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Abstract Background Mitochondrial dysfunction is associated with various aging diseases. The copy number of mtDNA in human cells may therefore be a potential biomarker for diagnostics of aging. Here we propose a new computational method for the accurate assessment of mtDNA copies from whole genome sequencing data. Results Two families of the human whole genome sequencing datasets from the HapMap and the 1000 Genomes projects were used for the accurate counting of mitochondrial DNA copy numbers. The results revealed the parental mitochondrial DNA copy numbers are significantly lower than that of their children in these samples. There are 8%~21% more copies of mtDNA in samples from the children than from their parents. The experiment demonstrated the possible correlations between the quantity of mitochondrial DNA and aging-related diseases. Conclusions Since the next-generation sequencing technology strives to deliver affordable and non-biased sequencing results, accurate assessment of mtDNA copy numbers can be achieved effectively from the output of whole genome sequencing. We implemented the method as a software package MitoCounter with the source code and user's guide available to the public at http://sourceforge.net/projects/mitocounter/.

Abstract Background A genetic interaction refers to the deviation of phenotypes from the expected when perturbing two genes simultaneously. Studying genetic interactions help clarify relationships between genes, such as compensation and masking, and identify gene groups of functional modules. Recently, several genome-scale experiments for measuring quantitative (positive and negative) genetic interactions have been conducted. The results revealed that genes in the same module usually interact with each other in a consistent way (pure positive or negative); this phenomenon was designated as monochromaticity. Monochromaticity might be the underlying principle that can be utilized to unveil the modularity of cellular networks. However, no appropriate quantitative measurement for this phenomenon has been proposed. Results In this study, we propose the monochromatic index (MCI), which is able to quantitatively evaluate the monochromaticity of potential functional modules of genes, and the MCI was used to study genetic landscapes in different cellular subsystems. We demonstrated that MCI not only amend the deficiencies of MP-score but also properly incorporate the background effect. The results showed that not only within-complex but also between-complex connections present significant monochromatic tendency. Furthermore, we also found that significantly higher proportion of protein complexes are connected by negative genetic interactions in metabolic network, while transcription and translation system adopts relatively even number of positive and negative genetic interactions to link protein complexes. Conclusion In summary, we demonstrate that MCI improves deficiencies suffered by MP-score, and can be used to evaluate monochromaticity in a quantitative manner. In addition, it also helps to unveil features of genetic landscapes in different cellular subsystems. Moreover, MCI can be easily applied to data produced by different types of genetic interaction methodologies such as Synthetic Genetic Array (SGA), and epistatic miniarray profile (E-MAP).

This corrects the article DOI: 10.1038/srep09541 [ABSTRACT FROM AUTHOR]

Background: Discussing the quality measurements based on interrupted time series in ischemic stroke, delays are often attributed to weekends effect. This study compared the metrics and outcomes of emergent endovascular thrombectomy (EST) during working hours versus non-working hours in the emergency department of an Asian medical center., Methods: A total of 297 patients who underwent EST between January 2015 and December 2018 were retrospectively included, with 52.5% of patients presenting during working hours and 47.5% presenting during nights, weekends, or holidays., Results: Patients with diabetes were more in non-working hours than in working hours (53.9% vs. 41.0%; p=0.026). It took longer during nonworking hours than working hours in door-to -image times (13 min vs. 12 min; p=0.04) and door-to-groin puncture times (median: 112 min vs. 104 min; p=0.042). Significant statistical differences were not observed between the two groups in neurological outcomes, including successful reperfusion and complications such as intracranial hemorrhage and mortality. However, the change in National Institute of Health Stroke Scale (NIHSS) scores in 24 hours was better in the working-hour group than in the nonworking-hour group (4 vs. 2; p=0.058)., Conclusion: This study revealed that nonworking-hour effects truly exist in patients who received EST. Although delays in door-to-groin puncture times were noticed during nonworking hours, significant differences in neurological functions and mortality were not observed between working and non-working hours. Nevertheless, methods to improve the process during non-working hours should be explored in the future., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

The occurrence of chimeric transcripts has been reported in many cancer cells and seen as potential biomarkers and therapeutic targets. Modern high-throughput sequencing technologies offer a way to investigate individual chimeric transcripts and the systematic information of associated gene expressions about underlying genome structural variations and genomic interactions. The detection methods of finding chimeric transcripts from massive amount of short read sequence data are discussed here. Both assembly-based and alignment-based methods are used for the investigation of chimeric transcripts.