cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data

Recent advances in sequencing technologies provide the means for identifying copy number variation (CNV) at an unprecedented resolution. A single next-generation sequencing experiment offers several features that can be used to detect CNV, yet current methods do not incorporate all available signatures into a unified model. cnvHiTSeq is an integrative probabilistic method for CNV discovery and genotyping that jointly analyzes multiple features at the population level. By combining evidence from complementary sources, cnvHiTSeq achieves high genotyping accuracy and a substantial improvement in CNV detection sensitivity over existing methods, while maintaining a low false discovery rate. cnvHiTSeq is available at http://sourceforge.net/projects/cnvhitse

Bioinformatics: living on the edge

A report on the 11th European Conference on Computational Biology (ECCB), Basel, Switzerland, September 9-12, 2012

Lung Microbiome in Asthma : Current Perspectives

A growing body of evidence implicates the human microbiome as a potentially influential player actively engaged in shaping the pathogenetic processes underlying the endotypes and phenotypes of chronic respiratory diseases, particularly of the airways. In this article, we specifically review current evidence on the characteristics of lung microbiome, and specifically the bacteriome, the modes of interaction between lung microbiota and host immune system, the role of the "lung-gut axis", and the functional effects thereof on asthma pathogenesis. We also attempt to explore the possibilities of therapeutic manipulation of the microbiome, aiming at the establishment of asthma prevention strategies and the optimization of asthma treatment

Method and reliability of measuring midurethral area and echogenicity, and changes during and after pregnancy

INTRODUCTION AND HYPOTHESIS: Internal closure of the urethral sphincter is one of the mechanisms in maintaining continence. Little is known about changes in the urethral sphincter during pregnancy. We designed this study to develop a reliable method to measure the area and mean echogenicity of the midurethra during and after pregnancy and to assess changes over time. METHODS: Two observers independently segmented the urethra as follows: in the sagittal plane, the urethra was positioned vertically, the marker was placed in the middle section of the lumen of the urethra, and eight tomographic US images of 2.5 -mm slices were obtained. The central image was selected, and area and mean echogenicity were calculated automatically. Intra- and interobserver reliability were determined by intraclass correlation coefficients (ICC) and their 95% confidence intervals (CI). Two hundred and eighty women underwent TPUS at 12 weeks and 36 weeks of gestation and 6 months postpartum, and 3D/4D transperineal ultrasound (TPUS) images of 40 pregnant nulliparous women were used for the reliability study. Paired t tests were used to assess changes in echogenicity and area. RESULTS: The ICC for measuring the area was substantial, at 0.77 and for measuring mean echogenicity was almost perfect, at 0.86. In the total study group (n = 280), midurethral area and mean echogenicity were significantly lower 6 months after delivery compared with 12 and 36 weeks of gestation. CONCLUSIONS: Our protocol for measuring area and mean echogenicity of the midurethra is reliable. This study indicates that structural changes in the midurethraoccur during pregnancy