Additional file 1: of Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma

Supplementary tables. Table S1. Cancer genes in detected amplification regions. Table S2. Cancer genes in detected deletion regions. Table S3. Comparison of results of Frankel to our results. Table S4. Comparison of results of Paulson to our results. Table S5. Comparison of results of Beroukhim to our results. Table S6. Comparison of results of Zack to our results. Table S7. Ploidy information of the 15 EA samples. (XLSX 57.4 kb

Modeling of IFN-γ producing cytotoxic CD8+ T cells (CD8+ IFN-γ+ T cells) as a function of IL-2 producing CD4+ helper T cells (CD4+ IL-2+ T cells) and time (model 1 and model 2) in the rAd5-rAd5 group, HVTN 068 trial.

<p>Modeling of IFN-γ producing cytotoxic CD8+ T cells (CD8+ IFN-γ+ T cells) as a function of IL-2 producing CD4+ helper T cells (CD4+ IL-2+ T cells) and time (model 1 and model 2) in the rAd5-rAd5 group, HVTN 068 trial.</p

Kinetics of IL-2 producing CD4+ helper T cells (CD4+ IL-2+ T cells) and IFN-γ producing cytotoxic CD8+ T (CD8+ IFN-γ+ T cells) responses over time after Env ex-vivo stimulation of PBMC in the rAd5-rAd5 and DNA-rAd5 groups respectively, HVTN 068 trial.

<p>(A) CD4+ IL-2+ T cells responses in the rAd5-rAd5 group. (B) CD8+ IFN-γ+ T cells responses in the rAd5-rAd5 group. (C) CD4+ IL-2+ T cells responses in the DNA-rAd5 group. (D) CD8+ IFN-γ+ T cells responses in the DNA-rAd5 group.</p

The neutralization of nine HIV-1 pseudoviruses by mAb 2191 using U87 as target cells.

<p>The neutralization curves of anti-V3 mAb 2191 against nine selected HIV-1 pseudoviruses are shown with their corresponding AUC and IC₅₀ values. Fifty percent neutralization is denoted by the dashed line. Significant neutralization at the confidence level of p<0.001 (denoted with * after AUC values) was determined statistically based on comparison with the AUC values of the negative controls together with the slopes of the titration curves as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010254#s2" target="_blank">Materials and Methods</a>. For viruses coming from patients where the date of infection is known, viruses are denoted as coming from acutely- or chronically-infected patients, and the clade of the virus is denoted by the capital letter in its name (A, B, C or D).</p

Neutralization curves of anti-V3 mAbs against representative HIV-1 psVs tested using the TZM.bl target cell line.

<p>Seven anti-V3 mAbs were tested against HIV-1 psVs in the TZM.bl experiment. The titration curves observed against nine selected viruses are shown. The background neutralization observed with the irrelevant control mAb 860 is also shown for comparison. Curve fitting was performed using the polynomial regression (quadratic) model described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010254#s2" target="_blank">Materials and Methods</a>. Fifty percent neutralization is denoted by the dashed line.</p

HVTN 068 trial design with repeated immunogenicity measurements–cellular and antibody responses—during the 52 weeks of follow-up.

<p>HVTN 068 trial design with repeated immunogenicity measurements–cellular and antibody responses—during the 52 weeks of follow-up.</p

The IC₅₀ values of anti-V3 mAbs against 57 HIV-1 pseudoviruses tested using the U87 target cell line.

<p>The IC₅₀ values were estimated from the titration curves of all mAb/psV combinations and are highlighted according to the color-coded scale. Pseudoviruses expressing Envs of JRCSF, NL3.4, and SF162 were tested as positive controls, whereas the irrelevant anti-parvovirus mAb 860 and aMLV Env-expressing psV were used as negative controls. When 50% neutralization was not achieved at the highest mAb concentration tested (50 µg/ml), the IC₅₀ values are shown as >50.</p

Characteristics of human mAbs used for this study.

<p>nd – not determined.</p><p>PA – protective antigen of anthrax.</p><p>§– Gorny et al., unpublished data.</p

Neutralization curves of anti-V3 mAbs against representative HIV-1 psVs tested using the U87 target cell.

<p>Seven anti-V3 mAbs (2191, 2219, 2557, 2558, 3074, 3869, and 447) were tested for neutralization against HIV-1 pseudoviruses using the U87 cell line as target cells. MAb 860, specific for parvovirus, and a pseudovirus expressing the aMLV Env were used as negative controls in this assay. The titration curves from eight selected psVs and the aMLV psV control are shown. Curve fitting was performed using the polynomial regression (quadratic) model described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010254#s2" target="_blank">Materials and Methods</a>. Fifty percent neutralization is denoted by the dashed line. Virus nomenclature is denoted as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010254#pone-0010254-g001" target="_blank">Figure 1</a>.</p

The AUC values of anti-V3 mAbs against 41 HIV-1 pseudoviruses tested using the TZM.bl target cell line.

<p>The AUC values were calculated from the titration curves as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010254#s2" target="_blank">Materials and Methods</a> section. All mAb/psV pairs with statistically significant neutralization at p<0.001 are color-coded according to the designated scale. The irrelevant anti-parvovirus mAb 1418 was used together with three other control mAbs (data not shown) as negative controls.</p