Objective method of comparing DNA microarray image analysis systems

Many image analysis systems are available for processing the images produced by laser scanning of DNA microarrays. The image processing system takes pixel-level intensity data and converts it to a set of gene-level expression or copy number summaries that will be used in further analyses. Image analysis systems currently in use differ with regard to the specific algorithms they implement, ease of use, and cost. Thus, it would be desirable to have an objective means of comparing systems. Here we describe a systematic method of comparing image processing results produced by different image analysis systems using a series of replicate microarray experiments. We demonstrate the method with a comparison of cDNA microarray data generated by the UCSF Spot and the GenePix® image processing systems

Supplementary Material for: Associations between Exposure to Persistent Organic Pollutants in Childhood and Overweight up to 12 Years Later in a Low Exposed Danish Population

<b><i>Background: </i></b>Persistent organic pollutants (POPs) have metabolic disrupting abilities and are suggested to contribute to the obesity epidemic. We investigated whether serum concentrations of POPs at 8-10 years of age were associated with subsequent development of overweight at age 14-16 and 20-22 years. <b><i>Methods: </i></b>The study was based on data from the European Youth Heart Study, Danish component (1997). Concentrations of several polychlorinated biphenyls (PCBs) and the organochlorine pesticides p,p-dichlorodiphenyldichloroethylene (DDE) and hexachlorobenzene (HCB) were measured in serum from children aged 8-10 years (n = 509). Information on BMI z-scores, waist circumference and % body fat were collected at clinical examinations at ages 8-10, 14-16 and 20-22 years. Multiple linear regression analyses were performed taking potential confounders into account. <b><i>Results: </i></b>Overall, POP serum concentrations were low: median ΣPCB 0.18 µg/g lipid, DDE 0.04 µg/g lipid and HCB 0.03 µg/g lipid. POPs were generally not associated with weight gain at 14-16 and 20-22 years of age, except for an inverse association among the highest exposed girls at 20-22 years of age, which might possibly be explained by multiple testing or residual confounding. <b><i>Conclusion: </i></b>This study suggests that, in a low exposed population, childhood serum concentrations of PCB, DDE, and HCB are not associated with subsequent weight gain