylaxis. METHODS: We performed a review of the literature in February 2019 using Medline database to identify relevant studies published in the last 10 years. We arbitrarily decided to fix our limit to the 10 last years considering that the resistance rate of bacteria to antibiotics and the surgical technics evolve over time. This search identified 229 studies. We included 53 studies selected upon the title or the abstract. RESULTS: Forty-four studies were finally included. We evaluated the efficacy to prevent SSI by skin antisepsis, surgical hand hygiene and technique, type of surgeons' caps, preservation of normothermia, hair removal, increased oxygen delivery, wound protectors, bathing, normoglycemia and immunonutrition. CONCLUSIONS: Antibiotic prophylaxis represents one way to prevent SSI but various other measures should be known and considered by anesthesiologists and surgeons. Some measures to reduce post-operative infections are not clearly established yet and more studies are needed.

2.
Brain Struct Funct ; 224(6): 2269-2280, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31098764

RESUMO

In cortical circuits, the vasoactive intestinal peptide (VIP+)-expressing GABAergic cells represent a heterogeneous but unique group of interneurons that is mainly specialized in network disinhibition. While the physiological properties and connectivity patterns have been elucidated in several types of VIP+ interneurons, little is known about the cell type-specific molecular repertoires important for selective targeting of VIP+ cell types and understanding their functions. Using patch-sequencing approach, we analyzed the transcriptomic profile of anatomically identified subiculum-projecting VIP+ GABAergic neurons that reside in the mouse hippocampal CA1 area, express muscarinic receptor 2 and coordinate the hippocampo-subicular interactions via selective innervation of interneurons in the CA1 area and of interneurons and pyramidal cells in subiculum. We explored the VIP+ cell gene expression within major gene families including ion channels, neurotransmitter receptors, neuromodulators, cell adhesion and myelination molecules. Among others, a large variety of genes involved in neuromodulatory signaling, including acetylcholine (Chrna4), norepinephrin (Adrb1), dopamine (Drd1), serotonin (Htr1d), cannabinoid (Cnr1), opioid (Oprd1, Oprl1) and neuropeptide Y (Npy1r) receptors was detected in these cells. Many genes that were enriched in other local VIP+ cell types, including the interneuron-selective interneurons and the cholecystokinin-coexpressing basket cells, were detected in VIP+ subiculum-projecting cells. In addition, the neuronatin (Nnat) and the Purkinje Cell Protein 4 (Pcp4) genes, which were detected previously in long-range projecting GABAergic neurons, were also common for the subiculum-projecting VIP+ cells. The expression of some genes was validated at the protein level, with proenkephalin being identified as an additional molecular marker of this VIP+ cell type. Together, our data indicate that the VIP+ subiculum-projecting cells share molecular identity with other VIP+ and long-range projecting GABAergic neurons, which can be important for specific function of these cells associated with their local and distant projection patterns.

5.
Genetics ; 207(1): 139-151, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-28679547

RESUMO

Cornelia de Lange syndrome (CdLS) is a complex multisystem developmental disorder caused by mutations in cohesin subunits and regulators. While its precise molecular mechanisms are not well defined, they point toward a global deregulation of the transcriptional gene expression program. Cohesin is associated with the boundaries of chromosome domains and with enhancer and promoter regions connecting the three-dimensional genome organization with transcriptional regulation. Here, we show that connected gene communities, structures emerging from the interactions of noncoding regulatory elements and genes in the three-dimensional chromosomal space, provide a molecular explanation for the pathoetiology of CdLS associated with mutations in the cohesin-loading factor NIPBL and the cohesin subunit SMC1A NIPBL and cohesin are important constituents of connected gene communities that are centrally positioned at noncoding regulatory elements. Accordingly, genes deregulated in CdLS are positioned within reach of NIPBL- and cohesin-occupied regions through promoter-promoter interactions. Our findings suggest a dynamic model where NIPBL loads cohesin to connect genes in communities, offering an explanation for the gene expression deregulation in the CdLS.


