Fig. 1

scDRS identifies significant association with nsCL/P candidate genes in epithelium and HAND2+ pharyngeal arches (a) UMAP plot of scRNA-seq data from the heads of five unaffected human embryos from Carnegie stages 12–16. (b) UMAP plot from a colored according to the normalized scDRS for nsCL/P association at the single-cell level in the unweighted setting. (c) Ridgeplot of normalized scDRS according to cell type in the unweighted setting. (d) scDRS disease association at the cell type level in the unweighted setting. Cell types above the dashed line showed significant association with the nsCL/P gene set. Bold cell type labels indicate significant within-cell type heterogeneity in terms of disease association. Anterior presomitic mesoderm (aPSM), frontonasal mesenchyme (FM), log₂ fold change (log₂FC), pharyngeal arches (PA), posterior presomitic mesoderm (pPSM), sympathetic neurons (SN), single-cell disease relevance score (scDRS).