Characterization of the nasopharyngeal microbiome in health and during rhinovirus challenge

<p>Additional files for the manuscript entitiled "Characterization of the nasopharyngeal microbiome in health and during rhinovirus challenge."</p

Top SNPs from the Raine cohort GWAS that were genotyped in our GWAS of COME/ROM.

<p>We report our OR and allele frequency using the Risk Allele corresponding to the Risk Allele listed in the Raine cohort GWAS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104212#pone.0104212-Rye1" target="_blank">[9]</a>.</p><p>*Indicates SNP is intergenic and therefore reports the nearest gene.</p>∧<p>Indicates the SNP was a top genotyped SNP from a subset of Raine study participants with full covariate data.</p

Power was computed using TDT Power Calculator [15] varying SNP minor allele frequency (MAF) and genetic relative risk (GRR).

<p>Power was computed using TDT Power Calculator <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104212#pone.0104212-Chen1" target="_blank">[15]</a> varying SNP minor allele frequency (MAF) and genetic relative risk (GRR).</p

Illustration of model-based clustering results from ADMIXTURE, based on 1,374 unrelated individuals of self-reported Hispanic origin from the Multi-Ethnic Study of Atherosclerosis (MESA), shown for K = 3, 4, and 5.

<p>Results are displayed only for individuals from MESA whose self-reported country/region of origin was reported unambiguously as Central America, Cuba, Dominican Republic, Mexico, Puerto Rico, or South America.</p

Proportion of ancestry estimates averaged within each Hispanic country/region of origin, from model-based clustering analysis of 1,374 unrelated MESA individuals in ADMIXTURE with K = 3, 4, and 5.

<p>Inferred ancestral populations from ADMIXTURE analysis are labeled based on putative assignments (<i>e.g.</i> Caucasian, African or Native American), as interpreted by the authors.</p

Summary of regional association for SNPs in the <i>TRIB1</i> gene region with triglycerides (modeled on a log scale).

<p>(A) Strength of association versus SNP position on chromosome 8 based on pooled analysis of MESA Hispanic individuals; (B) Forest plot of effects (with 95% CIs) reported in subsets of the MESA Hispanic cohort, using subgroups obtained from PCA-based cluster-analysis; and Strength of association versus SNP position on chromosome 8 based on stratified analysis of inferred clusters corresponding to (C) Central/South America, (D) the Dominican Republic and Cuba, (E) Mexico, and (F) Puerto Rico. In plots (A) and (C–F), genotyped SNPs are indicated as solid black dots, imputed SNPs as solid gray dots, the genotyped SNP rs4351435 as an open black diamond, and horizontal dashed gray lines indicate a conservative Bonferroni-threshold for statistical significance based on multiple testing of 45 SNPs.</p

Summary of regional association for SNPs in the <i>LPL</i> gene region with triglycerides (modeled on a log scale).

<p>(A) Strength of association versus SNP position on chromosome 8 based on pooled analysis of MESA Hispanic individuals; (B) Forest plot of effects (with 95% CIs) reported in subsets of the MESA Hispanic cohort, using subgroups obtained from PCA-based cluster-analysis; and Strength of association versus SNP position on chromosome 8 based on stratified analysis of inferred clusters corresponding to (C) Central/South America, (D) the Dominican Republic and Cuba, (E) Mexico, and (F) Puerto Rico. In plots (A) and (C–F), genotyped SNPs are indicated as solid black dots, imputed SNPs as solid gray dots, the imputed SNP rs328 as an open gray diamond, and horizontal dashed gray lines indicate a conservative Bonferroni-threshold for statistical significance based on multiple testing of 33 SNPs.</p

Principal component analysis of 1,374 unrelated individuals of self-reported Hispanic origin from the Multi-Ethnic Study of Atherosclerosis (MESA), displayed by country/region of origin, with projection to key reference populations.

<p>Individuals are labeled according to group inclusion: MESAHispNOS="MESA Hispanic, Other or Unspecified country/region of origin”, other labels are self-explanatory.</p

Variance and effect size explained by risk score.

<p>RS#-SNP annotation, dbSNP build 137. Chr-Chromosome. Position from dbSNP build 137. V.E.-Variance explained.</p><p>* = Average ΔPOST increase per risk variant added.</p

Haplotype analysis of Chr6 SNPs significantly-associated with ΔPOST in the VISP cohort.

<p>Haplotype analyses of the 10 most-associated SNPs, which are all genome wide significant, from chromosome 6, were performed using Haploview version 4.2 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004214#pgen.1004214-Barrett1" target="_blank">[13]</a>. (A) Shows results for the chromosome 6 genomic haplotype structure in VISP, encompassing the <i>GNMT</i> gene. Genetic coordinates, Entrez gene structure, haplotype blocks and linkage disequilibrium (LD) pattern between SNPs are shown. Within LD pattern, r² values are shown and are represented by shading. The darker the shading the closer the r² value is to 1.0. All SNPs assessed were genotyped. (B) Shows haplotypes generated by Haploview for haplotype blocks 1 and 2. Haplotype block 2 is characterized by two major haplotypes, which account for 80% of haplotypes observed. (C) Shows the mean ΔPOST values in the VISP sample for each of the 2 major haplotype block 2 haplotypes. (_*) p≤0.001 by student's T-test; error bars represent standard deviation from the mean (SD).</p