Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology

BACKGROUND: The arrival of RNA-seq as a high-throughput method competitive to the established microarray technologies has necessarily driven a need for comparative evaluation. To date, cross-platform comparisons of these technologies have been relatively few in number of platforms analyzed and were typically gene name annotation oriented. Here, we present a more extensive and yet precise assessment to elucidate differences and similarities in performance of numerous aspects including dynamic range, fidelity of raw signal and fold-change with sample titration, and concordance with qRT-PCR (TaqMan). To ensure that these results were not confounded by incompatible comparisons, we introduce the concept of probe mapping directed “transcript pattern”. A transcript pattern identifies probe(set)s across platforms that target a common set of transcripts for a specific gene. Thus, three levels of data were examined: entire data sets, data derived from a subset of 15,442 RefSeq genes common across platforms, and data derived from the transcript pattern defined subset of 7,034 RefSeq genes. RESULTS: In general, there were substantial core similarities between all 6 platforms evaluated; but, to varying degrees, the two RNA-seq protocols outperformed three of the four microarray platforms in most categories. Notably, a fourth microarray platform, Agilent with a modified protocol, was comparable, or marginally superior, to the RNA-seq protocols within these same assessments, especially in regards to fold-change evaluation. Furthermore, these 3 platforms (Agilent and two RNA-seq methods) demonstrated over 80 % fold-change concordance with the gold standard qRT-PCR (TaqMan). CONCLUSIONS: This study suggests that microarrays can perform on nearly equal footing with RNA-seq, in certain key features, specifically when the dynamic range is comparable. Furthermore, the concept of a transcript pattern has been introduced that may minimize potential confounding factors of multi-platform comparison and may be useful for similar evaluations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1913-6) contains supplementary material, which is available to authorized users

Increased complement activation is a distinctive feature of severe SARS-CoV-2 infection

Complement activation has been implicated in the pathogenesis of severe SARS-CoV-2 infection. However, it remains to be determined whether increased complement activation is a broad indicator of critical illness (and thus, no different in COVID-19). It is also unclear which pathways are contributing to complement activation in COVID-19, and if complement activation is associated with certain features of severe SARS-CoV-2 infection, such as endothelial injury and hypercoagulability. To address these questions, we investigated complement activation in the plasma from patients with COVID-19 prospectively enrolled at two tertiary care centers: Washington University School of Medicine (n=134) and Yale School of Medicine (n=49). We compared our patients to two non-COVID cohorts: (a) patients hospitalized with influenza (n=54), and (b) patients admitted to the intensive care unit (ICU) with acute respiratory failure requiring invasive mechanical ventilation (IMV, n=22). We demonstrate that circulating markers of complement activation are elevated in patients with COVID-19 compared to those with influenza and to patients with non-COVID-19 respiratory failure. Further, the results facilitate distinguishing those who are at higher risk of worse outcomes such as requiring ICU admission, or IMV. Moreover, the results indicate enhanced activation of the alternative complement pathway is most prevalent in patients with severe COVID-19 and is associated with markers of endothelial injury (i.e., angiopoietin-2) as well as hypercoagulability (i.e., thrombomodulin and von Willebrand factor). Our findings identify complement activation to be a distinctive feature of COVID-19, and provide specific targets that may be utilized for risk prognostication, drug discovery and personalized clinical trials

Current Guidelines, Common Clinical Pitfalls, and Future Directions for Laboratory Diagnosis of Lyme Disease, United States

In the United States, Lyme disease is caused by Borrelia burgdorferi and transmitted to humans by blacklegged ticks. Patients with an erythema migrans lesion and epidemiologic risk can receive a diagnosis without laboratory testing. For all other patients, laboratory testing is necessary to confirm the diagnosis, but proper interpretation depends on symptoms and timing of illness. The recommended laboratory test in the United States is 2-tiered serologic analysis consisting of an enzyme-linked immunoassay or immunofluorescence assay, followed by reflexive immunoblotting. Sensitivity of 2-tiered testing is low (30%–40%) during early infection while the antibody response is developing (window period). For disseminated Lyme disease, sensitivity is 70%–100%. Specificity is high (>95%) during all stages of disease. Use of other diagnostic tests for Lyme disease is limited. We review the rationale behind current US testing guidelines, appropriate use and interpretation of tests, and recent developments in Lyme disease diagnostics

Evaluation of a Sequential Enzyme Immunoassay Testing Algorithm for Lyme Disease Demonstrates Lack of Test Independence but High Diagnostic Specificity

To diagnose Lyme disease, a two-tier testing algorithm is used in which supplemental IgM and IgG immunoblots to detect antibody to Borrelia burgdorferi are reflexively performed if a first-tier assay, such as a whole-cell sonicate-based enzyme immunoassay (WCS EIA), is reactive. Recent data suggest that equal specificity is found by substituting the C6 peptide EIA for immunoblots. In this study using 3956 control sera, we demonstrated that although this two-tier testing algorithm does significantly improve diagnostic specificity compared with each of the EIAs individually, the WCS EIA and the C6 peptide EIA are not independent tests. Therefore, when the C6 peptide EIA is used as the second-tier test, it should be regarded as a supplemental rather than a confirmatory test

Additional file 2: Figure S2. of Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology

Overall average absolute fold-change comparisons across platforms with entire set and transcript pattern (TP) defined subset data, with a focus on the effect of Affymetrix “Signal Space Transformation” (SST) algorithm on the overall platform fold-change magnitude. The SST, in conjunction with the regular robust multiple-array average normalization method (SST-RMA, the dark blue bars), was able to improve the fold-change in the HTA2.0 arrays, and provided a 2-5x greater fold-change estimates overall, as compared to conventional data processing method (regular RMA, the light blue bars). (TIFF 491 kb

Additional file 1: Figure S1. of Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology

Box-Whisker plot for illustration of fold-change variability in each platform. (A) and (B) are for fold-change data in the 4 sample titrations in entire set and transcript pattern (TP) defined 7,034 RefSeq genes subset data, respectively; (C) and (D) are for fold-change data at overall platform level in the entire set and TP-defiend subset data, respectively. The frame boxes are the inter-quartile range (i.e. 25 % to 75 %). (TIFF 867 kb