The impact of developmental genes in non-syndromic cleft lip and/or palate


  • Nihal Şahin Uysal
  • Feride İffet Şahin
  • Yunus Kasım Terzi

Received Date: 18.10.2022 Accepted Date: 09.11.2022 J Turk Ger Gynecol Assoc 2023;24(1):57-64 PMID: 36919534

Non-syndromic cleft lip and/or palate (NSCL/P) is a congenital malformation with a prevalence of 1:700 births. It has a multifactorial etiology. Human craniofacial development takes place during the first 10 weeks of pregnancy. Normal craniofacial development arises from the convergence and fusion of the facial and palatal processes and involves interactions between genes that regulate cell growth, proliferation, differentiation, epithelial-to-mesenchymal transition, and apoptosis. Whole genome/exome analysis, and also genome-wide association studies give us to chance to identify the genetic factors which contribute to the development of NSCL/P. After detecting a cleft lip and/or palate on ultrasonography without associated anomalies, the patient should be evaluated in collaboration with a clinical geneticist, taking into account the many genes and environmental factors involved in NSCL/P etiopathogenesis, and a roadmap for possible genetic diagnosis should be drawn.

Keywords: Cleft lip and/or palate, developmental genes, prenatal evaluation


Non-syndromic cleft lip and/or palate (NSCL/P) is one of the most common congenital malformations with a prevalence of 1:700 (1,2). NSCL/P is a multifactorial condition caused by an inadequate partition of the nasal and oral cavities with no other anomaly (3,4). Orofacial clefts (OFC) are classified according to their facial position; unilateral or bilateral, involved parts; lip, palate, and lip and palate, and/or their underlying pathogenesis i.e. syndromic and non-syndromic.

Of all cases with cleft lip and/or palate (CLP), 30% are syndromic. The rest of the cases are NSCL/P, and of them 20% are familial and 80% are sporadic (2,5). As an isolated condition, 50% of all CLP patients are syndromic, the rest are sporadic (3). CLP is observed twice as frequently in males than in females (6). Unilateral clefts of the lip account for approximately 75% of all patients and among them the left side is affected twice as frequently as the right side (7).

The development of palate and lip involves a complex process including the organization of cells in tissues through cell growth, migration, differentiation, and apoptosis, which are controlled by gene expression and signaling molecules. Both genes and environmental factors, such as drugs and chemical exposure of the parent, as well as dietary habits, contribute to the occurrence of the disease pathogenesis (8). Hereditary factors are estimated to be 90% effective in the development of NSCL/P (9). Contribution of epigenetic factors and gene-gene/environment interactions make the pathogenesis of NSCL/P complex. This complex nature makes it difficult to understand the exact reason for the clinical condition. To diagnose genetic factors playing a role in disease pathogenesis, prenatally detected cases may be referred to genetic testing and counseling. Due to the complex nature of the disease, it is not always possible to define the exact gene/gene(s) involved. This information should be emphasized during pre- and post-test genetic counseling sessions. The aim of this study was to review the genes involved in NSCL/P.


Human craniofacial development takes place during the first 10 weeks of pregnancy. The fourth and eighth gestational weeks are the time point where normal lip development occurs (10). The early formative systems of vertebrates are firmly controlled and closely monitored biologically, and hereditary and environmental components influence this sensitive interaction (8,11).

Neural crest cells (NCCs) differentiate to cranial processes by migrating (day 21) and differentiating to maxillary, lateral, and medial nasal processes (12). NCCs undergo epithelial-mesenchymal transition before moving to the craniofacial region and constitute the antecedents of the processes that will develop basic facial structures (13).

Head and neck develop from two-sided transient outgrowths called pharyngeal arches, which take 23-24 days and marks the beginning of early facial development. These swellings of tissue are coated by ectodermal epithelial cells, with a center of NCC-determined mesenchyme (14). A medial outgrowth of the first frontonasal prominence (FNP) is involved in the upper lip, roof of the palate, and lower jaw development (14). The FNP is responsible for the development of bilateral nasal pits and extends into the primitive oral cavity (12). The development of the FNP continues by dividing into paired medial and lateral nasal processes. They fuse with the maxillary process to form an intact upper lip (12).