Assuntos
Síndrome de Lange/genética , Redes Reguladoras de Genes , Transcriptoma , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Linhagem Celular Tumoral , Proteínas Cromossômicas não Histona/genética , Proteínas Cromossômicas não Histona/metabolismo , Genoma Humano , Humanos , Mutação , Regiões Promotoras Genéticas , Proteínas/genética
8.
Oncotarget ; 7(48): 78827-78840, 2016 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-27705932

RESUMO

The utility of KRAS mutations in plasma circulating cell-free DNA (cfDNA) samples as non-invasive biomarkers for the detection of pancreatic cancer has never been evaluated in a large case-control series. We applied a KRAS amplicon-based deep sequencing strategy combined with analytical pipeline specifically designed for the detection of low-abundance mutations to screen plasma samples of 437 pancreatic cancer cases, 141 chronic pancreatitis subjects, and 394 healthy controls. We detected mutations in 21.1% (N=92) of cases, of whom 82 (89.1%) carried at least one mutation at hotspot codons 12, 13 or 61, with mutant allelic fractions from 0.08% to 79%. Advanced stages were associated with an increased proportion of detection, with KRAS cfDNA mutations detected in 10.3%, 17,5% and 33.3% of cases with local, regional and systemic stages, respectively. We also detected KRAS cfDNA mutations in 3.7% (N=14) of healthy controls and in 4.3% (N=6) of subjects with chronic pancreatitis, but at significantly lower allelic fractions than in cases. Combining cfDNA KRAS mutations and CA19-9 plasma levels on a limited set of case-control samples did not improve the overall performance of the biomarkers as compared to CA19-9 alone. Whether the limited sensitivity and specificity observed in our series of KRAS mutations in plasma cfDNA as biomarkers for pancreatic cancer detection are attributable to methodological limitations or to the biology of cfDNA should be further assessed in large case-control series.


Assuntos
Biomarcadores Tumorais/genética , Carcinoma Ductal Pancreático/genética , DNA Tumoral Circulante/genética , Mutação , Neoplasias Pancreáticas/genética , Proteínas Proto-Oncogênicas p21(ras)/genética , Idoso , Biomarcadores Tumorais/sangue , Antígeno CA-19-9/sangue , Carcinoma Ductal Pancreático/sangue , Carcinoma Ductal Pancreático/patologia , Estudos de Casos e Controles , DNA Tumoral Circulante/sangue , República Tcheca , Análise Mutacional de DNA , Feminino , Frequência do Gene , Predisposição Genética para Doença , Humanos , Masculino , Pessoa de Meia-Idade , Estadiamento de Neoplasias , Neoplasias Pancreáticas/sangue , Neoplasias Pancreáticas/patologia , Fenótipo , Projetos Piloto , Valor Preditivo dos Testes , Proteínas Proto-Oncogênicas p21(ras)/sangue , Reprodutibilidade dos Testes , Eslováquia
9.
Sci Rep ; 6: 31628, 2016 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-27545006

RESUMO

To examine the diversity of somatic alterations and clonal evolution according to aggressiveness of disease, nineteen tumor-blood pairs of 'formerly bronchiolo-alveolar carcinoma (BAC)' which had been reclassified into preinvasive lesion (adenocarcinoma in situ; AIS), focal invasive lesion (minimally invasive adenocarcinoma; MIA), and invasive lesion (lepidic predominant adenocarcinoma; LPA and non-lepidic predominant adenocarcinoma; non-LPA) according to IASLC/ATS/ERS 2011 classification were explored by whole exome sequencing. Several distinct somatic alterations were observed compare to the lung adenocarcinoma study from the Cancer Genome Atlas (TCGA). There were higher numbers of tumors with significant APOBEC mutation fold enrichment (73% vs. 58% TCGA). The frequency of KRAS mutations was lower in our study (5% vs. 32% TCGA), while a higher number of mutations of RNA-splicing genes, RBM10 and U2AF1, were found (37% vs. 11% TCGA). We found neither mutational pattern nor somatic copy number alterations that were specific to AIS/MIA. We demonstrated that clonal cell fraction was the only distinctive feature that discriminated LPA/non-LPA from AIS/MIA. The broad range of clonal frequency signified a more branched clonal evolution at the time of diagnosis. Assessment of tumor clonal cell fraction might provide critical information for individualized therapy as a prognostic factor, however this needs further study.


