samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

MOTIVATION: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.

RESULTS: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.

AVAILABILITY: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).

Socio-economic inequalities in cerebral palsy prevalence in the United Kingdom: a register-based study

Evidence is unclear as to whether there is a socio-economic gradient in cerebral palsy (CP) prevalence beyond what would be expected from the socio-economic gradient for low birthweight, a strong risk factor for CP. We conducted a population-based study in five regions of the UK with CP registers, to investigate the relationship between CP prevalence and socio-economic deprivation, and how it varies by region, by birthweight and by severity and type of CP. The total study population was 1 657 569 livebirths, born between 1984 and 1997. Wards of residence were classified into five quintiles according to a census-based deprivation index, from Q1 (least deprived) to Q5 (most deprived). Socio-economic gradients were modelled by Poisson regression, and region-specific estimates combined by meta-analysis.

The prevalence of postneonatally acquired CP was 0.14 per 1000 livebirths overall. The mean deprivation gradient, expressed as the relative risk in the most deprived vs. the least deprived quintile, was 1.86 (95% confidence interval [95% CI 1.19, 2.88]). The prevalence of non-acquired CP was 2.22 per 1000 livebirths. For non-acquired CP the gradient was 1.16 [95% CI 1.00, 1.35]. Evidence for a socio-economic gradient was strongest for spastic bilateral cases (1.32 [95% CI 1.09, 1.59]) and cases with severe intellectual impairment (1.59 [95% CI 1.06, 2.39]). There was evidence for differences in gradient between regions. The gradient of risk of CP among normal birthweight births was not statistically significant overall (1.21 [95% CI 0.95, 1.54]), but was significant in two regions. There was non-significant evidence of a reduction in gradients over time.

The reduction of the higher rates of postneonatally acquired CP in the more socioeconomically deprived areas is a clear goal for prevention. While we found evidence for a socio-economic gradient for non-acquired CP of antenatal or perinatal origin, the picture was not consistent across regions, and there was some evidence of a decline in inequalities over time. The steeper gradients in some regions for normal birthweight cases and cases with severe intellectual impairment require further investigation.

The application of Reporter Gene Assays for the detection of endocrine disruptors in sport supplements.

The increasing availability and use of sports supplements is of concern as highlighted by a number of studies reporting endocrine disruptor contamination in such products. The health food supplement market, including sport supplements, is growing across the Developed World. Therefore, the need to ensure the quality and safety of sport supplements for the consumer is essential. The development and validation of two reporter gene assays coupled with solid phase sample preparation enabling the detection of estrogenic and androgenic constituents in sport supplements is reported. Both assays were shown to be of high sensitivity with the estrogen and androgen reporter gene assays having an EC50 of 0.01 ng mL-1 and 0.16 ng mL-1 respectively. The developed assays were applied in a survey of 63 sport supplements samples obtained across the Island of Ireland with an additional seven reference samples previously investigated using LC–MS/MS. Androgen and estrogen bio-activity was found in 71% of the investigated samples. Bio-activity profiling was further broken down into agonists, partial agonists and antagonists. Supplements (13) with the strongest estrogenic bio-activity were chosen for further investigation. LC–MS/MS analysis of these samples determined the presence of phytoestrogens in seven of them. Supplements (38) with androgen bio-activity were also selected for further investigation. Androgen agonist bio-activity was detected in 12 supplements, antagonistic bio-activity was detected in 16 and partial antagonistic bio-activity was detected in 10. A further group of supplements (7) did not present androgenic bio-activity when tested alone but enhanced the androgenic agonist bio-activity of dihydrotestosterone when combined. The developed assays offer advantages in detection of known, unknown and low-level mixtures of endocrine disruptors over existing analytical screening techniques. For the detection and identification of constituent hormonally active compounds the combination of biological and physio-chemical techniques is optimal.