As palate development is an early event during embryogenesis and takes a relatively long time, probable exposure to teratogens increases the risk of CLP formation in mammalian embryos (1). The palate develops in two parts. By the sixth week of development, the primary palate formation occurs from the bilateral medial nasal processes (15). Between the sixth and twelfth weeks, the rest of the palate, termed the secondary palate, develops. At this stage, palatal shelves outgrow from the inner oral side of the maxillary processes (16). The tongue is required for true mammalian hard palate fusion (17). Mammalian palatal bone ossification is followed by bone fusion (16). Palatal bone develops through intramembranous ossification, in which osteoblasts directly lay down the bone matrix. Lip, palate, and nose deformities are caused by a disruption in normal development. The extent of the defect is dependent on the disruption time, severity and amount. For the formation of the primary palate and central lip, rapid cell division is required in the lateral nasal process region. The developing embryo is vulnerable to both genetic and environmental effects during this period (16).

Signaling pathways

With the development of technology, modern techniques including automated analyses have been used to study complex diseases. Whole genome/exome analyses, and also genome-wide association studies (GWAS) provide an opportunity to identify genetic factors that contribute to the development of NSCL/P. Different candidate genes have been reported in recent publications (1,5,18,19,20). GWAS also helps to identify rare, low-frequency coding variants (21,22). Besides point mutation, copy number variants (CNV), which disrupt the structure and also the regulatory region of the genes, can cause NSCL/P (23).

Signaling molecules and morphogens play a crucial role in mesenchymal proliferation and patterning during craniofacial development. These signaling molecules originate from the epithelial cells of the facial prominences and palate and create reciprocal epithelial-mesenchymal communications that is critical for palatal development (12). Wnt, TGF/BMP, Hedgehog, and Fgf-related signaling cascades are involved in these interactions, and mutations of the genes of these signaling pathways may be the underlying reason for CLP and CP (24).

MSX1, BMP4, BMP2, FGF10, and SHOX2 are among the genes involved in anterior palate development. BMP4 expression is regulated by a transcription factor called MSX1. BMP4 regulates sonic hedgehog (Shh) expression in the palatal epithelium, and BMP2 expression takes place downstream of the Shh signaling cascades. Simultaneously, FGF10 uses the FGFR2 receptor to regulate the Shh signaling cascade in the palatal epithelium in a paracrine manner. Activated Shh promotes cell proliferation in the mesenchyme by using the BMP2 signaling cascade. These findings suggest that the growth of the anterior area of the palatal shelf is a very tightly controlled process, and BMP and FGF canonical pathways play a critical role in this process. However, less is known about the function of the genes expressed in the posterior area of the palate but it is understood that FGF8 is the first step in one of the pathways that promote the expression of PAX9 in the posterior area of the palatal mesenchyme. A deficiency in PAX9 results in a developmental defect of the palatal shelf and a cleft palate (CLP) (25).

Palatal shelf development defects are classified into five categories by Chai and Maxson (25): failure of palatal shelf formation due to mutations in activin-βA and FGFR2; a fusion of the palatal shelf with the tongue or mandible arising from TBX22 mutations and loss of function mutations in FGF10; failure of palatal shelf elevation resulting from mutations in the PAX9, PITX1, and OSR2 genes; failure of palatal shelves to meet after elevation as a consequence of mutations in MSX1 and LHX8, TGFBR2 in NCCs, or Shh in the epithelium; and persistence of medial edge epithelium caused by TGFB3 and EGFR mutations (25).

Further hereditary investigations identified variants in the MMP3, MMP25, TIMP2, and TIMP3 genes to be causative in the development of NSCL/P. Besides point mutations in coding regions, variants that affect functional promoter activity in MMP3 and TIMP2 have also been found to be related to NSCL/P (26,27).

As an oncogene, FOS promotes epithelial-to-mesenchymal transition, which is essential for craniofacial development (28). In embryonic development, apoptosis is an important mechanism for maintaining tissue homeostasis. CASP8 is one of the vital genes involved in craniofacial development (29).