Assuntos
Desaminases APOBEC/genética , Adenocarcinoma/genética , Neoplasias Pulmonares/genética , Mutação , Proteínas Proto-Oncogênicas p21(ras)/genética , Adenocarcinoma/patologia , Adenocarcinoma/terapia , Idoso , Feminino , Humanos , Neoplasias Pulmonares/patologia , Neoplasias Pulmonares/terapia , Masculino , Pessoa de Meia-Idade , Invasividade Neoplásica
10.
Sci Rep ; 6: 30953, 2016 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-27484949

RESUMO

The abnormal regulation of amyloid-ß (Aß) metabolism (e.g., production, cleavage, clearance) plays a central role in Alzheimer's disease (AD). Among endogenous factors believed to participate in AD progression are the small regulatory non-coding microRNAs (miRs). In particular, the miR-132/212 cluster is severely reduced in the AD brain. In previous studies we have shown that miR-132/212 deficiency in mice leads to impaired memory and enhanced Tau pathology as seen in AD patients. Here we demonstrate that the genetic deletion of miR-132/212 promotes Aß production and amyloid (senile) plaque formation in triple transgenic AD (3xTg-AD) mice. Using RNA-Seq and bioinformatics, we identified genes of the miR-132/212 network with documented roles in the regulation of Aß metabolism, including Tau, Mapk, and Sirt1. Consistent with these findings, we show that the modulation of miR-132, or its target Sirt1, can directly regulate Aß production in cells. Finally, both miR-132 and Sirt1 levels correlated with Aß load in humans. Overall, our results support the hypothesis that the miR-132/212 network, including Sirt1 and likely other target genes, contributes to abnormal Aß metabolism and senile plaque deposition in AD. This study strengthens the importance of miR-dependent networks in neurodegenerative disorders, and opens the door to multifactorial drug targets of AD by targeting Aß and Tau.


Assuntos
Doença de Alzheimer , Peptídeos beta-Amiloides/biossíntese , MicroRNAs/genética , Doença de Alzheimer/genética , Doença de Alzheimer/metabolismo , Doença de Alzheimer/patologia , Peptídeos beta-Amiloides/genética , Animais , Modelos Animais de Doenças , Humanos , Camundongos , Camundongos Transgênicos , MicroRNAs/metabolismo , Sirtuína 1/genética , Sirtuína 1/metabolismo
11.
PLoS One ; 11(6): e0156820, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27270457

RESUMO

Approximately half of the familial aggregation of breast cancer remains unexplained. This proportion is less for early-onset disease where familial aggregation is greater, suggesting that other susceptibility genes remain to be discovered. The majority of known breast cancer susceptibility genes are involved in the DNA double-strand break repair pathway. ABRAXAS is involved in this pathway and mutations in this gene impair BRCA1 recruitment to DNA damage foci and increase cell sensitivity to ionizing radiation. Moreover, a recurrent germline mutation was reported in Finnish high-risk breast cancer families. To determine if ABRAXAS could be a breast cancer susceptibility gene in other populations, we conducted a population-based case-control mutation screening study of the coding exons and exon/intron boundaries of ABRAXAS in the Breast Cancer Family Registry. In addition to the common variant p.Asp373Asn, sixteen distinct rare variants were identified. Although no significant difference in allele frequencies between cases and controls was observed for the identified variants, two variants, p.Gly39Val and p.Thr141Ile, were shown to diminish phosphorylation of gamma-H2AX in MCF7 human breast adenocarcinoma cells, an important biomarker of DNA double-strand breaks. Overall, likely damaging or neutral variants were evenly represented among cases and controls suggesting that rare variants in ABRAXAS may explain only a small proportion of hereditary breast cancer.


