MOESM1 of Lipid levels in HIV-positive men receiving anti-retroviral therapy are not associated with copy number variation of reverse cholesterol transport pathway genes

Additional file 1.  Supplementary Methods. File Format: PDF

Supplemental Material - Comparison of anal pre-cancer screening strategies among men who have sex with men

Supplemental Material for Comparison of anal pre-cancer screening strategies among men who have sex with men by Jing Sun, Dorothy Wiley, Benjamin W Barrett, Hilary Hsu, Frank J Palella, Jennafer Kwait, Jeremy Martinson and Gypsyamber D’Souza in International Journal of STD & AIDS</p

Distribution of the cases and controls haplotypes.

<p>Distribution of the cases and controls haplotypes.</p

Haploview APOBEC3G linkage disequilibrium plots for case and controls.

<p>The figures are oriented 5’ to 3’, right to left, relative to the gene orientation on the minus strand. Fig 1a represents the LD plot of the case pairwise D’ between markers, and Fig 1b shows the LD plot of the control pairwise D’ between markers. Strong LD is indicated by red, while pink indicate uninformative values. LD blocks were created with the default algorithm in the Haploview software (version 4.1) that creates 95% confidence bounds. D’ was considered strong where 95% of the comparisons made are informative.</p

LILRB2 binding strength and odds ratios for viral load control for individual <i>HLA-B</i> alleles.

<p>The data plotted includes only alleles with significant association (p<0.05) for white (A) and black (B) patients in a univariate analysis for each <i>HLA-B</i> allele. Spearman correlation coefficient and p values are indicated.</p

Spearman correlation between LILRB2 binding strength and mVL in HIV-1-infected individuals.

<p>Spearman correlation between LILRB2 binding strength and mVL in HIV-1-infected individuals.</p

Effect of LILRB2-HLA binding strength and individual class I alleles on viral control (controllers vs. non-controllers) in white patients.

<p>Logistic regression model with stepwise selection included all <i>HLA</i> class I alleles with phenotypic frequencies of >2% and one of the A, B, C or ABC binding scores at a time. The results are shown for the p<0.05 cut-off. The C binding score did not stay in the model. ORs for binding scores reflect a change of 0.1 units.</p>1<p>stayed in the model with the p<0.01 cut-off but not with the p<0.001 cut-off.</p>2<p>stayed in the model with the p<0.01 and p<0.001 cut-offs.</p

LILRB2-HLA binding score variations in 2900 white (A) and 1490 black (B) patients.

<p>A, B and C binding scores represent the sum of the binding scores for two alleles of the corresponding <i>HLA</i> class I locus. ABC binding score represents the sum of the locus-specific binding scores with the C scores counted at 1/10 level. Alleles with undefined scores were assigned the average of the scores for a given locus. Box and Whisker plots reflect median, the 25% and 75% percentiles and the minimum and maximum of all data.</p

Spearman correlation between LILRB2 binding strength and odds ratios of <i>HLA</i> alleles (p<0.05) for viral load control in HIV-1-infected individuals.

<p>Spearman correlation between LILRB2 binding strength and odds ratios of <i>HLA</i> alleles (p<0.05) for viral load control in HIV-1-infected individuals.</p

Impact of LILRB2-HLA interactions on functional properties of dendritic cells.

<p>(A) Fold changes in proliferative activities of allogeneic CD4⁺ T cells after exposure to MDDC treated with indicated HLA-A, -B or -C allotypes normalized to MDDC treated with negative beads (N. Bead), in the absence (white bars, n = 5, 8, 5 for HLA-A, -B, -C allotypes, respectively) or presence (gray bars, n = 5, 6, 5 for HLA-A, -B, -C allotypes, respectively) of siRNA-mediated downregulation of LILRB2 surface expression on MDDC. Significance was tested using one-way ANOVA followed by post-hoc analysis with the Tukey multiple comparison test, or using paired t-tests, as appropriate, (^▪p<0.05, ^Xp<0.01, *p<0.001). (B): Spearman correlation between proliferative activities of allogeneic CD4⁺ T cells after incubation with MDDC treated with indicated HLA-A, -B and -C allotypes and corresponding LILRB2-HLA binding scores. (C): Spearman correlation between the ratios of MDDC function in the presence or absence of siRNA-mediated LILRB2 downregulation, and corresponding LILRB2-HLA-A, -B, -C binding scores.</p