A gene list is provided in Table 1 related to NSCL/P and craniofacial development.


Epigenetics is described as the regulation of gene expression through reversible chemical modifications without affecting the DNA sequence (61).

Among the best understood epigenetic modifications in animals are histone modifications, which regulate chromatin accessibility during transcription, and DNA methylation, which plays a critical role in many biological processes, and also contributes to the regulation of gene expression during palatal fusion (2,62).

The expression of the several genes that are associated with NSCL/P is controlled by epigenetic modifications. Epigenetically controlled genes include transcription factors (LHX8, PRDM16, PBX1, GSC, VAX1, MYC), growth factors and their modulators (WNT9B, BMP4, EPHB2, BICC1, DHRS2), and microRNAs (miRNAs) including MIR140 and MIR300 (63,64,65,66,67). Xu et al. (66) and Sharp et al. (68) reported methylation position variations in OFC subsets; and emphasized many methylation positions related to genes that differentiated between cleft lip with CLP, cleft lip only, and cleft palate only (CPO).

miRNAs have been reported to regulate the expression of 60% of genes encoding proteins (69), but abnormalities of expression are linked to a variety of diseases, including OFCs (70). An SNP in miR-140 was found to have a significant correlation with NSCL/P (71). Rattanasopha et al. (72) reported a role for miR-140 in PDGFRA regulation in association with human CPO. miR-140 was likewise found to control the expression of BMP2 and FGF9 genes in human palatal mesenchyme cells (73). These discoveries highlighted two significant focuses for craniofacial development: (a) Bmp signaling can be carried on by Smad factors and miRNA-17-92, and (b) miR-17-92 can have multiple effects by focusing on a few pathways, including TGF, FGF, Wnt, and others.

Environmental factors influence epigenetic modifications in both cells and organisms, which can result in different developmental outcomes (74). Van Rooij et al. (75) reported that maternal glutathione s-transferase genotype, and smoking as an environmental factor, increased the risk of CLP significantly. Joubert et al. (76) reported that maternal smoking was associated with differential methylation of some of the genes related to OFC, such as MSX1, PDGFRA, GRHL3, ZIC2, and HOXA2. Jugessur et al. (77) reported that alcohol dehydrogenase gene ADH1C variants are associated with clefting.

Human studies have also found that dietary folate plays a role in epigenetic-mediated CL/P (64). Gonseth et al. (64) conducted an epigenome-wide association study to investigate the correlation between epialleles and OFCs in the United States, before setting up mandatory folate treatment in 1998.

Prenatal evaluation

During diagnostic ultrasonography, the defined cleft lip is a direct imperfection stretching out between the lip side and the nostril. CLP with cleft lip might extend between the alveolar side and hard palate, reaching the nasal and oral cavities, and may also extend to the orbits. Diagnosis requires the use of both the transverse and coronal planes. During visualization of cleft and palate, color Doppler might be valuable in showing flow across the palate. The diagnosis of isolated CP is difficult. Even between 11 and 13 gestational weeks, diagnosis of CLP may be possible but mostly CLP is diagnosed by detailed ultrasound examination at 18-22 gestational weeks. Retronasal triangle and maxillary gap views should be obtained during ultrasonographic evaluation of the fetus in screening for OFCs.

Magnetic resonance imaging may be an adjunct to prenatal diagnosis of CLP. After the prenatal ultrasound diagnosis of CLP, other system anomalies should be screened and invasive testing for karyotyping and microarray testing should be offered. Prenatal consultation with a multidisciplinary team, including clinical geneticists, should be performed during prenatal evaluation (78). Clinical geneticists take a detailed pedigree and family history followed by reviewing the ultrasonography findings. The finding can be isolated or associated with a specific syndrome (79). After genetic counseling and risk calculation, clinical geneticists decide about appropriate genetic tests (78). Karyotype analysis is necessary to exclude trisomy 13 and other chromosome abnormalities for fetuses with multiple abnormal ultrasonographic findings (80). If there is a suggestion of a specific syndrome due to the associated anomalies, targeted genetic studies including fluorescent in situ hybridization or multiplex ligation-dependent probe amplification can be performed before the microarrayor testing may proceed directly to microarray following the karyotyping. If these test results are normal, whole exome sequencing can be the next step to detect point mutations.

