Medical Sequencing of Candidate Genes for Nonsyndromic Cleft Lip and Palate

Abstract

Nonsyndromic or isolated cleft lip with or without cleft palate (CL/P) occurs in wide geographic distribution with an average birth prevalence of 1/700. We used direct sequencing as an approach to study candidate genes for CL/P. We report here the results of sequencing on 20 candidate genes for clefts in 184 cases with CL/P selected with an emphasis on severity and positive family history. Genes were selected based on expression patterns, animal models, and/or role in known human clefting syndromes. For seven genes with identified coding mutations that are potentially etiologic, we performed linkage disequilibrium studies as well in 501 family triads (affected child/mother/father). The recently reported MSX1 P147Q mutation was also studied in an additional 1,098 cleft cases. Selected missense mutations were screened in 1,064 controls from unrelated individuals on the Centre d'Étude du Polymorphisme Humain (CEPH) diversity cell line panel. Our aggregate data suggest that point mutations in these candidate genes are likely to contribute to 6% of isolated clefts, particularly those with more severe phenotypes (bilateral cleft of the lip with cleft palate). Additional cases, possibly due to microdeletions or isodisomy, were also detected and may contribute to clefts as well. Sequence analysis alone suggests that point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated cleft lip with or without cleft palate, and the linkage disequilibrium data support a larger, as yet unspecified, role for variants in or near MSX2, JAG2, and SKI. This study also illustrates the need to test large numbers of controls to distinguish rare polymorphic variants and prioritize functional studies for rare point mutations.

Contribution of MSX1 variants to the risk of non-syndromic cleft lip and palate in a Malay population

“…Of these variants, only the P147Q variant, which has been detected in a number of Southeast Asian populations, is a relatively common variation in the MSX1 gene. In addition to the present study, this variant has been detected in three Vietnamese families, 17 two Filipino families 9 and three Thai families. 26 The prevalence of this variant may reflect a Founder effect in these populations.…”

“…Consistent with the present study, it has been detected across affected and non-affected members of the same family and in unrelated healthy controls. 9,17,26 Although this variant is located within a conserved phosphorylation motif within the MH3 domain, 23 it is revealed that it may not be pathogenic. 26 Therefore, it, at best, may contribute to clefting with other genetic and environmental risk factors in a complex inheritance pattern.…”

“…[5][6][7][8] Although no deleterious mutation has been reported in TGFB3. 7,9 MSX1 has been suggested to function upstream of TGFB3 in the development of oral cleft. 10 The aim of the current research was to investigate the genetic association of MSX1 and TGFB3 in a Malay population with non-syndromic orofacial cleft.…”

The MSX1 allele 4 homozygous child exposed to smoking at periconception is most sensitive in developing nonsyndromic orofacial clefts

“…Extensive studies in knockout mice have also demonstrated that Msx1-Bmp signaling, regulating expression of Shh, is essential for palate development (Zhang et al 2002) and the identiWcation of a MSX1 stop mutation in a Dutch family with a combination of tooth agenesis and OFC conWrmed MSX1 as a candidate gene for clefting in humans (van den Boogaard et al 2000). Sequencing-and association studies have indicated a role for MSX1 in the etiology of nonsyndromic orofacial clefting (Lidral et al 1998;Beaty et al 2001;Blanco et al 2004;Fallin et al 2003;Jezewski et al 2003;Jugessur et al 2003;Vieira et al 2003;Moreno et al 2004;Vieira et al 2005;Modesto et al 2006;Tongkobpetch et al 2006;Park et al 2007), although results published by others question this role (Mitchell et al 2001;Koillinen et al 2003;Etheredge et al 2005).…”

Triagem de mutação no éxon 3 do gene IRF6 em indivíduos com fissura labiopalatina e agenesia dentária: padronização de protocolo para seqüenciamento de DNA genômico a partir de saliva

“…Estudos examinando o padrão de recorrência das fissuras não-sindrômicas estimam que cerca de 3 a 14 genes possam estar envolvidos na determinação desse fenótipo (SCHLIEKELMAN; SLATKIN, 2002;RILEY et al, 2007;VIEIRA , 2008a). Estudos de ligação e associação têm indicado alguns genes candidatos, dentre eles: TGFA, TGFB2, TGFB3, FGF, FOXE1, GLI2, JAG2, LHX8, SATB2, SKI, ERBB2, SPRY2, TBX10, MSX 2, MSX1 e IRF6 (MURRAY, 1995;JEZEWSKI et al, 2003;BLANTON et al, 2005;VIEIRA et al, 2005;VIEIRA, 2008a;VIEIRA et al, 2008b;VIEIRA et al, 2008d;TANG et al, 2009;MARAZITA et al, 2009;JUGESSUR et al, 2009;SULL et al, 2009 ZUCCHERO et al, 2004;RILEY et al, 2007;VIEIRA, 2008a).…”