Assuntos
Neoplasias da Mama/genética , Proteínas de Transporte/genética , Estudos de Associação Genética/métodos , Polimorfismo de Nucleotídeo Único , Idade de Início , Estudos de Casos e Controles , Feminino , Frequência do Gene , Predisposição Genética para Doença , Mutação em Linhagem Germinativa , Humanos , Células MCF-7 , Linhagem , Quebeque
12.
Hum Mutat ; 37(7): 627-39, 2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-26913838

RESUMO

Clinical mutation screening of the cancer susceptibility genes BRCA1 and BRCA2 generates many unclassified variants (UVs). Most of these UVs are either rare missense substitutions or nucleotide substitutions near the splice junctions of the protein coding exons. Previously, we developed a quantitative method for evaluation of BRCA gene UVs-the "integrated evaluation"-that combines a sequence analysis-based prior probability of pathogenicity with patient and/or tumor observational data to arrive at a posterior probability of pathogenicity. One limitation of the sequence analysis-based prior has been that it evaluates UVs from the perspective of missense substitution severity but not probability to disrupt normal mRNA splicing. Here, we calibrated output from the splice-site fitness program MaxEntScan to generate spliceogenicity-based prior probabilities of pathogenicity for BRCA gene variants; these range from 0.97 for variants with high probability to damage a donor or acceptor to 0.02 for exonic variants that do not impact a splice junction and are unlikely to create a de novo donor. We created a database http://priors.hci.utah.edu/PRIORS/ that provides the combined missense substitution severity and spliceogenicity-based probability of pathogenicity for BRCA gene single-nucleotide substitutions. We also updated the BRCA gene Ex-UV LOVD, available at http://hci-exlovd.hci.utah.edu, with 77 re-evaluable variants.


Assuntos
Proteína BRCA1/genética , Proteína BRCA2/genética , Neoplasias da Mama/genética , Biologia Computacional/métodos , Substituição de Aminoácidos , Simulação por Computador , Bases de Dados Genéticas , Feminino , Predisposição Genética para Doença , Humanos , Mutação de Sentido Incorreto , Processamento de RNA
13.
PLoS One ; 10(9): e0136505, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26352266

RESUMO

The MYD88 L265P is a recurrent somatic mutation in neoplastic cells from patients with Waldenström Macroglobulinemia (WM). We identified the MYD88 L265P mutation in three individuals from unrelated families, but its presence did not explain the disease segregation within these WM pedigrees. We observed the mutation in these three individuals at high allele fractions in DNA extracted from EBV-immortalized Lymphoblastoid cell lines established from peripheral blood (LCL), but at much lower allele fractions in DNA extracted directly from peripheral blood, suggesting that this mutation is present in a clonal cell subpopulation rather than of germ-line origin. Furthermore, we observed that the MYD88 L265P mutation is enriched in WM families, detected in 40.5% of patients with familial WM or MGUS (10/22 WM, 5/15 MGUS), compared to 3.5% of patients with familial MM or MGUS (0/72 MM, 4/41 MGUS) (p = 10-7). The mutant allele frequency increased with passages in vitro after immortalization with Epstein-Barr virus (EBV) consistent with the MYD88 L265P described gain-of-function proposed for this mutation. The MYD88 L265P mutation appears to be frequently present in circulating cells in patients with WM, and MGUS, and these cells are amenable to immortalization by EBV.


Assuntos
Transformação Celular Viral , Células Clonais/patologia , Linfócitos/patologia , Mutação de Sentido Incorreto , Fator 88 de Diferenciação Mieloide/genética , Mutação Puntual , Macroglobulinemia de Waldenstrom/patologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Alelos , Divisão Celular , Células Cultivadas , Células Clonais/metabolismo , Células Clonais/virologia , Feminino , Predisposição Genética para Doença , Herpesvirus Humano 4/fisiologia , Humanos , Imunoglobulina M/genética , Linfócitos/metabolismo , Linfócitos/virologia , Masculino , Pessoa de Meia-Idade , Gamopatia Monoclonal de Significância Indeterminada/sangue , Gamopatia Monoclonal de Significância Indeterminada/genética , Gamopatia Monoclonal de Significância Indeterminada/patologia , Macroglobulinemia de Waldenstrom/sangue , Macroglobulinemia de Waldenstrom/genética
14.
PLoS One ; 10(5): e0126762, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25961742

RESUMO

Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer.