Prognosis relies upon the presence and kind of related abnormalities. If it is isolated, the prognosis is good and normal survival can be achieved with appropriate management. Surgical intervention is frequently performed between postnatal 3-6 months. The recurrence risk can be defined as 5% if one sibling or parent is affected and 10% if two siblings are affected in isolated cases. If the genetic alteration is disclosed during genetic work up, genetic counseling should be given to the family about the recurrence risk after trying to determine the inheritance pattern together with the parental genetic evaluation.


Pathogenesis of OFCs is complex and may frequently include hereditary and environmental interactions that are yet to be fully understood. As the condition is complex, epigenetic modifications may also contribute to the clinical condition if there is no defined genetic reason.

When a cleft lip and/or palate is detected by ultrasonography, in the absence of associated anomalies, the patient should be evaluated in consultation with the clinical geneticist, taking into account many genes and environmental factors involved in NSCL/P etiopathogenesis. A roadmap for possible prenatal genetic diagnosis should be devised, as genetic testing is an important component of pre- and post-natal management of cases.

Peer-review: Externally peer-reviewed.

Author Contributions: Concept: F.İ.Ş., Y.K.T.; Design: F.İ.Ş.; Data Collection or Processing: N.Ş.U.; Analysis or Interpretation: N.Ş.U.; Literature Search: N.Ş.U.; Writing: N.Ş.U., F.İ.Ş., Y.K.T.

Conflict of Interest: No conflict of interest is declared by the authors.

Financial Disclosure: The authors declared that this study received no financial support.


