The Effect of False-Positive Results on Subsequent Participation in Chest X-ray Screening for Lung Cancer

COVID-19 chest X-ray image analysis by threshold-based segmentation

COVID-19 is a severe acute respiratory syndrome that has caused a major ongoing pandemic worldwide. Imaging systems such as conventional chest X-ray (CXR) and computed tomography (CT) were proven essential for patients due to the lack of information about the complications that could result from this disease. In this study, the aim was to develop and evaluate a method for automatic diagnosis of COVID-19 using binary segmentation of chest X-ray images. The study used frontal chest X-ray images of 27 infected and 19 uninfected individuals from Kaggle COVID-19 Radiography Database, and applied binary segmentation and quartering in MATLAB to analyze the images. The binary images of the lung were split into four quarters; Q1 = right upper quarter, Q2 = left upper quarter, Q3 = right lower, and Q4 = left lower. The results showed that COVID-19 patients had a higher percentage of attenuation in the lower lobes of the lungs (p-value < 0.00001) compared to healthy individuals, which is likely due to ground-glass opacities and consolidations caused by the infection. The ratios of white pixels in the four quarters of the X-ray images were calculated, and it was found that the left lower quarter had the highest number of white pixels but without a statistical significance compared to right lower quarter (p-value = 0.102792). This supports the theory that COVID-19 primarily affects the lower and lateral fields of the lungs, and suggests that the virus is accumulated mostly in the lower left quarter of the lungs. Overall, this study contributes to the understanding of the impact of COVID-19 on the respiratory system and can help in the development of accurate diagnostic methods.

GLM-based optimization of NGS data analysis: A case study of Roche 454, Ion Torrent PGM and Illumina NextSeq sequencing data

BACKGROUND

There are various next-generation sequencing techniques, all of them striving to replace Sanger sequencing as the gold standard. However, false positive calls of single nucleotide variants and especially indels are a widely known problem of basically all sequencing platforms.

METHODS

We considered three common next-generation sequencers-Roche 454, Ion Torrent PGM and Illumina NextSeq-and applied standard as well as optimized variant calling pipelines. Optimization was achieved by combining information of 23 diverse parameters characterizing the reported variants and generating individually calibrated generalized linear models. Models were calibrated using amplicon-based targeted sequencing data (19 genes, 28,775 bp) from seven to 12 myelodysplastic syndrome patients. Evaluation of the optimized pipelines and platforms was performed using sequencing data from three additional myelodysplastic syndrome patients.

RESULTS

Using standard analysis methods, true mutations were missed and the obtained results contained many artifacts-no matter which platform was considered. Analysis of the parameters characterizing the true and false positive calls revealed significant platform- and variant specific differences. Application of optimized variant calling pipelines considerably improved results. 76% of all false positive single nucleotide variants and 97% of all false positive indels could be filtered out. Positive predictive values could be increased by factors of 1.07 to 1.27 in case of single nucleotide variant calling and by factors of 3.33 to 53.87 in case of indel calling. Application of the optimized variant calling pipelines leads to comparable results for all next-generation sequencing platforms analyzed. However, regarding clinical diagnostics it needs to be considered that even the optimized results still contained false positive as well as false negative calls.