A Distributed Whole Genome Sequencing Benchmark Study.

Population sequencing often requires collaboration across a distributed network of sequencing centers for the timely processing of thousands of samples. In such massive efforts, it is important that participating scientists can be confident that the accuracy of the sequence data produced is not affected by which center generates the data. A study was conducted across three established sequencing centers, located in Montreal, Toronto, and Vancouver, constituting Canada's Genomics Enterprise (www.cgen.ca). Whole genome sequencing was performed at each center, on three genomic DNA replicates from three well-characterized cell lines. Secondary analysis pipelines employed by each site were applied to sequence data from each of the sites, resulting in three datasets for each of four variables (cell line, replicate, sequencing center, and analysis pipeline), for a total of 81 datasets. These datasets were each assessed according to multiple quality metrics including concordance with benchmark variant truth sets to assess consistent quality across all three conditions for each variable. Three-way concordance analysis of variants across conditions for each variable was performed. Our results showed that the variant concordance between datasets differing only by sequencing center was similar to the concordance for datasets differing only by replicate, using the same analysis pipeline. We also showed that the statistically significant differences between datasets result from the analysis pipeline used, which can be unified and updated as new approaches become available. We conclude that genome sequencing projects can rely on the quality and reproducibility of aggregate data generated across a network of distributed sites.

Epidermal barrier treatments based on vernix caseosa.

BACKGROUND/AIMS: Premature infants lack the vernix caseosa, have an incompetent stratum corneum (SC) barrier and are predisposed to infection. Use of topical agents to improve barrier function has had mixed outcomes. The aim was to determine the effect of vernix versus common barrier creams on the rate and quality of the epidermal barrier repair following controlled wounding. METHODS: Minor wounds were created with (1) laser ablation in the minipig and (2) tape stripping of mother's volar skin as a model for premature skin. Native vernix was applied to the mother's tape-stripped skin. Treatments were no occlusion (NO), vernix and a petrolatum-based cream (PBC) in the pig, and NO, vernix, PBC, an oil-in-water cream (OWC), a semipermeable film (SP) and full occlusion (FO) in adults. RESULTS: Outcomes for both trials were barrier recovery and skin hydration (moisture accumulation rate, MAT), initial hydration, erythema and dryness in adults. Vernix and PBC produced greater barrier repair than NO in the pig. SP produced greater recovery than NO and FO in adults. Vernix yielded greater recovery than FO and was similar to PBC, OWC and NO. Vernix had a directionally higher MAT than OWC and directionally higher initial hydration than NO. CONCLUSIONS: The findings suggest that vernix-based topical creams would be effective for the treatment of epidermal wounds and show promise to augment SC repair and maturation in infants.

Improved barrier function observed in cultured skin substitutes developed under anchored conditions.

BACKGROUND/PURPOSE: The current method of producing cultured skin substitutes (CSS) is focused on providing treatments for severe skin wounds/burns. We have developed a modified growth method to make them more suitable for in vitro product-testing/toxicity-testing purposes. METHOD: CSS grown in Petri dishes were either transferred to Franz diffusion cells on day 5 (modified method) or left in the Petri dish (standard method) and maintained in these environments for the remainder of the growth phase. Mitochondrial metabolism (MTT assay) was measured on days 5, 10 and 14 and histology was studied on days 5, 10 and 14. Barrier function for all tissues was evaluated by transferring them to Franz cells (standard method) and measuring transepidermal water loss (TEWL), 3H2O penetration and 14C-niacinamide permeability on days 7, 14 and 21. RESULTS: CSS grown by the standard and modified methods showed comparable cell viability and tissue morphology. Barrier function, however, was markedly improved in CSS grown by the modified method. The average improvement at days 7 and 14 was 1.3-fold for TEWL, 2.1-fold for 3H2O penetration and 6.4-fold for 14C-niacinamide permeability. The barrier function of CSS grown by the modified method was still significantly lower than that of human cadaver skin tested by the same methods. CONCLUSIONS: CSS developed using the anchored multi-cell system showed similar cell viability and morphology and improved barrier function compared with CSS produced by the standard Petri dish method, thereby improving its potential as an in vitro skin permeability and toxicity model.

Improvement of epidermal barrier properties in cultured skin substitutes after grafting onto athymic mice.

Barrier function in cultured skin substitutes (CSS) prepared from human cell sources was measured by noninvasive (surface hydration, transepidermal water loss) and invasive methods (water permeation, niacinamide flux) before and after grafting onto athymic mice. In vitro measurements were made on days 7 and 14. Although three of the four measures of barrier function improved markedly from day 7 to 14, the values obtained were still far from those obtained with native human skin controls. Additional CSS were grafted onto athymic mice on day 14, and skin was harvested 2 and 6 weeks after grafting. Grafting brought about a substantial decrease in all measurements by 2 weeks and almost complete normalization of barrier function after 6 weeks. The most sensitive measure of this recovery was niacinamide permeability, which decreased from (280 +/- 40) x 10(-4) cm/h in vitro to (17 +/- 30) x 10(-4) cm/h 2 weeks after grafting and (5 +/- 2) x 10(-4) cm/h 6 weeks after grafting, versus control values of (2 +/- 2) x 10(-4) cm/h in human cadaver skin and (0.6 +/- 0.4) x 10(-4) cm/h in human epidermal membrane prepared from freshly excised breast skin. These results demonstrate the reformation of epidermal barrier function after transplantation and provide insights for the development of a functional epidermal barrier in CSS in vitro.

Mobility of water in human stratum corneum.

At low water activities, stratum corneum (SC) water sorption resembles that in other keratinized tissues (i.e., wool and horn), whereas at high water activities, it resembles that in polymeric hydrogels. We propose that the concentration-dependent water diffusivity observed in these other systems applies to the corneocyte phase of the SC. An increase in SC hydration leads to increased water diffusivity in the corneocytes, in accordance with the predictions of both effective diffusion and free volume theories. Thus, theoretical results on effective diffusivity in a composite medium with random fiber obstacles and a free volume theory for water diffusivity in hydrogels (calibrated using data from wool and horn) have been applied to human SC water sorption data to estimate and establish theoretical limits on water diffusivity in corneocytes as a function of water activity. These results are used in conjunction with steady-state water permeability data to estimate the water permeability of both corneocyte and lipid phases of the SC under hydrated and partially hydrated conditions. The results of the analysis, when combined with previous spectroscopic analyses, strongly suggest that the lipids provide most of the SC water barrier in either case; thus, the diffusion pathway for water is primarily transcellular.

Equilibrium water sorption in human stratum corneum.

The water content of the stratum corneum (SC) is a key factor in skin barrier homeostasis; it is intimately related to both skin condition and skin permeability. Studies of water uptake in excised human SC show strong similarities and allow characterization of the equilibrium SC water sorption isotherm in terms of widely used theoretical models. At low water activities, SC water sorption resembles that in other keratinized tissues (i.e., wool and horn), whereas at high water activities, it resembles that in polymeric hydrogels. In this paper, theoretical water sorption models [Brunauer-Emmett-Teller (BET), D'Arcy-Watt, and Frenkel-Halsey-Hill] are fit to the combined human SC water sorption data from our laboratories and others. Each of these models provides a satisfactory description of the equilibrium water content of human SC over the water activity range 0.03-1.0. An accompanying paper discusses the implications of SC water sorption on water mobility in corneocytes and on SC permeability.