  1. Dixon MJ, Marazita ML, Beaty TH, Murray JC. Cleft lip and palate: Understanding genetic and environmental influences. Nat Rev Genet 2011; 12: 167-78.
  2. Beaty TH, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, et al. Evidence for gene-environment interaction in a genome-wide study of nonsyndromic cleft palate. Genet Epidemiol 2011; 35: 469-78.
  3. Carinci F, Scapoli L, Palmieri A, Zollino I, Pezzetti F. Human genetic factors in nonsyndromic cleft lip and palate: an update. Int J Pediatr Otorhinolaryngol 2007; 71: 1509-19.
  4. Mossey PA, Modell B. Epidemiology of oral clefts 2012: an international perspective. Front Oral Biol 2012; 16: 1-18.
  5. Yu Y, Zuo X, He M, Gao J, Fu Y, Qin C, et al. Genome-wide analyses of non-syndromic cleft lip with palate identify 14 novel loci and genetic heterogeneity. Nat. Commun. 2017; 8: 14364.
  6. Mossey PA, Little J, Munger RG, Dixon MJ, Shaw WC. Cleft lip and palate. Lancet 2009; 374: 1773-85.
  7. Gundlach KK, Maus C. Epidemiological studies on the frequency of clefts in Europe and world-wide. J Craniomaxillofac Surg 2006; 34(Suppl 2): 1-2.
  8. Murray JC. Gene/environment causes of cleft lip and/or palate. Clinical Genetics 2002; 61: 248-56.
  9. Grosen D, Bille C, Petersen I, Skytthe A, von Hjelmborg JB, Pedersen JK, et al. Risk of oral clefts in twins. Epidemiology 2011; 22: 313-9.
  10. Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-resolution epigenomic atlas of human embryonic craniofacial development. Cell Reports 2018; 23: 1581-97.
  11. Johnston MC, Hassell JR, Brown KS. The embryology of cleft lip and cleft palate. Clin Plast Surg 1975; 2: 195-203.
  12. Jiang R, Bush JO, Lidral AC. Development of the upper lip: morphogenetic and molecular mechanisms. Dev Dyn 2006; 235: 1152-66.
  13. Kang P, Svoboda KK. Epithelial-mesenchymal transformation during craniofacial development. J Dent Res 2005; 84: 678-90.
  14. Noden DM, Trainor PA. Relations and interactions between cranial mesoderm and neural crest populations. J Anat 2005; 207: 575-601.
  15. Bush JO, Jiang R. Palatogenesis: Morphogenetic and molecular mechanisms of secondary palate development. Development 2012; 139: 231-43.
  16. Gritli-Linde A. The etiopathogenesis of cleft lip and cleft palate: Usefulness and caveats of mouse models. Curr Top Dev Biol 2008; 84: 37-138.
  17. Lough KJ, Byrd KM, Spitzer DC, Williams SE. Closing the gap: Mouse models to study adhesion in secondary palatogenesis. J Dent Res 2017; 96: 1210-20.
  18. Beaty TH, Marazita ML, Leslie EJ. Genetic factors influencing risk to orofacial clefts: today’s challenges and tomorrow’s opportunities. F1000Res 2016; 5: 2800.
  19. Khandelwal KD, van Bokhoven H, Roscioli T, Carels CE, Zhou H. Genomic approaches for studying craniofacial disorders. Am J Med Genet C Semin Med Genet 2013; 163C: 218-31.
  20. Ludwig KU, Böhmer AC, Bowes J, Nikolic M, Ishorst N, Wyatt, N, et al. Imputation of orofacial clefting data identifies novel risk loci and sheds light on the genetic background of cleft lip ± cleft palate and cleft palate only. Hum Mol Genet 2017; 26: 829-42.
  21. Leslie EJ, Carlson JC, Shaffer JR, Buxo CJ, Castilla EE, Christensen K, et al. Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate. Am J Med Genet 2017; 173: 1531-8.
  22. Aylward A, Cai Y, Lee A, Blue E, Rabinowitz D, Haddad Jr J. University of Washington Center for Mendelian Genomics. Using Whole Exome Sequencing to Identify Candidate Genes With Rare Variants In Nonsyndromic Cleft Lip and Palate. Genet Epidemiol 2016; 40: 432-41.
  23. da Silva HPV, Oliveira GHM, Ururahy MAG, Bezerra JF, de Souza KSC, Bortolin, RH, et al. Application of high-resolution array platform for genome-wide copy number variation analysis in patients with nonsyndromic cleft lip and palate. J Clin Lab Anal 2018; 32: e22428.
