Additional file 1 of chngpt: threshold regression model estimation and inference

Supplementary tables and a short tutorial on using chngpt. (PDF 63.5 kb

Epitope hotspots and their relationship to evolutionary conservation as measured by the HLA targeting efficiency scores.

<p>Scores can range from −1 to 1. Positive scores indicate that epitopes tend to be in the more conserved regions of the targeted protein, while negative scores indicate targeting of the more variable sites along the insert. P-values were computed using the bootstrap procedure, and denote the significance of the correlation between epitope hotspot location and evolutionary conservation.</p

Epitope hotspots observed in each vaccine trial.

<p>The four dominant hotspots for each protein are presented. Restricting HLAs were imputed using HLA binding predictors.</p

HLA binding prediction algorithms can be used to identify vaccine-induced immunodominant hotspots.

<p>A comparison of the measured (black) vs. predicted (dashed) population-based epitope maps in HVTN 502/Step. Predictions were computed using the HLA alleles of trial participants and were weighted by HLA frequencies in this cohort. (a) Predicted vs. measured map for Gag. (b) Predicted vs. measured map for Nef. (c) Spearman correlation coefficients between measured and predicted epitope maps. Predicted maps were generated using three different IC50 thresholds on predicted binders: low (50 nM), intermediate (150 nM) and high (500 nM). Different thresholds yield higher correlations for different proteins: for all proteins but Pol, lower thresholds yield higher correlations, suggesting that the responses detected by the experimental assay are focused on the most immunogenic, high-affinity HLA binders. Since predicted population-based maps were obtained using predicted 9-mers, peaks in these maps are by definition more narrow than the experimentally measured maps in which 15 mers were used for epitope mapping.</p

Clinical datasets used in this study.

<p>Clinical datasets used in this study.</p

Post-Infection Magnitude of CD8+ T-Cell Response.

<p>Magnitude of the post-infection CD8+ T-cell response measured by ICS, as quantified by the percentage of CD8+ T-cells producing IFN or IL-2 when stimulated with the vaccine-insert-matched peptide pools (Gag, Pol, and Nef) and other non-vaccine-insert peptide pools, for vaccine and placebo groups. Positive responses are indicated using closed red circles and negative responses using open blue circles. The p-values refer to tests comparing response magnitudes between the vaccine and placebo positive responders.</p

Signature Sites in Relation to T-Cell Responses.

<p>Locations of the signature sites and pre- and post-infection T-cell responses for Gag, Nef, and Pol. For each protein, the top graph represents the location of post-infection IFNγ ELISpot responses detected in 19 vaccine and 11 placebo recipients (light and medium blue columns, respectively), signature K-mers (red horizontal bars), amino acid signature sites (dashed vertical lines), and sites where an insert-mismatch was found to be associated with viral load in the vaccine group alone (dotted vertical lines; Materials S1 Section 5). The bottom graph corresponds to pre-infection IFNγ ELISpot responses detected in 27 vaccine recipients (green columns). The region covered by each responsive peptide is indicated by the box width, and the number of subjects reacting to that peptide is indicated by the box height.</p

Post-Infection Breadth of T-Cell Response.

<p>Breath of the post-infection T-cell response as measured by IFNγ ELISpot, as quantified by the number of reactive 15-mers, for the vaccine (grey) and placebo (black) groups. The distribution of breadth is shown for all proteins in aggregate; for Gag, Pol, and Nef combined; for other non-insert proteins; and for Gag, Pol, and Nef individually. The p-values refer to tests comparing breadth between vaccine and placebo groups.</p

Some vaccine-induced hotspots target highly variable regions of HIV.

<p>Population epitope maps of HVTN 502/Step for Gag (a) and Nef (b) overlaid with conservation scores (red line). Conservation scores were scaled to the range of 0–1, where lower scores correspond to more variable sites. The four immunodominant hotspots are shaded in blue. (c) Boxplots comparing the conservation patterns of hotspots vs. non-targeted sites along each protein are presented. Targeted hotspots were defined as areas targeted by more than 15% of individuals in a trial vs. all other sites along the protein. P-values reported are based on the Wilcoxon rank sum test. Medians are represented by black lines, and the bottom and top of the box denotes the 25^th and 75^th percentiles, respectively. The whiskers extend to the most extreme data point, which is no more than 1.5 times the interquartile range from the box and outliers are marked by circles.</p

Acute Log₁₀ Viral Load.

<p>The distribution of acute log₁₀ viral load values in vaccine and placebo groups. Solid lines correspond to observed means and dashed lines correspond to means estimated using the multiple imputation approach.</p