Rare functional variants in genome–wide association identified candidate genes for nonsyndromic clefts in the African population

Abstract

Nonsyndromic clefts of the lip and palate [NSCLP] are complex genetic traits. Together, they are classified as one of the most common birth defects with a prevalence of 1/700 live births. Genome-wide association studies [GWAS] for non-syndromic cleft lip with or without cleft palate [NSCL[P]] revealed significant association for common single nucleotide polymorphisms near genes involved in craniofacial development i.e. MAFB, PAX7, VAX1, ARHGAP29 (ABCA4 locus), and IRF6. Sequencing of protein coding regions of the NSCL[P] GWAS candidate genes or adjacent genes suggest a role for rare functional variants. Replication studies in the African population did not observe any significant association with the GWAS candidate genes. On the other hand, the role of rare functional variants in GWAS candidate genes has not been evaluated in the African population. We obtained saliva samples from case triads in Nigeria and Ethiopia for Sanger sequencing of the GWAS candidate genes [MAFB, PAX7, VAX1, ARHGAP29, and IRF6] in order to identify rare functional variants. A total of 220 African samples [140 Nigerians and 80 Ethiopians] were sequenced and we found the following new rare variants— p.His165Asn in the MAFB gene, p.Asp428Asn in the PAX7, a splice-site variant that creates a new donor splice-site in PAX7. We also found three previously reported missense variants p.Gly466Ser in PAX7; p.Leu913Ser and Arg955His in ARHGAP29. No de novo mutations were found. Future genome-wide association and sequencing studies should be conducted using samples from Africa in order to identify new molecular genetic factors that contribute to the etiology of NSCLP.

PAX7nucleotide variants and the risk of non‐syndromic orofacial clefts in the Polish population

“…The PAX7 status as a cleft candidate gene has been further confirmed by a number of independent follow‐up replication studies conducted in various populations and meta‐analysis (Beaty et al, ; Böhmer et al, ; Butali et al, ; Gowans et al, ; Leslie et al, , ; Ludwig et al, ). Both common and rare PAX7 variants have been correlated with the increased risk of nsCL/P (Butali et al, , ; Leslie et al, ). Identification of de novo mutations disrupting the function of PAX7 transcription factor in patients with nsCL/P may indicate that the GWAS association signal in the 1p36.13 locus reflects a strong LD with a variant that alters the level of PAX7 expression or function of the encoded protein (Butali et al, ; Leslie et al, ).…”

“…Both common and rare PAX7 variants have been correlated with the increased risk of nsCL/P (Butali et al, , ; Leslie et al, ). Identification of de novo mutations disrupting the function of PAX7 transcription factor in patients with nsCL/P may indicate that the GWAS association signal in the 1p36.13 locus reflects a strong LD with a variant that alters the level of PAX7 expression or function of the encoded protein (Butali et al, ; Leslie et al, ). The most important result of our sequencing analysis was the identification of a novel PAX7 synonymous variant in a single patient with nsCLP.…”

“…In the meta‐analyses of genome‐wide association studies (GWASs) for nsCL/P, the results for the PAX7 variants reached the genome‐wide significance (Leslie et al, ; Ludwig et al, ). Moreover, several rare and potentially pathogenic variants located in or near the PAX7 gene have recently been detected in patients with orofacial clefts (Butali et al, ; Gowans et al, ; Leslie et al, ).…”

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

“…2009; Butali et al. 2014a,b). All DNA processing protocols, PCR conditions and electrophoretic procedure are available at the Murray laboratory website (http://genetics.uiowa.edu/protocols.php).…”

Variantes genéticas de risco às fissuras orofaciais

“…At the cellular level, the authors verified that deletion of these regions were correlated with lower Myc expression and enriched expression of genes involved with ribosome assembly and transcriptional, suggesting that abnormal cell proliferation is a possible mechanism by which deletion of these elements causes Sequencing strategies have been the most suitable approach to detect rare variants implicated with diseases (Manolio et al, 2009). Resequencing of genes associated with NSCL/P by GWAS has found possibly pathogenic rare variants in ARGHAP29 (Leslie and Murray, 2012), MAFB and PAX7 (Butali et al, 2014). In addition, the advent of next-generation sequencing (NGS) technologies stimulated a genome-wide hunt for rare variants, by means of exome and genome sequencing.…”