  24. Chiquet BT, Yuan Q, Swindell EC, Maili L, Plant R, Dyke J, et al. Knockdown of Crispld2 in zebrafish identifies a novel network for nonsyndromic cleft lip with or without cleft palate candidate genes. Eur J Hum Genet 2018; 26: 1441-50.
  25. Chai Y, Maxson RE Jr. Recent advances in craniofacial morphogenesis. Dev Dyn 2006; 235: 2353-75.
  26. Letra A, Silva RA, Menezes R, Astolfi CM, Shinohara A, de Souza AP, et al. MMP gene polymorphisms as contributors for cleft lip/palate: association with MMP3 but not MMP1. Arch Oral Biol 2007; 52: 954-60.
  27. Letra A, Zhao M, Silva RM, Vieira AR, Hecht JT. Functional Significance of MMP3 and TIMP2 Polymorphisms in Cleft Lip/Palate. J Dent Res 2014; 93: 651-6.
  28. Reichmann E, Schwarz H, Deiner EM, Leitner I, Eilers M, Berger J, et al. Activation of an inducible c-FosER fusion protein causes loss of epithelial polarity and triggers epithelial-fibroblastoid cell conversion. Cell 1992; 71: 1103-16.
  29. Thompson CB. Apoptosis in the pathogenesis and treatment of disease. Science 1995; 267: 1456-62.
  30. Davies AF, Stephens RJ, Olavesen MG, Heather L, Dixon MJ, Magee A, et al. Evidence of a locus for orofacial clefting on human chromosome 6p24 and STS content map of the region. Hum Mol Genet 1995; 4: 121-8.
  31. Ardinger HH, Buetow KH, Bell GI, Bardach J, VanDemark DR, Murray JC. Association of genetic variation of the transforming growth factor-alpha gene with cleft lip and palate. Am. J. Hum. Genet 1989; 45: 348-53.
  32. Lace B, Kempa I, Klovins J, Stavusis J, Krumina A, Akota I, et al. BCL3 gene role in facial morphology. Birth Defects Res A Clin Mol Teratol 2012; 94: 918-24.
  33. Beiraghi S, Zhou M, Talmadge CB, Went-Sumegi N, Davis JR, Huang D, et al. Identification and characterization of a novel gene disrupted by a pericentric inversion inv(4)(p13.1q21.1) in a family with cleft lip. Gene 2003; 309: 11-21.
  34. Indencleef K, Roosenboom J, Hoskens H, White JD, Shriver MD, Richmond S, et al. Six NSCL/P loci show associations with normal-range craniofacial variation. Front. Genet 2018; 9: 502.
  35. Vieira AR, Meira R, Modesto A, Murray JC. MSX1, PAX9, and TGFA contribute to tooth agenesis in humans. J Dent Res 2004; 83: 723-7.
  36. Scapoli L, Palmieri A, Martinelli M, Vaccari C, Marchesini J, Pezzetti F, et al. Study of the PVRL1 gene in Italian nonsyndromic cleft lip patients with or without cleft palate. Ann. Hum. Genet 2006; 70: 410-3.
  37. Basha M, Demeer B, Revencu N, Helaers R, Theys S, Bou Saba S, et al. Whole exome sequencing identifies mutations in 10% of patients with familial non-syndromic cleft lip and/or palate in genes mutated in well-known syndromes. J Med Genet 2018; 55: 449-58.
  38. Radhakrishna U, Ratnamala U, Gaines M, Beiraghi S, Hutchings D, et al. Genomewide scan for nonsyndromic cleft lip and palate in multigenerational Indian families reveals significant evidence of linkage at 13q33.1- 34. Am. J. Hum. Genet 2006; 79: 580-5.
  39. Shi M, Mostowska A, Jugessur A, Johnson MK, Mansilla MA, Christensen K, et al. Identification of microdeletions in candidate genes for cleft lip and/or palate. Birth Defects Res A Clin Mol Teratol 2009; 85: 42-51.
  40. Suzuki S, Marazita ML, Cooper ME, Miwa N, Hing A, Jugessur A, et al. Mutations in BMP4 are associated with subepithelial, microform, and overt cleft lip. Am J Hum Genet 2009; 84: 406-11.
  41. Leslie EJ, Carlson JC, Shaffer JR, Feingold E, Wehby G, Laurie CA, et al. A multi-ethnic genome-wide association study identifies novel loci for non-syndromic cleft lip with or without cleft palate on 2p24.2, 17q23 and 19q13. Hum Mol Genet 2016; 25: 2862-72.