Assuntos
Formaldeído/química , Parafina/química , Neoplasias de Mama Triplo Negativas/metabolismo , Neoplasias de Mama Triplo Negativas/patologia , Adulto , Feminino , Humanos , Técnicas In Vitro , Pessoa de Meia-Idade , Estudos Retrospectivos , Fixação de Tecidos
15.
J Natl Cancer Inst ; 107(5)2015 May.
Artigo em Inglês | MEDLINE | ID: mdl-25838448

RESUMO

Deleterious BRCA2 genetic variants markedly increase risk of developing breast cancer. A rare truncating BRCA2 genetic variant, rs11571833 (K3326X), has been associated with a 2.5-fold risk of lung squamous cell carcinoma but only a modest 26% increase in breast cancer risk. We analyzed the association between BRCA2 SNP rs11571833 and upper aerodigestive tract (UADT) cancer risk with multivariable unconditional logistic regression adjusted by sex and combinations of study and country for 5942 UADT squamous cell carcinoma case patients and 8086 control patients from nine different studies. All statistical tests were two-sided. rs11571833 was associated with UADT cancers (odds ratio = 2.53, 95% confidence interval = 1.89 to 3.38, P = 3x10(-10)) and was present in European, Latin American, and Indian populations but extremely rare in Japanese populations. The association appeared more apparent in smokers (current or former) compared with never smokers (P het = .026). A robust association between a truncating BRCA2 variant and UADT cancer risk suggests that treatment strategies orientated towards BRCA2 mutations may warrant further investigation in UADT tumors.


Assuntos
Proteína BRCA2/genética , Carcinoma de Células Escamosas/genética , Neoplasias de Cabeça e Pescoço/genética , Polimorfismo de Nucleotídeo Único , Adulto , Idoso , Consumo de Bebidas Alcoólicas/efeitos adversos , Consumo de Bebidas Alcoólicas/epidemiologia , Estudos de Casos e Controles , Feminino , Predisposição Genética para Doença , Humanos , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Razão de Chances , Medição de Risco , Fatores de Risco , Fumar/efeitos adversos , Fumar/epidemiologia
16.
PLoS One ; 10(3): e0117639, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25793373

RESUMO

Genetic variants located within the 12p13.33/RAD52 locus have been associated with lung squamous cell carcinoma (LUSC). Here, within 5,947 UADT cancers and 7,789 controls from 9 different studies, we found rs10849605, a common intronic variant in RAD52, to be also associated with upper aerodigestive tract (UADT) squamous cell carcinoma cases (OR = 1.09, 95% CI: 1.04-1.15, p = 6x10(-4)). We additionally identified rs10849605 as a RAD52 cis-eQTL inUADT(p = 1x10(-3)) and LUSC (p = 9x10(-4)) tumours, with the UADT/LUSC risk allele correlated with increased RAD52 expression levels. The 12p13.33 locus, encompassing rs10849605/RAD52, was identified as a significant somatic focal copy number amplification in UADT(n = 374, q-value = 0.075) and LUSC (n = 464, q-value = 0.007) tumors and correlated with higher RAD52 tumor expression levels (p = 6x10(-48) and p = 3x10(-29) in UADT and LUSC, respectively). In combination, these results implicate increased RAD52 expression in both genetic susceptibility and tumorigenesis of UADT and LUSC tumors.


Assuntos
Carcinoma de Células Escamosas/genética , Cromossomos Humanos Par 12/genética , Loci Gênicos , Predisposição Genética para Doença , Neoplasias de Cabeça e Pescoço/genética , Proteína Rad52 de Recombinação e Reparo de DNA/genética , Estudos de Casos e Controles , Simulação por Computador , Demografia , Feminino , Células Germinativas , Humanos , Neoplasias Pulmonares/genética , Masculino , Pessoa de Meia-Idade , Mapeamento Físico do Cromossomo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Fatores de Risco
17.
J Med Genet ; 52(4): 224-30, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25643705

