Quantile-Quantile Plot (Q-Q Plot) of P-values distribution from the GWAS on HIV-1 specific cross-reactive neutralizing activity.

<p>The comparison of the distribution of observed Chi-Square values against the theoretical model distribution of expected Chi-Square values is shown.</p

Heatmap and clustering analysis of HIV-1 specific cross-reactive neutralizing activity in serum.

<p>IC₅₀ values of sera from 292 HIV-1 infected individuals at ∼35 months post (imputed) seroconversion (rows) against 6 viral isolates (columns) are shown. Darker colors represent more potent neutralization. Kmeans clustering was performed on the rows and the columns and the rows/columns that fall in the same cluster are represented by the same colors on the row/column side bar. Patients with cross-reactive neutralizing activity (CrNA) cluster together in the upper heatmap and patients with no CrNA cluster in the bottom of the heatmap.</p

P-values for top ranking associations of SNPs with HIV-1-specific cross-reactive neutralizing activity, as well as P-values after correction for viral load and CD4⁺ T-cell count at set-point as covariates.

<p>Chr; chromosome.</p

Genome overview of P-values for associations of SNPs with HIV-1-specific cross-reactive neutralizing activity.

<p>Genome overview (A) and Major Histocompatibility Complex region (B).</p

P-values for different endpoints in survival analysis and viral load at set-point of top ranking SNPs associated in GWA study with HIV-1-specific cross-reactive neutralizing activity.

<p>P-values for different endpoints in survival analysis and viral load at set-point of top ranking SNPs associated in GWA study with HIV-1-specific cross-reactive neutralizing activity.</p

Survival Analysis for the −2G/C Genotype in Combination with the 136Q Genotype

<p>Kaplan Meier analysis for time in years from seroconversion to AIDS according to the CDC 1993 definition. Bold black lines indicate individuals with the −2GG genotype; dashed black lines indicate individuals with the −2GC genotype; thin black lines indicate individuals with the −2CC genotype.</p

Survival Analysis for the H43Y Genotype

<p>Kaplan Meier analysis for time in years from seroconversion to AIDS according to the CDC 1987 definition (A), to AIDS according to the CDC 1993 definition (B), to CD4 count below 200 cells/μl blood (C), to viral RNA load above 10^4.5 copies per ml plasma (D), and to first detection of X4-variants (E) based on the H43Y genotype. Bold lines indicate individuals with the wild type genotype (43HH); dashed black lines indicate individuals heterozygous for the 43Y genotype (43HY); thin black lines indicate individuals homozygous for the 43Y genotype (43YY).</p

Analysis of Trim5α mRNA Levels in Naïve and Memory CD4 T Cells

<div><p>(A) Trim5α mRNA levels in naïve CD4 T cells (CD45RO-CD27+) and memory CD4 T cells (CD45RO+) obtained from healthy controls.</p><p>(B) Average Trim5α mRNA levels in naïve and memory CD4 T cells during the course of infection from HIV-1 infected individuals. Trim5α mRNA levels are normalized for β-actin mRNA levels. Different symbols represent Trim5α mRNA levels of naïve and memory CD4 T cells from the different individuals.</p></div

Genotype distribution among HAD (cases) and non-HAD (controls) HIV-1-infected patients for all polymorphisms tested.

1<p>Polymorphisms selected from earlier studies that tested for association between genotype and HAD.</p>2<p>In the case of <i>APOE</i> AA, AB and BB refer to no APO E4, one APO E4 allele and two APO E4 alleles, respectively.</p>3<p>SNPs selected from a previous study that found associations between these SNPs and HIV-1 replication in macrophages.</p><p>*Significant difference after correction for multiple testing (n = 12); Bonferroni threshold <i>p</i> = 4.2×10⁻³.</p

Characteristics of the studied population consisting of AIDS patients with or without HAD.

<p>N.A., not applicable; HAD, HIV-1-associated dementia; IDU, injecting drug user.</p>1<p>Mann Whitney test.</p>2<p>Time to develop HAD after AIDS diagnosis among the cases was compared to the time from AIDS diagnosis to death or to start cART in the control group.</p>3<p>unpaired t test.</p>4<p>CD4+ T cell counts within 6 months to the date of AIDS diagnosis.</p>5<p>Fisher's exact test.</p