Association of <i>CAV2</i> and <i>TMC6</i> variants with lung function.

<p>Each small dot in each panel represents one CF-specific FEV1 percentile value in the data set (percentiles are age- and sex-adjusted); and each individual has an average of 3.5 percentile values per year in the data set. (<b>A</b>) Mean CF-specific FEV1 percentile by age for 289 EPIC validation individuals with (red) and 283 without at least one CAV2 rs8940 derived allele (blue). FEV1 was an average of 5.5 percentile points higher among individuals with the rs8940 derived allele (p = 0.001). (<b>B</b>) Mean CF-specific FEV1 percentile by age for 59 EPIC validation individuals with (red) and 513 without at least one TMC6 rs34712518 derived allele (blue). FEV1 was an average of 8.0 percentile points lower among individuals with the rs34712518 derived allele (p = 0.01). The apparent age interaction in the diagram (growing distance between lines) was not significant here, though power is limited by the lower numbers of observations at older ages.</p

Primary results for <i>TMC6</i> from exome discovery and validation phases and its interaction with <i>CAV2</i>.

<p>(<b>A</b>) QQ-plot of p-values from the discovery analysis of exomes from 65 CF individuals with late onset chronic <i>P</i>. <i>aeruginosa</i> infection versus exomes from 3275 non-lung disease European American population control exomes. P-values are from the SKAT-O test with the small sample adjustment applied to non-synonymous variants grouped by gene to discover genes with differing distributions of these variants between groups. The most significant gene (highest point) is <i>CFTR</i> (p<1x10^-16), followed by <i>TMC6</i> (p = 9.5x10^-7). (<b>B</b>) Kaplan Meier curves for age-of-onset of chronic <i>P</i>. <i>aeruginosa</i> in individuals in validation cohort with cystic fibrosis with at least one <i>TMC6</i> rs3412518 derived allele versus those with ancestral alleles. Individuals with at least one <i>TMC6</i> rs3412518 derived allele had a higher risk for early onset chronic <i>P</i>. <i>aeruginosa</i> and this risk increased significantly over time (p = 0.01 for age interaction; HR = 5.2 at age 10, p = 0.00046, 95% CI = [2.1–43.0]). (<b>C</b>) Kaplan Meier curves for age-of-onset of chronic <i>P</i>. <i>aeruginosa</i> in individuals in validation cohort with cystic fibrosis showing <i>TMC6</i> risk groups among individuals <i>without</i> the <i>CAV2</i> rs8940 protective (derived) allele. Individuals with at least one <i>TMC6</i> rs34712518 derived allele had higher risk for early onset and this risk increased significantly over time (HR = 12.1 at age 10, p = 2.6x10^-5, 95% CI = [3.8–38.8]). (<b>D</b>) Kaplan Meier curves for age-of-onset of chronic <i>P</i>. <i>aeruginosa</i> in individuals in validation cohort with cystic fibrosis showing <i>TMC6</i> risk groups among individuals with the <i>CAV2</i> rs8940 protective (derived) allele. There was no significant difference in risk between individuals with and without <i>TMC6</i> rs34712518 among these children with the <i>CAV2</i> protective allele (HR = 2.1, p = 0.41, 95% CI = [0.38–11.3]).</p

Genetic architecture of age-of-onset of chronic <i>P</i>. <i>aeruginosa</i> infection and TMC6 rs34712518.

<p>(<b>A</b>) Observed age of onset for children with at least one rs34712518 allele (blue) and without (red), compared to Weibull distribution models for age of onset among children with at least one rs34712518 allele (light blue) and without (green). (<b>B</b>) Blue: The probability of carrying at least one rs34712518 allele given age of onset is beyond age X (i.e. one does not have chronic <i>P</i>. <i>aeruginosa</i> infection by age X) based on the event probabilities for each carrier state shown in (A). The probability of being a carrier declines markedly between ages 6 and 25 among “survivors;” the more extreme (later) ages of onset have a growing difference in proportion of carriers compared to the general population (dotted red line), conferring greater power when included in the sample. Power provided by a single extreme vs. control design can be calculated from this plot, given the ages of the individuals in the single extreme.</p

Primary results for <i>CAV2</i> from exome discovery and validation phases.

<p>(A) QQ-plot of p-values from the discovery analysis of exomes from 85 CF individuals with early onset chronic <i>P</i>. <i>aeruginosa</i> infection versus exomes from 3329 non-lung disease European American population controls. P-values are from the SKAT-O test with the small sample adjustment applied to non-synonymous variants grouped by gene to discover genes with differing distributions of these variants between groups. The most significant gene (highest point) is <i>CFTR</i> (p<1x10^-16), followed by CAV2 (p = 1.1x10^-6). 1(B) Kaplan Meier curves for age-of-onset of chronic <i>P</i>. <i>aeruginosa</i> infection among individuals in the validation cohort with (blue) and without (red) the <i>CAV2</i> rs8940 derived allele. Individuals in with at least one rs8940 variant had significantly later age-of-onset (HR = 0.53, p = 0.01, 95% CI = [0.32–0.88]).</p

Power to discover <i>TMC6</i> with aSKAT-O for a test of size α under the actual ages of the individuals in the extreme samples in this study.

<p>(<b>A</b>) Power to detect a difference between groups at <i>TMC6 rs34712518</i> for three study designs based on the allele distributions for actual ages of individuals in the extremes in this study: extreme phenotypes (i.e. extreme versus extreme; black); the single extreme versus population control study reported here (blue); hypothetical single extreme versus control study if all exome resources had been devoted to the late onset extreme, which provides near 99% power to detect this variant (red). (<b>B</b>) Power to detect a difference between groups for <i>TMC6</i> by-gene assuming the observed allele frequencies in the validation set (for CF individuals) and in ESP controls. Study designs are the same as in (A). The power of the single extreme versus control design to detect <i>TMC6</i> at the exome-wide significance level of 2x10^-6 is approximately 20% (blue), which is an order of magnitude higher than that of the extreme phenotypes design (black), while devoting all exomes to one extreme would provide nearly 80% power (red).</p

Identification of four independent LD blocks in the 8p23.1 region <i>(~3</i>.<i>3 MBs</i>).

<p>Identification of four independent LD blocks in the 8p23.1 region <i>(~3</i>.<i>3 MBs</i>).</p

Novel SNVs/Genes associated with BP traits in Multi-ancestry meta-analysis in combined Stage 1 and Stage 2.

<p>Novel SNVs/Genes associated with BP traits in Multi-ancestry meta-analysis in combined Stage 1 and Stage 2.</p

Novel SNVs/Genes associated with BP traits in European ancestry.

<p>Novel SNVs/Genes associated with BP traits in European ancestry.</p

Potential novel SNVs/Genes associated with BP traits in African ancestry.

<p>Potential novel SNVs/Genes associated with BP traits in African ancestry.</p

Novel SNVs/Genes associated with BP traits in European ancestry.

<p>Novel SNVs/Genes associated with BP traits in European ancestry.</p