A commentary on this article appears in this issue on page 1331.

The prognostic value of pN stratification depends on the thoroughness of examination. Differences in thoroughness of nodal staging may explain a large proportion of intercontinental survival differences. More thorough nodal examination practice must be disseminated to improve the prognostic value of the TNM staging system. Future updates of the TNM staging system should incorporate more quality restraints.

BackgroundWhole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. These associations can be confounded by cellular heterogeneity. Algorithms have been developed to measure or adjust for this heterogeneity, and some have been compared in the literature. However, with new methods available, it is unknown whether the findings will be consistent, if not which method(s) perform better.Results Methods: We compared eight cell-type correction methods including the method in the minfi R package, the method by Houseman et al., the Removing unwanted variation (RUV) approach, the methods in FaST-LMM-EWASher, ReFACTor, RefFreeEWAS, and RefFreeCellMix R programs, along with one approach utilizing surrogate variables (SVAs). We first evaluated the association of DNA methylation at each CpG across the whole genome with prenatal arsenic exposure levels and with cancer status, adjusted for estimated cell-type information obtained from different methods. We then compared CpGs showing statistical significance from different approaches. For the methods implemented in minfi and proposed by Houseman et al., we utilized homogeneous data with composition of some blood cells available and compared them with the estimated cell compositions. Finally, for methods not explicitly estimating cell compositions, we evaluated their performance using simulated DNA methylation data with a set of latent variables representing “cell types”. Results: Results from the SVA-based method overall showed the highest agreement with all other methods except for FaST-LMM-EWASher. Using homogeneous data, minfi provided better estimations on cell types compared to the originally proposed method by Houseman et al. Further simulation studies on methods free of reference data revealed that SVA provided good sensitivities and specificities, RefFreeCellMix in general produced high sensitivities but specificities tended to be low when confounding is present, and FaST-LMM-EWASher gave the lowest sensitivity but highest specificity.ConclusionsResults from real data and simulations indicated that SVA is recommended when the focus is on the identification of informative CpGs. When appropriate reference data are available, the method implemented in the minfi package is recommended. However, if no such reference data are available or if the focus is not on estimating cell proportions, the SVA method is suggested.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1611-2) contains supplementary material, which is available to authorized users.

Background Season of birth influences allergy risk, however the biological mechanisms underlying this observation are unclear. The environment affects DNA methylation, with potentially long-lasting effects on gene expression and disease. This study examined whether DNA methylation could underlie the association between season of birth and allergy. Methods In a subset of 18-year-old participants from the Isle of Wight (IoW) birth cohort (n=367), the risks of birth season on allergic outcomes were estimated. Whole blood epigenome-wide DNA methylation was measured, and season-associated CpGs detected using a training-and-testing-based technique. Validation examined the 8-year-old Prevention and Incidence of Asthma and Mite Allergy (PIAMA) cohort. The relationships between DNA methylation, season of birth and allergy were examined. CpGs were analysed in IoW third generation cohort newborns. Results Autumn birth increased risk of eczema, relative to spring birth. Methylation at 92 CpGs showed association with season of birth in the epigenome-wide association study. In validation significantly more CpGs had the same directionality than expected by chance, and four were statistically significant. Season-associated methylation was enriched among networks relating to development, the cell cycle, and apoptosis. Twenty CpGs were nominally associated with allergic outcomes. Two CpGs were marginally on the causal pathway to allergy. Season-associated methylation was largely absent in newborns, suggesting it arises postnatally. Conclusions This study demonstrates that DNA methylation in adulthood is associated with season of birth, supporting the hypothesis that DNA methylation could mechanistically underlie the effect of season of birth on allergy, though other mechanisms are also likely to be involved.

IntroductionPatients frequently present to the emergency department (ED) with migraine headaches. Although low-dose ketamine demonstrates analgesic efficacy for acute pain complaints in the ED, headaches have historically been excluded from these trials. This study evaluates the efficacy and safety of low-dose ketamine for treatment of acute migraine in the ED.MethodsThis randomized, double-blinded, placebo-controlled trial evaluated adults 18 to 65 years of age with acute migraine at a single academic ED. Subjects were randomized to receive 0.2 milligrams per kilogram of intravenous (IV) ketamine or an equivalent volume of normal saline. Numeric Rating Scale (NRS-11) pain scores, categorical pain scores, functional disability scores, side effects, and adverse events were assessed at baseline (T0) and 30 minutes post-treatment (T30). The primary outcome was between-group difference in NRS score reduction at 30 minutes.ResultsWe enrolled 34 subjects (ketamine=16, placebo=18). Demographics were similar between treatment groups. There was no statistically significant difference in NRS score reductions between ketamine and placebo-treated groups after 30 minutes. Median NRS score reductions at 30 minutes were 1.0 (interquartile range [IQR] 0 to 2.25) for the ketamine group and 2.0 (IQR 0 to 3.75) for the placebo group. Between-group median difference at 30 minutes was −1.0 (IQR −2 to 1, p=0.5035). No significant differences between treatment groups occurred in categorical pain scores, functional disability scores, rescue medication request rate, and treatment satisfaction. Side Effect Rating Scale for Dissociative Anesthetics scores in the ketamine group were significantly greater for generalized discomfort at 30 minutes (p=0.008) and fatigue at 60 minutes (p=0.0216). No serious adverse events occurred in this study.ConclusionWe found that 0.2mg/kg IV ketamine did not produce a greater reduction in NRS score compared to placebo for treatment of acute migraine in the ED. Generalized discomfort at 30 minutes was significantly greater in the ketamine group. Overall, ketamine was well tolerated by migraine-suffering subjects. To optimize low-dose ketamine as an acute migraine treatment, future studies should investigate more effective dosing and routes of administration.