Motivation: Quantitative real-time PCR (qPCR) is one of the most widely used methods to measure gene expression. Despite extensive research in qPCR laboratory protocols, normalization and statistical analysis, little attention has been given to qPCR non-detects—those reactions failing to produce a minimum amount of signal.Results: We show that the common methods of handling qPCR non-detects lead to biased inference. Furthermore, we show that non-detects do not represent data missing completely at random and likely represent missing data occurring not at random. We propose a model of the missing data mechanism and develop a method to directly model non-detects as missing data. Finally, we show that our approach results in a sizeable reduction in bias when estimating both absolute and differential gene expression.Availability and implementation: The proposed algorithm is implemented in the R package, . This package also contains the raw data for the three example datasets used in this manuscript. The package is freely available at http://mnmccall.com/software and as part of the Bioconductor project.Contact: mccallm@gmail.com

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Rheumatoid arthritis (RA) is mediated by a proinflammatory cytokine network with TNF at its apex. Accordingly, drugs that block TNF have demonstrated significant efficacy in the treatment of RA. A great deal of experimental evidence also strongly implicates B cells in the pathogenesis of RA. Yet, it remains unclear whether these two important players and the therapies that target them are mechanistically linked. In this study we demonstrate that RA patients on anti-TNF (etanercept) display a paucity of follicular dendritic cell networks and germinal center (GC) structures accompanied by a reduction in CD38+ GC B cells and peripheral blood memory B cell lymphopenia compared with healthy controls and RA patients on methotrexate. This study provides initial evidence in humans to support the notion that anti-TNF treatment disrupts GC reactions at least in part via effects on follicular dendritic cells.

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Development of natural antibodies to 3 nontypeable Haemophilus influenzae (NTHi) outer membrane proteins (D, P6 and OMP26) was prospectively studied in 168 children 6–30 months of age during NP colonization and AOM. IgG antibody to protein D, P6 and OMP26 increased with age (p<0.001). Serum IgG responses to NP colonization were different for the 3 proteins: protein D responses occurred at a later age than P6, and OMP26 responses were minimal. For all 3 proteins serum antibody levels in the convalescent phase of AOM infection were not as high as after NP colonization. Antibodies to protein D and P6 but not OMP26 were bactericidal.