Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2

Abstract

A combined genome-wide association and linkage study was used to identify loci causing variation in cystic fibrosis lung disease severity. We identified a significant association (P = 3.34 × 10(-8)) near EHF and APIP (chr11p13) in p.Phe508del homozygotes (n = 1,978). The association replicated in p.Phe508del homozygotes (P = 0.006) from a separate family based study (n = 557), with P = 1.49 × 10(-9) for the three-study joint meta-analysis. Linkage analysis of 486 sibling pairs from the family based study identified a significant quantitative trait locus on chromosome 20q13.2 (log(10) odds = 5.03). Our findings provide insight into the causes of variation in lung disease severity in cystic fibrosis and suggest new therapeutic targets for this life-limiting disorder.

Figure 1

Histograms of the Consortium lung phenotype for the three cystic fibrosis studies show similar average phenotypes. The phenotype mean is above zero due to a lower bound placed by the survival correction, as well as cohort effects of improving lung function. (a) The two designs using unrelated individuals. All of the patients in the Genetic Modifier Study (GMS) are F508del/F508del at CFTR. These patients were oversampled at extremes of an initial entry phenotype, in order to improve power, and the original severe/mild designations are colored separately. In contrast, the Canadian Consortium for Genetic Studies (CGS) is population based, representing a range of pancreatic insufficient CFTR genotypes. (b) Patients enrolled in the family-based Twin and Sibling Study (TSS) show a similar distribution of the Consortium lung phenotype as the population-based CGS.

Figure 2

Genome-wide Manhattan plots for the cystic fibrosis Consortium lung function phenotype, combining the association evidence from GMS and CGS samples across 570,725 SNPs. The black dashed line represents the Bonferroni threshold for genome-wide α=0.05, while the green dashed line is the suggestive association threshold, expected once per genome scan. SNPs are plotted in Mb relative to their position on each chromosome (alternating blue and black) (a) Results from GMS (n=1137, all of whom are F508del/F508del) combined with all of the CGS patients (n=1357). Seven regions reach suggestive significance. (b) Results from the combined evidence of GMS (n=1137) and the CGS F508del/F508del (n=841). A region on chromosome 11p13 reaches genome-wide significance (P=3.34 × 10^-8).

Figure 3

A plot of the association evidence in GMS and CGS F508del/F508del in the chromosome 11p13 EHF/APIP region (NCBI build 36, LocusZoom viewer). Colors represent HapMap CEU linkage disequilibrium r² with the most significant SNP, rs12793173 (P=3.34 × 10^-8). The secondary peak at rs286873 has relatively low r² with the primary peak.

Figure 4

Genome-wide linkage scan for the Consortium lung phenotype of 486 sibling pairs in the family-based TSS, adjusted for sex. A QTL with a genome-wide significant LOD=5.03 was found on 20q13.2. LOD scores with SNPs used in the linkage panel are plotted in cM relative to their position on each chromosome (alternating blue and black).

Figure 5

Regional analysis of the QTL on chromosome 20q13.2 (a) A detailed chromosome 20 linkage plot for the Consortium lung phenotype in the TSS study, with covariates sex (essentially the same result as for no covariates) and with covariates sex and BMI. (b) Association evidence from the GMS and CGS F508del/F508del patients, in the 1-LOD support interval provided by TSS. A region centromeric to CBLN4 and MC3R on 20q13.2 shows suggestive evidence of association, with the greatest evidence at rs6024460 (P=1.34 × 10^-4).