  42. Saleem K, Zaib T, Sun W, Fu S. Assessment of candidate genes and genetic heterogeneity in human non syndromic orofacial clefts specifically non syndromic cleft lip with or without palate. Heliyon 2019; 5: e03019.
  43. Yıldırım Y, Kerem M, Köroğlu Ç, Tolun A. 2014. A homozygous 237-kb deletion at 1p31 identified as the locus for midline cleft of the upper and lower lip in a consanguineous family. Eur J Hum Genet 2014; 22: 333-7.
  44. He M, Bian Z. Association between DLX4 polymorphisms and nonsyndromic orofacial clefts in a Chinese han population. Cleft Palate Craniofac J 2019; 56: 357-62.
  45. de Aguiar PK, Coletta RD, de Oliveira AM, Machado RA, Furtado PG, de Oliveira, et al. rs1801133C>T polymorphism in MTHFR is a risk factor for nonsyndromic cleft lip with or without cleft palate in the Brazilian population. Birth Defects Res A Clin Mol Teratol 2015; 103: 292-8.
  46. Mijiti A, Ling W, Maimaiti A, Tuerdi M, Tuerxun J, Moming A. Preliminary evidence of an interaction between the CRISPLD2 gene and non-syndromic cleft lip with or without cleft palate (nsCL/P) in Xinjiang Uyghur population, China. Int. J. Pediatr. Otorhinolaryngol 2015; 79: 94-100.
  47. Wang H, Zhang T, Wu T, Hetmanski JB, Ruczinski I, Schwender H, et al. The FGF and FGFR gene family and risk of cleft lip with or without cleft palate. Cleft Palate-Craniofac J 2013; 50: 96-103.
  48. Dickinson AJ, Sive HL. The Wnt antagonists Frzb-1 and Crescent locally regulate basement membrane dissolution in the developing primary mouth. Development 2009; 136: 1071-81.
  49. Yamamoto T, Cui XM, Shuler CF. Role of ERK1/2 signal- ing during EGF-induced inhibition of palatal fusion. Dev Biol 2003; 260: 512-21.
  50. Vieira AR, de Carvalho FM, Johnson L, DeVos L, Swailes AL, Weber ML, et al. Fine Mapping of 6q23.1 Identifies TULP4 as Contributing to Clefts. Cleft Palate Craniofac J 2015; 52: 128-34.
  51. Conte F, Oti M, Dixon J, Carels CE, Rubini M, Zhou H. Systematic analysis of copy number variants of a large cohort of orofacial cleft patients identifies candidate genes for orofacial clefts. Hum Genet 2016; 135: 41-59.
  52. Suazo J, Santos JL, Scapoli L, Jara L, Blanco R. Association between TGFB3 and nonsyndromic cleft lip with or without cleft palate in a Chilean population. Cleft Palate Craniofac J 2010; 47: 513-7.
  53. Beaty TH, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, et al. A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet 2010; 42: 525-9.
  54. Moreno LM, Mansilla MA, Bullard SA, Cooper ME, Busch TD, Machida, J, et al. FOXE1 Association with Both Isolated Cleft Lip with or without Cleft Palate, and Isolated Cleft Palate. Hum Mol Genet 2009; 18: 4879-96.
  55. Torres-Juan L, Rosell J, Morla M, Vidal-Pou C, García-Algas F, de la Fuente MA, et al. Mutations in TBX1 genocopy the 22q11.2 deletion and duplication syndromes: a new susceptibility factor for mental retardation. Eur J Hum Genet 2007; 15: 658-63.
  56. Blavier L, Lazaryev A, Groffen J, Heisterkamp N, DeClerck YA, Kaartinen V. TGF-beta3-induced palatogenesis requires matrix metalloproteinases. Mol Biol Cell 2001; 12: 1457-66.
  57. Mangold E, Böhmer AC, Ishorst N, Hoebel AK, Gültepe P, Schuenke H, et al. Sequencing the GRHL3 coding region reveals rare truncating mutations and a common susceptibil- ity variant for nonsyndromic cleft palate. Am J Hum Genet 2016; 98: 755-62.
  58. Proetzel G, Pawlowski SA, Wiles MV, Yin M, Boivin GP, Howles PN, et al. Transforming growth factor-beta 3 is required for secondary palate fusion. Nat Genet 1995; 11: 409-14.
  59. Lu YP, Han WT, Liu Q, Li JX, Li ZJ, Jiang M. Variations in WNT3 gene are associated with incidence of non-syndromic cleft lip with or without cleft palate in a northeast Chinese population. Genet Mol Res 2015; 14: 12646-53.
