Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Toracoscopia no tratamento do empiema pleural em pacientes pediátricos Thoracoscopy in the treatment of pleural empyema in pediatric patients

OBJETIVO: Apresentar resultados obtidos com a toracoscopia no tratamento do empiema pleural em pacientes pediátricos. MÉTODOS: Foram avaliados 117 empiemas pleurais, utilizando-se o mediastinoscópio ou a videotoracoscopia, com anestesia geral e sonda de intubação simples. As indicações para a intervenção cirúrgica foram: derrame pleural com ausência de resposta clínica e radiológica ao tratamento clínico (antibióticos, fisioterapia e toracocentese) ou sepse grave, e derrame pleural loculado (documentado por ultrassonografia ou tomografia computadorizada do tórax). RESULTADOS: De fevereiro de 1983 a julho de 2006, 117 toracoscopias foram realizadas em pacientes com idade entre 5 meses e 17 anos (média, 4 anos). O tempo médio de permanência do dreno torácico foi de 9 dias (2 a 33), e o tempo de internação hospitalar foi de 16,44 dias (4 a 49). Houve apenas um óbito (0,8%), e 33 pacientes (28%) tiveram como complicação fístula aérea prolongada. Em 7 pacientes (6%), houve necessidade de conversão para toracotomia com decorticação pulmonar em decorrência da organização do empiema. CONCLUSÕES: Não existe consenso para o tratamento do empiema pleural nesta faixa etária. A terapêutica cirúrgica é geralmente requisitada tardiamente no curso da doença, particularmente quando já existem múltiplas loculações ou quadro séptico grave. A toracoscopia indicada mais precocemente no tratamento do empiema pleural em pacientes pediátricos proporcionou uma melhor resposta à terapêutica clínica, aparentemente reduzindo o índice de morbi-mortalidade, o tempo de permanência do dreno torácico, o tempo de internação hospitalar e o tempo de antibioticoterapia.<br>OBJECTIVE: To evaluate the results of thoracoscopy for the treatment of pleural empyema in pediatric patients. METHODS: A retrospective study of 117 patients who underwent mediastinoscopy or video-assisted thoracoscopy for pleural empyema treatment. General anesthesia and single-lumen oral intubation were used. Surgery was indicated when there was pleural effusion and no clinical and radiological response to clinical treatment (antibiotics, physiotherapy and thoracocentesis) or severe sepsis, together with loculated pleural effusion (confirmed through ultrasound or computed tomography of the chest). RESULTS: Between February of 1983 and July of 2006, 117 thoracoscopies were performed in patients ranging in age from 5 months to 17 years (mean, 4 years). Mean time for thoracic drainage was 9 days (range, 2-33 days), and mean period of hospitalization was 16.4 days (range, 4 to 49 days). One patient (0.8%) died after surgery, and persistent fistula was observed in 33 patients (28%). In 7 cases (6%), open thoracotomy with pulmonary decortication was performed due to the disposition of the empyema. CONCLUSIONS: Management of pleural empyema in this age bracket is still controversial, and surgical indication is often delayed, particularly when there are multiple loculations or severe sepsis. Early thoracoscopy yields a better clinical outcome for pediatric patients with pleural empyema, with apparent decreased morbidity and mortality, earlier chest tube removal, earlier hospital discharge and improved response to antibiotic therapy

Pleuropericardial cyst torsion: case report

ABSTRACT Pericardial cysts account for 12-18% of all mediastinal masses. They are usually asymptomatic and incidentally detected. However, when large, they can cause symptoms. Most pericardial cysts are located in the right cardiophrenic angle, but they can be anywhere in the mediastinum. We reported a pleuropericardial cyst torsion after physical stress, a very rare complication of this condition. The diagnosis was made by computed tomography and confirmed by video-assisted thoracoscopy

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts