Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies

A diversity of tools is available for identification of variants from genome sequence data. Given the current complexity of incorporating external software into a genome analysis infrastructure, a tendency exists to rely on the results from a single tool alone. The quality of the output variant calls is highly variable however, depending on factors such as sequence library quality as well as the choice of short-read aligner, variant caller, and variant caller filtering strategy. Here we present a two-part study first using the high quality ‘genome in a bottle’ reference set to demonstrate the significant impact the choice of aligner, variant caller, and variant caller filtering strategy has on overall variant call quality and further how certain variant callers outperform others with increased sample contamination, an important consideration when analyzing sequenced cancer samples. This analysis confirms previous work showing that combining variant calls of multiple tools results in the best quality resultant variant set, for either specificity or sensitivity, depending on whether the intersection or union, of all variant calls is used respectively. Second, we analyze a melanoma cell line derived from a control lymphocyte sample to determine whether software choices affect the detection of clinically important melanoma risk-factor variants finding that only one of the three such variants is unanimously detected under all conditions. Finally, we describe a cogent strategy for implementing a clinical variant detection pipeline; a strategy that requires careful software selection, variant caller filtering optimizing, and combined variant calls in order to effectively minimize false negative variants. While implementing such features represents an increase in complexity and computation the results offer indisputable improvements in data quality.     

Microparticle-Induced Activation of the Vascular Endothelium Requires Caveolin-1/Caveolae

Microparticles (MPs) are small membrane fragments shed from normal as well as activated, apoptotic or injured cells. Emerging evidence implicates MPs as a causal and/or contributing factor in altering normal vascular cell phenotype through initiation of proinflammatory signal transduction events and paracrine delivery of proteins, mRNA and miRNA. However, little is known regarding the mechanism by which MPs influence these events. Caveolae are important membrane microdomains that function as centers of signal transduction and endocytosis. Here, we tested the concept that the MP-induced pro-inflammatory phenotype shift in endothelial cells (ECs) depends on caveolae. Consistent with previous reports, MP challenge activated ECs as evidenced by upregulation of intracellular adhesion molecule-1 (ICAM-1) expression. ICAM-1 upregulation was mediated by activation of NF-κB, Poly [ADP-ribose] polymerase 1 (PARP-1) and the epidermal growth factor receptor (EGFR). This response was absent in ECs lacking caveolin-1/caveolae. To test whether caveolae-mediated endocytosis, a dynamin-2 dependent process, is a feature of the proinflammatory response, EC’s were pretreated with the dynamin-2 inhibitor dynasore. Similar to observations in cells lacking caveolin-1, inhibition of endocytosis significantly attenuated MPs effects including, EGFR phosphorylation, activation of NF-κB and upregulation of ICAM-1 expression. Thus, our results indicate that caveolae play a role in mediating the pro-inflammatory signaling pathways which lead to EC activation in response to MPs.     

Comparison of two techniques for quantifying environmental contaminants in human serum

Peak area matching and linear regression were used to quantify eight chlorinated pesticides and polychlorinated biphenyls (as Aroclor 1260) in human serum. There are no statistically significant differences in data obtained by these two quantifying techniques which were indicated by the paired t-test. For chlorinated pesticides, p = 0.053-0.62, and for polychlorinated biphenyls (as Aroclor 1260), p = 0.64. Analyte residues for the chlorinated pesticides ranged from 0.5 ppb for hexachlorobenzene (HCB) to 186 ppb for dichlorodiphenyldichloroethylene (DDE). Analyte residues for the polychlorinated biphenyls (as Aroclor 1260) ranged from 5-114 ppb. The absolute mean percent difference between the two quantifying techniques ranged from 0.06% for DDE to 8.06% for dieldrin (HEOD) among the chlorinated pesticides. The absolute mean percent difference between the two quantifying techniques for the polychlorinated biphenyls (as Aroclor 1260) was 3.4%. Peak area matching and linear regression were found to be comparable for quantifying these environmental residues in serum when the following conditions apply: 1) the concentration of the chlorinated pesticides is greater than or equal to 0.5 ppb (e.g., HCB, hexachlorocyclohexane (HCCH), oxychlordane (OC), heptachlor epoxide (HE), transnonachlor (TN), HEOD, and dichlorodiphenyltrichloroethane (DDT); 2) the concentration of the chlorinated pesticide is greater than or equal to 3 ppb (e.g., DDE); and 3) the total concentration of polychlorinated biphenyls (e.g., as Aroclor 1260) is greater than or equal to 5 ppb.     

Early growth and final yield of autumn sownVicia faba L cultivars given different forms of fertiliser N over winter

Summary Between 3 Nov. 1983 and 9 Apr. 1984, six applications of fertiliser N (ammonium, nitrate or urea) were given to four autumn sown (26 Oct. 1983)Vicia faba L cultivars, Banner Winter (BW) and Maris Beagle (MBg), cold tolerant cultivars normally sown in the autumn, and Herz Freya (HF) and Maris Bead (MBd), cold sensitive cultivars more commonly sown in the spring. The effects of additional N were determined by comparison with plants given zero-N (controls). Application of N, regardless of form, had no effect on % emergence at the first sampling (15 Dec. 1983); >90% for BW, MBg and HF, but only 40–60% for MBd. At this time the dry weight, carbon content and nitrogen content of all cultivars was approximately 20% less than that of the seed on planting. No more plants emerged after 15 Dec. 1983. Between 15 Dec. 1983 and 20 Feb. 1984, all cultivars, regardless of N treatment, showed little change in dry weight, carbon content and nitrogen content but the proportion of total plant dry weight, carbon content and nitrogen content in the cotyledons decreased while the proportions in root, stem and leaf tissue increased. On 20 Feb. 1984 there were no N effects. All cultivars but especially BW and MBg, showed progressive increases in dry weight, carbon content and nitrogen content during the period 20 Feb. 1984 to 8 May 1984. Pooled results for all four cultivars indicated that on 8 May 1984, plants given ammonium and urea had a greater dry weight, carbon content and nitrogen content than controls. At harvest (1–3 Sep. 1984), BW and MBg outyielded (g dw seed m⁻²) HF and MBd. Pooled results for all cultivars indicated that application of N regardless of form gave increased yield and an increased N concentration (mg N g⁻¹ dw) in the seed.     

Metabolic and thermoregulatory consequences of social behaviors between Microtus townsendii

1. Townsend voles responded to each other by raising their core temperatures. 2. Increments of temperature increases that accompanied hostile reactions between voles, were proportional to the intensity of the behavioral displays. 3. Amicable behaviors (huddling) were also associated with higher body temperatures that were proportional to group size. 4. Huddling voles conserved metabolic energy expenditure by reducing their metabolic rates and thermal conductances. 5. Such conservation required 1 or more days of amicable behavior to develop, and to be reversed. 6. The degree of metabolic rate reduction that accompanied amicable huddling behavior and the associated reduction of thermal conductance was independent of group size.