RESUMO

BACKGROUND: Inactivating germline mutations in the tumour suppressor gene BRCA1 are associated with a significantly increased risk of developing breast and ovarian cancer. A large number (>1500) of unique BRCA1 variants have been identified in the population and can be classified as pathogenic, non-pathogenic or as variants of unknown significance (VUS). Many VUS are rare missense variants leading to single amino acid changes. Their impact on protein function cannot be directly inferred from sequence information, precluding assessment of their pathogenicity. Thus, functional assays are critical to assess the impact of these VUS on protein activity. BRCA1 is a multifunctional protein and different assays have been used to assess the impact of variants on different biochemical activities and biological processes. METHODS AND RESULTS: To facilitate VUS analysis, we have developed a visualisation resource that compiles and displays functional data on all documented BRCA1 missense variants. BRCA1 Circos is a web-based visualisation tool based on the freely available Circos software package. The BRCA1 Circos web tool (http://research.nhgri.nih.gov/bic/circos/) aggregates data from all published BRCA1 missense variants for functional studies, harmonises their results and presents various functionalities to search and interpret individual-level functional information for each BRCA1 missense variant. CONCLUSIONS: This research visualisation tool will serve as a quick one-stop publically available reference for all the BRCA1 missense variants that have been functionally assessed. It will facilitate meta-analysis of functional data and improve assessment of pathogenicity of VUS.


Assuntos
Proteína BRCA1/genética , Biologia Computacional/métodos , Gráficos por Computador , Internet , Mutação de Sentido Incorreto , Software , Neoplasias da Mama/genética , Análise Mutacional de DNA , Sistemas de Gerenciamento de Base de Dados , Bases de Dados Genéticas , Conjuntos de Dados como Assunto , Feminino , Predisposição Genética para Doença , Testes Genéticos , Humanos , Neoplasias Ovarianas/genética
18.
Clin Cancer Res ; 20(17): 4613-24, 2014 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-25013125

RESUMO

PURPOSE: Tumor somatic mutation analysis is part of the standard management of metastatic lung cancer. However, physicians often have to deal with small biopsies and consequently with challenging mutation testing. Circulating free DNA (cfDNA) is a promising tool for accessing the tumor genome as a liquid biopsy. Here, we evaluated next-generation sequencing (NGS) on cfDNA samples obtained from a consecutive series of patients for the screening of a range of clinically relevant mutations. EXPERIMENTAL DESIGN: A total of 107 plasma samples were collected from the BioCAST/IFCT-1002 lung cancer study (never-smokers cohort). Matched tumor DNA (tDNA) was obtained for 68 cases. Multiplex PCR-based assays were designed to target specific coding regions in EGFR, KRAS, BRAF, ERBB2, and PI3KCA genes, and amplicon sequencing was performed at deep coverage on the cfDNA/tDNA pairs using the NGS IonTorrent Personal Genome Machine Platform. RESULTS: CfDNA concentration in plasma was significantly associated with both stage and number of metastatic sites. In tDNA, 50 mutations (36 EGFR, 5 ERBB2, 4 KRAS, 3 BRAF, and 2 PIK3CA) were identified, of which 26 were detected in cfDNA. Sensitivity of the test was 58% (95% confidence interval, 43%-71%) and the estimated specificity was 87% (62%-96%). CONCLUSION: These data demonstrate the feasibility and potential utility of mutation screening in cfDNA using IonTorrent NGS for the detection of a range of tumor biomarkers in patients with metastatic lung cancer.


Assuntos
Receptores ErbB/genética , Neoplasias Pulmonares/genética , Fosfatidilinositol 3-Quinases/genética , Proteínas Proto-Oncogênicas B-raf/genética , Proteínas Proto-Oncogênicas/genética , Receptor ErbB-2/genética , Proteínas ras/genética , Adulto , Idoso , Biomarcadores Tumorais/sangue , Biomarcadores Tumorais/genética , Classe I de Fosfatidilinositol 3-Quinases , Análise Mutacional de DNA , DNA de Neoplasias/sangue , Receptores ErbB/sangue , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Neoplasias Pulmonares/sangue , Neoplasias Pulmonares/patologia , Pessoa de Meia-Idade , Células Neoplásicas Circulantes/patologia , Proteínas Proto-Oncogênicas/sangue , Proteínas Proto-Oncogênicas B-raf/sangue , Proteínas Proto-Oncogênicas p21(ras) , Receptor ErbB-2/sangue , Fumar , Proteínas ras/sangue
19.
Nat Genet ; 46(7): 736-41, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24880342

