Nonsyndromic orofacial clefts are a common complex birth defect caused by genetic and environmental factors and/or their interactions. A previous genome-wide linkage scan discovered a novel locus for cleft lip with or without cleft palate (CL/P) at 9q22-q33. To identify the etiologic gene, we undertook an iterative and complementary fine mapping strategy using family-based CL/P samples from Colombia, USA and the Philippines. Candidate genes within 9q22-q33 were sequenced, revealing 32 new variants. Concurrently, 397 SNPs spanning the 9q22-q33 2-LOD-unit interval were tested for association. Significant SNP and haplotype association signals (P = 1.45E - 08) narrowed the interval to a 200 kb region containing: FOXE1, C9ORF156 and HEMGN. Association results were replicated in CL/P families of European descent and when all populations were combined the two most associated SNPs, rs3758249 (P = 5.01E - 13) and rs4460498 (P = 6.51E - 12), were located inside a 70 kb high linkage disequilibrium block containing FOXE1. Association signals for Caucasians and Asians clustered 5' and 3' of FOXE1, respectively. Isolated cleft palate (CP) was also associated, indicating that FOXE1 plays a role in two phenotypes thought to be genetically distinct. Foxe1 expression was found in the epithelium undergoing fusion between the medial nasal and maxillary processes. Mutation screens of FOXE1 identified two family-specific missense mutations at highly conserved amino acids. These data indicate that FOXE1 is a major gene for CL/P and provides new insights for improved counseling and genetic interaction studies.

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Surgical transfer of embryos is carried out daily in animal facilities worldwide for the rederivation of mouse strains/lines, among other purposes. Current protocols described in laboratory manuals recommend using a high number of embryos during transfer, typically in the range of 15 up to 25. To optimize the use of resources it is necessary to estimate and relate the effort required and the yield obtained. Here, we analyse the balance between the number of embryos transferred (the effort), and the yield as the number of born pups obtained from surgical embryo transfer. To accomplish this, we have analyzed data obtained during rederivation of nearly one hundred lines of mice to a new animal facility. Our results confirm that the use of increasing numbers of embryos per transfer increases the yields of born pups, as has been described previously in the literature, but they also highlight the disproportionate effort required, i.e. in the number of embryos that needed to be transferred. An estimate of the mean expected yields of surgical transfers and their comparison with the actual observed yields indicated that the balance between effort and yield is optimized when using lower numbers of embryos than in currently used protocols, in the range of 8 to 12. Given the heterogeneous nature of the data presented and analyzed here, which is from a population of mice that may be considered as representative of any animal facility, our optimization approach should help save resources in similar facilities and improve the yields of embryo transfer procedures.