Abstract / Description
Nonsyndromic cleft lip (nsCL) exhibits a non-random laterality pattern, with left-sided clefts occurring twice as frequently as right-sided clefts. The molecular mechanisms underlying this laterality bias remain poorly understood. We performed whole-genome sequencing and methylation profiling on a family comprising monozygotic twins with mirror-image nsCL, their affected mother, and unaffected father and brother. We conducted three independent replications via publicly available whole genome data; genome-wide methylation analysis in 38 individuals with unilateral cleft; and validation of methylation results in the top 3 candidate genes in 385 unrelated individuals with unilateral nonsyndromic cleft lip with or without cleft palate (nsCL/P) (DNA from blood or saliva). We identified a variant in FGF20 (p.Ile79Val) shared by the twins and their mother. We observed laterality and severity-associated methylation differences in three main genes. ARID5B showed higher methylation in left clefts (saliva, P = .001; blood, P = .032). ZFP57 demonstrated a strong cleft-extent effect, with cleft lip and palate (CLP) showing markedly higher methylation than cleft lip only (CL) (LCLP vs. RCL padj = 0.0004; LCLP vs. LCL padj = 0.019). HOOK2 displayed a cross-tissue cleft-extent effect in the opposite direction-CLP subtypes were hypomethylated relative to CL-only subtypes in blood (P