Genome Scan, Fine-Mapping, and Candidate Gene Analysis of Non-Syndromic Cleft Lip with or without Cleft Palate Reveals Phenotype-Specific Differences in Linkage and Association Results

Abstract

Objectives: Non-syndromic orofacial clefts, i.e. cleft lip (CL) and cleft palate (CP), are among the most common birth defects. The goal of this study was to identify genomic regions and genes for CL with or without CP (CL/P). Methods: We performed linkage analyses of a 10 cM genome scan in 820 multiplex CL/P families (6,565 individuals). Significant linkage results were followed by association analyses of 1,476 SNPs in candidate genes and regions, utilizing a weighted false discovery rate (wFDR) approach to control for multiple testing and incorporate the genome scan results. Results: Significant (multipoint HLOD ≥3.2) or genome-wide-significant (HLOD ≥4.02) linkage results were found for regions 1q32, 2p13, 3q27-28, 9q21, 12p11, 14q21-24 and 16q24. SNPs in IRF6 (1q32) and in or near FOXE1 (9q21) reached formal genome-wide wFDR-adjusted significance. Further, results were phenotype dependent in that the IRF6 region results were most significant for families in which affected individuals have CL alone, and the FOXE1 region results were most significant in families in which some or all of the affected individuals have CL with CP. Conclusions: These results highlight the importance of careful phenotypic delineation in large samples of families for genetic analyses of complex, heterogeneous traits such as CL/P.

The prevalence, penetrance, and expressivity of etiologicIRF6variants in orofacial clefts patients from sub‐Saharan Africa

“…Thus, our study and other studies (Marazita et al. 2009; Dixon et al. 2011) presuppose the need to carry out deep subclinical phenotyping in families with history of clefts.…”

The potential for next generation sequencing to characterise the genetic variation underlying nonsyndromic cleft lip and palate phenotypes

“…Murray 10 and Grosen et al 11 found heritability estimates exceeding 90% for CLP phenotypes. Genetic studies including linkage analysis 12,13 , genome-wide association, and GWASbased meta-analysis 14 , have yielded reproducible evidence for several genes and gene regions 8 . Results from Ludwig et al…”

“…But, although many of these signals have been replicated in independent samples, several of the linkage regions are broad and the underlying causal gene(s) are poorly established. Incomplete knowledge about gene function presents difficulties for selecting the most likely 12 have not replicated subsequently in independent samples 13 . Successful replication is difficult to achieve and it is perhaps too early to dismiss some of the more uncertain signals.…”

Genetic and epigenetic mechanisms in the aetiology of orofacial clefts

“…ARDINGER et al, 1989;MARAZITA et al, 2009;MORENO et al, 2009;VIEIRA et al, 2005). On the other hand, common variants conferring susceptibility to NSCL/P have been mostly identified by Genome-Wide Association Studies (GWAS) and the most replicated genomic region lies in a gene desert at 8q24.21, in which rs987525 emerges as the most significant SNP, including in the Brazilian population .…”