The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes.

paper Cited Public

Authors: Cusanovich, Darren A; Billstrand, Christine; Zhou, Xiang; Chavarria, Claudia; De Leon, Sherryl; Michelini, Katelyn; Pai, Athma A; Ober, Carole; Gilad, Yoav
Year: 2012
Journal: Human molecular genetics
PMID: 22286170
DOI: 10.1093/hmg/dds021
PMCID: PMC3315207

Figure 1.

Study design. We performed a gene expression profiling study (1a) to identify differentially expressed genes between individuals with low and high lymphocyte counts, as well as a GWAS (1b) to identify loci associated with lymphocyte counts. We integrated data from the two studies (2) to identify candidate genes that would have been missed by the GWAS alone. Ultimately, we asked whether these candidate genes are also associated with asthma (3).

Figure 2.

GWAS for lymphocyte count. (A) Manhattan plot displaying the −log10 (P-values) for a GWAS of lymphocyte counts in 462 Hutterites. The top two SNPs are circled. (B) Close-up of the region around the top SNP, rs2746347 (red point), which is located within the first intron of PRKAA2. The estimated recombination rate (based on HapMap data) in the region is also plotted. (C) Close-up of the region around the second most significant SNP, rs881827 (red point), located within an intron of S100B.

Figure 3.

Choice of samples for the gene expression profiling study. A histogram of the distribution of lymphocyte counts (x-axis; the transformed residuals after correcting for age) for all available samples (gray bars) and for the 96 individuals chosen for the gene expression profiling study (red bars).

Figure 4.

Integrating the GWAS and gene expression profiling studies. (A) The median lymphocyte count GWAS P-value (y-axis) for an expanding window of genes is plotted in red. Genes are ordered by the strength of evidence supporting differences in expression level between individuals with low and high lymphocyte counts. The blue curves indicate the confidence interval for median P-values for random sets of genes at each test set size (based on 10 000 permutations). (B) A box plot of the distribution of median lymphocyte count GWAS P-values for random sets of 193 genes (based on 10 000 permutations). The whiskers extend to the 5th and 95th percentile. Black points indicate the observed medians outside this range. The red ‘X’ indicates the median P-value observed for the top 193 differentially expressed genes.

Figure 5.

Integrating results with asthma meta-analyses. Box plots of the distribution of median GABRIEL meta-analysis P-values and median EVE meta-analysis P-value for random sets of 117 genes (based on 10 000 permutations). The whiskers extend to the 5th and 95th percentiles. Black points indicate the observed medians outside this range. For each box plot, the red ‘X’ indicates the median P-value observed for the 117 genes carried forward based on the analysis of association with lymphocyte counts.

#	Section	Preview
60	SUPPLEMENTARY MATERIAL	Supplementary Material is available at HMG online.
61	FUNDING	This work was supported by the National Institutes of Health (HL092206 to Y.G., HL085197 and…

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