  60. van Rooij IA, Ludwig KU, Welzenbach J, Ishorst N, Thonissen M, Galesloot TE, et al. Non-Syndromic Cleft Lip with or without Cleft Palate: Genome-Wide Association Study in Europeans Identifies a Suggestive Risk Locus at 16p12.1 and Supports SH3PXD2A as a Clefting Susceptibility Gene. Genes (Basel) 2019; 10: 1023.
  61. Kiefer JC. Epigenetics in development. Developmental Dynamics 2007; 236: 1144-56.
  62. Garland MA, Sun B, Zhang S, Reynolds K, Ji Y, Zhou CJ. Role of epigenetics and miRNAs in orofacial clefts. Birth Defects Res 2020; 112: 1635-59.
  63. Alvizi L, Ke X, Brito LA, Seselgyte R, Moore GE, Stanier P, et al. Differential methylation is associated with non-syndromic cleft lip and palate and contributes to penetrance effects. Scientific Reports 2017; 7: 2441.
  64. Gonseth S, Shaw GM, Roy R, Segal MR, Asrani K, Rine J, Marini NJ. Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions in disease risk. Epigenetics 2019; 14: 198-213.
  65. Howe LJ, Richardson TG, Arathimos R, Alvizi L, Passos-Bueno MR, Stanier P, et al. Evidence for DNA methylation mediating genetic liability to non-syndromic cleft lip/palate. Epigenomics 2019; 11: 133-45.
  66. Xu Z, Lie RT, Wilcox AJ, Saugstad OD, Taylor JA. A comparison of DNA methylation in newborn blood samples from infants with and without orofacial clefts. Clinical Epigenetics 2019; 11: 40.
  67. Zhao AD, Huang YJ, Zhang HF, Tang W, Zhang MF. Study on DNA methylation profiles in non-syndromic cleft lip/palate based on bioinformatics. Shanghai Kou Qiang Yi Xue 2019; 28: 57-62.
  68. Sharp GC, Ho K, Davies A, Stergiakouli E, Humphries K, McArdle W, et al. Distinct DNA methylation profiles in subtypes of orofacial cleft. Clinical Epigenetics 2017; 9: 63.
  69. Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009; 19: 92-105.
  70. Suzuki A, Abdallah N, Gajera M, Jun G, Jia P, Zhao Z, et al. Genes and microRNAs associated with mouse cleft palate: A systematic review and bioinformatics analysis. Mech Dev 2018; 150: 21-7.
  71. Li L, Meng T, Jia Z, Zhu G, Shi B. Single nucleotide polymorphism associated with nonsyndromic cleft palate influences the processing of miR-140. Am J Med Genet A 2010; 152A: 856-62.
  72. Rattanasopha S, Tongkobpetch S, Srichomthong C, Siriwan P, Suphapeetiporn K, Shotelersuk V. PDGFRa muta- tions in humans with isolated cleft palate. European J Hum Genet 2012; 20: 1058-62.
  73. Li A, Jia P, Mallik S, Fei R, Yoshioka H, Suzuki A, et al. Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice. Brief Bioinform 2020; 21: 1465-78.
  74. Feil R, Fraga MF. Epigenetics and the environment: Emerging patterns and implications. Nature Reviews. Genetics 2012; 13: 97-109.
  75. van Rooij IA, Wegerif MJ, Roelofs HM, Peters WH, Kuijpers-Jagtman AM, Zielhuis GA, et al. Smoking, genetic polymorphisms in biotransformation enzymes, and nonsyndromic oral clefting: A gene-environment interaction. Epidemiology 2001; 12: 502-7.
  76. Joubert BR, Felix JF, Yousefi P, Bakulski KM, Just AC, Breton C et al. DNA methylation in new- borns and maternal smoking in pregnancy: Genome-wide con- sortium meta-analysis. Am J Hum Genet 2016; 98: 680-96.
  77. Jugessur A, Shi M, Gjessing HK, Lie RT, Wilcox AJ, Weinberg CR, et al. Genetic determinants of facial clefting: analysis of 357 candidate genes using two national cleft studies from Scandinavia. PLoS One 2009; 4: e5385.
  78. Yılmaz Celik Z, Terzi YK, Sahin Fİ. Craniofacial Malformations. In:Dundar M, editor. Atlas of Dysmorphology and Diagnosis. Kayseri, Turkey: Mgroup Published; 2015. p. 226-30.
  79. Yilmaz Z, Gokdemir M, Derbent M, Sahin FI. Greig syndrome based on a de novo translocation. Pediatr Int 2008; 50: 248-50.
  80. Yaman D, Sahin FI. Down Sendromunda Genetik. In:Ustun Y, editör. Her Yönüyle Down Sendromu. Ankara/Turkey: Ozturk Ticaret; 2018. p. 5-18.