Quality control in microarray assessment of gene expression in human airway epithelium

<p>Abstract</p> <p>Background</p> <p>Microarray technology provides a powerful tool for defining gene expression profiles of airway epithelium that lend insight into the pathogenesis of human airway disorders. The focus of this study was to establish rigorous quality control parameters to ensure that microarray assessment of the airway epithelium is not confounded by experimental artifact. Samples (total n = 223) of trachea, large and small airway epithelium were collected by fiberoptic bronchoscopy of 144 individuals and hybridized to Affymetrix microarrays. The pre- and post-chip quality control (QC) criteria established, included: (1) RNA quality, assessed by RNA Integrity Number (RIN) ≥ 7.0; (2) cRNA transcript integrity, assessed by signal intensity ratio of GAPDH 3' to 5' probe sets ≤ 3.0; and (3) the multi-chip normalization scaling factor ≤ 10.0.</p> <p>Results</p> <p>Of the 223 samples, all three criteria were assessed in 191; of these 184 (96.3%) passed all three criteria. For the remaining 32 samples, the RIN was not available, and only the other two criteria were used; of these 29 (90.6%) passed these two criteria. Correlation coefficients for pairwise comparisons of expression levels for 100 maintenance genes in which at least one array failed the QC criteria (average Pearson r = 0.90 ± 0.04) were significantly lower (p < 0.0001) than correlation coefficients for pairwise comparisons between arrays that passed the QC criteria (average Pearson r = 0.97 ± 0.01). Inter-array variability was significantly decreased (p < 0.0001) among samples passing the QC criteria compared with samples failing the QC criteria.</p> <p>Conclusion</p> <p>Based on the aberrant maintenance gene data generated from samples failing the established QC criteria, we propose that the QC criteria outlined in this study can accurately distinguish high quality from low quality data, and can be used to delete poor quality microarray samples before proceeding to higher-order biological analyses and interpretation.</p

Systems Collaboration with Schools and Treatment of Severely Emotionally Disturbed Children or Adolescents

This study explored the relationship between the level of systems collaboration with schools and outcomes for children diagnosed with serious emotional disorder and their families involved in integrative family and systems treatment, a home-based treatment program. Using data collected from 38 clients and their families, this study used a structural equation model to explore how systems collaboration with schools influenced children\u27s behavioral outcomes, parental competence, and family functioning. The squared multiple correlations from endogenous variables of the final model accounted for 31 percent of the variance in problem severity in children, 38 percent of the variance in level of functioning in children, 30 percent of the variance in parental competence with children, and 41 percent of the variance in family functioning. The final model indicated the following: Systems collaboration with schools positively influenced parental competence with children, which positively predicted level of functioning in children and negatively predicted problem severity in children. Although the limited sample size of the study precludes any definitive conclusions, implications of the study on the potential role of systems collaboration with schools in treating families with at-risk children or adolescents are explored and discussed