Additional file 1: of TRIg: a robust alignment pipeline for non-regular T-cell receptor and immunoglobulin sequences

Is a pdf file containing Supplementary Results, Tables S1-S3 and Figures S1-S2 as described below. Table S1 PCR primer for 5′ RACE and the primer and barcode (MID) sequences used in 454 sequencing. Table S2 Number of VJ annotations by four programs to the SRR941034 data. Table S3 Consistency of VJ annotations to the SRR941034 data. Figure S1 Flow of 5′ RACE experiment. Figure S2 Comparison of alignments by different programs for the SRR941034 data. Please check Fig. 2 of the main text for explanations. Figure S3 Base quality of reads in the (a) first and (b) second quadrant of Fig. 2b of the main text when TRIg is compared to IgBLAST and IMGT. (PDF 312 kb

Antibody Profiling of Dengue Severities Using Flavivirus Protein Microarrays

Dengue is a viral disease transmitted by Aedes aegypti mosquitoes. According to the World Health Organization, about half of the world’s population is at risk of dengue. There are four serotypes of the dengue virus. After infection with one serotype, it will be immune to such a serotype. However, subsequent infection with other serotypes will increase the risk of severe outcomes, e.g., dengue hemorrhagic fever, dengue shock syndrome, and even death. Since severe dengue is challenging to predict and lacks molecular markers, we aim to build a multiplexed Flavivirus protein microarray (Flaviarray) that includes all of the common Flaviviruses to profile the humoral immunity and cross-reactivity in the dengue patients with different outcomes. The Flaviarrays we fabricated contained 17 Flavivirus antigens with high reproducibility (R-square = 0.96) and low detection limits (172–214 pg). We collected serums from healthy subjects (n = 36) and dengue patients within 7 days after symptom onset (mild dengue (n = 21), hospitalized nonsevere dengue (n = 29), and severe dengue (n = 36)). After profiling the serum antibodies using Flaviarrays, we found that patients with severe dengue showed higher IgG levels against multiple Flavivirus antigens. With logistic regression, we found groups of markers with high performance in distinguishing dengue patients from healthy controls as well as hospitalized from mild cases (AUC > 0.9). We further reported some single markers that were suitable to separate dengue patients from healthy controls (AUC > 0.9) and hospitalized from mild outcomes (AUC > 0.8). Together, Flaviarray is a valuable tool to profile antibody specificities, uncover novel markers for decision-making, and shed some light on early preventions and treatments