Differential expressions of 16 genes near 16 ear-associated loci in 50 cell types.

(A) Boxplots of normalized RNA-seq VST values for the 16 genes (in orange, details of genes shown in lower B plot) and 16 median gene expression value as control (randomly matched 1e-4 times using SNPsnap, in blue). Expression differences between the control genes and the 16 genes were tested in each cell type using the unpaired Wilcoxon rank-sum test. The expression of the 16 genes in CNCCs was also iteratively compared with that in all other cell types using paired Wilcoxon rank-sum test. Statistical significance was indicated: *P B) Normalized RNA-seq VST values in CNCCs were compared with those in other 49 types of cells (purple), in 20 tissue cell types (blue), in 20 primary cell types (green), and in nine embryonic stem cell types (orange), using one-sample Student’s t-test. Dotted line represents Bonferroni corrected significant threshold (P C) Partitioned heritability enrichments based on cell-type-specific regulatory annotations (More details see in Methods). Heritability enrichment Z-scores, as estimated by stratified linkage disequilibrium score regression (S-LDSC) of the C-GWAS summary data for GWASs of 136 ear traits. Trait abbreviations as in S10 Table.</p

In-vivo mouse models of <i>TBX15</i> deficiency.

Homozygous Tbx15-/- mutant mice (N = 9, 9 weeks), heterozygous Tbx15+/- (N = 18, 9 weeks) and C57BL/6 WT+/+ control mice (N = 10, 9 weeks) were compared for ear and body morphological differences. (A) The schematic diagram of the one-step CRISPR/Cas9 technology used in Tbx15 knockout mice. (B) Example of left profile craniofacial photo of Tbx15-/- mutant mice with removal hair. (C) The principal component analysis for 21 landmarks of Tbx15-/- mutant mice, heterozygous Tbx15+/- and WT+/+ mice. The upper layer shown the detailed contribution proportion of 21 landmarks to the first 10 principal components. The middle layer shown the screenplot of first 10 PCs, the significant association between the genotype and PCs which including PC1 and PC4 (* P P P Tbx15 knock-out on ear phenotypes in mice (blue for effect of heterozygote mutant and red for wildtype). (TIF)</p

16 ear-associated loci we identified in our current MinGWAS and C-GWAS.

The first 8 (A-H) were novel loci, others 8 were previously reported loci (I-P). Each figure includes three figures, LocusZoom (up) shows regional association plots for the top-associated ear phenotype (p values in CGWAS, except for the 6q21 PRDM1/ATG5, which solely identified by meta-analysis) with candidate genes aligned below according to the chromosomal positions (GRCh37.p13) followed by the linkage disequilibrium (LD) patterns (r2) of European. Ear map (left lower) shows the association (p values in Meta-analysis) between all ear phenotypes (P (DOCX)</p

Study design.

(A) The location of selected 17 ear landmarks. (B) Design of the current study. (TIF)</p

Effects of sex (left) and age (right) on 136 ear phenotypes in RS.

Please note the different figure legends in these two figures. (TIF)</p

The effects of age and sex on 136 ear phenotypes in the RS cohort.

The effects of age and sex on 136 ear phenotypes in the RS cohort.</p

Enhancer regions estimated based on the H3K27ac and ATAC-seq using ROSE.

Enhancer regions estimated based on the H3K27ac and ATAC-seq using ROSE.</p

Two distinct clusters of 136 ear phenotypes derived from unsupervised hierarchical clustering.

(A) Two clusters for 136 phenotypes. (B) Phenotypic (right up) and genetic correlation matrix (left down) within and between the cluster. (TIF)</p

Characteristics of 136 ear phenotypes in 5 cohorts.

Characteristics of 136 ear phenotypes in 5 cohorts.</p

Definition of 21 ear landmarks in mice.

Human ear morphology, a complex anatomical structure represented by a multidimensional set of correlated and heritable phenotypes, has a poorly understood genetic architecture. In this study, we quantitatively assessed 136 ear morphology traits using deep learning analysis of digital face images in 14,921 individuals from five different cohorts in Europe, Asia, and Latin America. Through GWAS meta-analysis and C-GWASs, a recently introduced method to effectively combine GWASs of many traits, we identified 16 genetic loci involved in various ear phenotypes, eight of which have not been previously associated with human ear features. Our findings suggest that ear morphology shares genetic determinants with other surface ectoderm-derived traits such as facial variation, mono eyebrow, and male pattern baldness. Our results enhance the genetic understanding of human ear morphology and shed light on the shared genetic contributors of different surface ectoderm-derived phenotypes. Additionally, gene editing experiments in mice have demonstrated that knocking out the newly ear-associated gene (Intu) and a previously ear-associated gene (Tbx15) causes deviating mouse ear morphology.</div