Set-theory based benchmarking of three different variant callers for targeted sequencing

Background

Next generation sequencing (NGS) technologies have improved the study of hereditary diseases. Since the evaluation of bioinformatics pipelines is not straightforward, NGS demands effective strategies to analyze data that is of paramount relevance for decision making under a clinical scenario. According to the benchmarking framework of the Global Alliance for Genomics and Health (GA4GH), we implemented a new simple and user-friendly set-theory based method to assess variant callers using a gold standard variant set and high confidence regions. As model, we used TruSight Cardio kit sequencing data of the reference genome NA12878. This targeted sequencing kit is used to identify variants in key genes related to Inherited Cardiac Conditions (ICCs), a group of cardiovascular diseases with high rates of morbidity and mortality.

Results

We implemented and compared three variant calling pipelines (Isaac, Freebayes, and VarScan). Performance metrics using our set-theory approach showed high-resolution pipelines and revealed: (1) a perfect recall of 1.000 for all three pipelines, (2) very high precision values, i.e. 0.987 for Freebayes, 0.928 for VarScan, and 1.000 for Isaac, when compared with the reference material, and (3) a ROC curve analysis with AUC > 0.94 for all cases. Moreover, significant differences were obtained between the three pipelines. In general, results indicate that the three pipelines were able to recognize the expected variants in the gold standard data set.

Conclusions

Our set-theory approach to calculate metrics was able to identify the expected ICCs related variants by the three selected pipelines, but results were completely dependent on the algorithms. We emphasize the importance to assess pipelines using gold standard materials to achieve the most reliable results for clinical application.

The resilience of coastal marshes to hurricanes: The potential impact of excess nutrients

Hurricanes pose an increasing threat to coastal environments as the intensity and severity of hurricanes are predicted to increase under the changing climate. Coastal wetlands are effective nature-based defenses of coastal cities against storms. However, the ecosystems themselves are also susceptible to the impacts of hurricanes, which are highly complex and not fully understood. Here we utilize multi-decadal satellite data archives (Landsat 1984-2014 and MODIS 2005-2015) and long-term coast-wide field-based environmental data (1978-2018) to investigate the impacts of hurricanes Katrina (2005), Gustav (2008), and Isaac (2012) on the coastal marshes in Louisiana, USA, where the hurricanes made landfall. While the hurricanes had immediate impacts on the marshes' biomass and area at an ecosystem scale, general recovery was observed in the next one and two years. We also found that the most severe damage always occurred in the intermediate and brackish marshes of the Breton Sound basin, where the nitrogen concentration in the water was significantly higher compared to areas with less damage (P < 0.01). Because excess nutrient can reduce the marshes' root growth and degrade their root mat, we posit that the long-term nutrient enrichment in the area, which resulted from the diverted Mississippi River water, has increased the marshes' susceptibility to hurricanes. The results highlight the resilience of coastal marsh ecosystems against hurricanes, but also underline the profound synergistic effects of climatic and anthropogenic factors on the sustainability of coastal ecosystems, which have important implications for coastal management under the current climate trend.

When Fathering Fails: Violence, Narcissism, and the Father Function in Ancient Tales and Clinical Analysis

Manifestations of failures in both symbolic and actual flesh-and-blood fathering reveal the inescapable role played by the father's unconscious transmissions in the ever present triadic matrix. Perelberg's crucial distinction between the murdered narcissistic father and the dead symbolic father suggests the problematic internalizations that fail to uphold the paternal law required for oedipal resolution. Three father-child narratives derived from classical literature and mythology are presented in order to elucidate significant unconscious paternal fantasies pertaining to lethal rivalry and neglect of the child's otherness. These narratives suggest how the father's insufficient management of rivalrous, envious, and murderously aggressive impulses-as well as narcissistic needs that fail to take into account the child's alterity-combine with the child's intrapsychic propensities to constrict triangular space and restrict development. Consequently, unavoidable father-child rivalries, absences, neglect, and desires often make it vital to recover the "missing" paternal function in analytic space. A clinical example illustrates the impact of this absence on the analyst's countertransference.