RESUMO

We conducted imputation to the 1000 Genomes Project of four genome-wide association studies of lung cancer in populations of European ancestry (11,348 cases and 15,861 controls) and genotyped an additional 10,246 cases and 38,295 controls for follow-up. We identified large-effect genome-wide associations for squamous lung cancer with the rare variants BRCA2 p.Lys3326X (rs11571833, odds ratio (OR) = 2.47, P = 4.74 × 10(-20)) and CHEK2 p.Ile157Thr (rs17879961, OR = 0.38, P = 1.27 × 10(-13)). We also showed an association between common variation at 3q28 (TP63, rs13314271, OR = 1.13, P = 7.22 × 10(-10)) and lung adenocarcinoma that had been previously reported only in Asians. These findings provide further evidence for inherited genetic susceptibility to lung cancer and its biological basis. Additionally, our analysis demonstrates that imputation can identify rare disease-causing variants with substantive effects on cancer risk from preexisting genome-wide association study data.


Assuntos
Adenocarcinoma/genética , Proteína BRCA2/genética , Carcinoma de Células Escamosas/genética , Quinase do Ponto de Checagem 2/genética , Neoplasias Pulmonares/genética , Polimorfismo de Nucleotídeo Único/genética , Estudos de Casos e Controles , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Metanálise como Assunto , Prognóstico , Fatores de Risco
20.
Breast Cancer Res ; 16(3): R58, 2014 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-24894818

RESUMO

INTRODUCTION: The MRE11A-RAD50-Nibrin (MRN) complex plays several critical roles related to repair of DNA double-strand breaks. Inherited mutations in the three components predispose to genetic instability disorders and the MRN genes have been implicated in breast cancer susceptibility, but the underlying data are not entirely convincing. Here, we address two related questions: (1) are some rare MRN variants intermediate-risk breast cancer susceptibility alleles, and if so (2) do the MRN genes follow a BRCA1/BRCA2 pattern wherein most susceptibility alleles are protein-truncating variants, or do they follow an ATM/CHEK2 pattern wherein half or more of the susceptibility alleles are missense substitutions? METHODS: Using high-resolution melt curve analysis followed by Sanger sequencing, we mutation screened the coding exons and proximal splice junction regions of the MRN genes in 1,313 early-onset breast cancer cases and 1,123 population controls. Rare variants in the three genes were pooled using bioinformatics methods similar to those previously applied to ATM, BRCA1, BRCA2, and CHEK2, and then assessed by logistic regression. RESULTS: Re-analysis of our ATM, BRCA1, and BRCA2 mutation screening data revealed that these genes do not harbor pathogenic alleles (other than modest-risk SNPs) with minor allele frequencies>0.1% in Caucasian Americans, African Americans, or East Asians. Limiting our MRN analyses to variants with allele frequencies of <0.1% and combining protein-truncating variants, likely spliceogenic variants, and key functional domain rare missense substitutions, we found significant evidence that the MRN genes are indeed intermediate-risk breast cancer susceptibility genes (odds ratio (OR)=2.88, P=0.0090). Key domain missense substitutions were more frequent than the truncating variants (24 versus 12 observations) and conferred a slightly higher OR (3.07 versus 2.61) with a lower P value (0.029 versus 0.14). CONCLUSIONS: These data establish that MRE11A, RAD50, and NBN are intermediate-risk breast cancer susceptibility genes. Like ATM and CHEK2, their spectrum of pathogenic variants includes a relatively high proportion of missense substitutions. However, the data neither establish whether variants in each of the three genes are best evaluated under the same analysis model nor achieve clinically actionable classification of individual variants observed in this study.


Assuntos
Neoplasias da Mama/genética , Proteínas de Ciclo Celular/genética , Enzimas Reparadoras do DNA/genética , Proteínas de Ligação a DNA/genética , Predisposição Genética para Doença , Proteínas Nucleares/genética , Adulto , Substituição de Aminoácidos , Proteínas Mutadas de Ataxia Telangiectasia/genética , Proteína BRCA1/genética , Proteína BRCA2/genética , Sequência de Bases , Estudos de Casos e Controles , Quinase do Ponto de Checagem 2/genética , Quebras de DNA de Cadeia Dupla , Reparo do DNA/genética , Feminino , Frequência do Gene , Testes Genéticos , Humanos , Proteína Homóloga a MRE11 , Pessoa de Meia-Idade , Mutação de Sentido Incorreto , Isoformas de Proteínas/genética , Alinhamento de Sequência , Análise de Sequência de DNA
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