Figure 6: Association analysis for CNV covering Alad and Hdhd3. | Nature Communications

Figure 6: Association analysis for CNV covering Alad and Hdhd3.

From: Joint mouse–human phenome-wide association to test gene function and disease risk

Figure 6

(a) The CNV region for Alad and Hdhd3 derived using read-depth information from genome sequencing. Red dots represent at least a two-fold increase in coverage compared with the reference genome. The x-axis shows the reference genomic position of the CNV. Two gene models (that is, Hdhd3 and Alad) are shown in the CNV plot. (b,c) Rank ordered mean expression levels of Hdhd3 and Alad across 67 BXD strains, their parental strains, and F1 crosses. Expression values are normalized on a log2 scale (mean±s.e.m.). Strains with D alleles (red) have higher levels of Alad and Hdhd3 compared with B alleles (green). F1 hybrids (blue) are intermediate. The comparison between B and D alleles for Alad and Hdhd3 are shown in an inset boxplot. (d) The phenome scan of the BXD cohort highlights several interesting potential phenotypes including pain response (thermal nociception), brain deoxycorticosterone levels, and antigenic activity in the spleen. Two triangles represent pigmentation traits that we know are associated with a variant in the linkage disequilibrium block. (e) Manhattan plot obtained after phenome scan of the BioVU EHR data showing the association in humans between a SNP (rs1800435) in ALAD and chronic pain syndrome and several other classic phenotypes.

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