Analysis of Single Nucleotide Polymorphisms on Locus 13q33.1-34 in Multigenerational Families of Cleft Lip Palate using MassArray

Praveen Kumar Neela, Srinivas Reddy Gosla, Akhter Husain, Vasavi Mohan, Sravya Thumoju, Rajeshwari Rajeshwari

Abstract


BACKGROUND: Cleft lip palate is a common congenital anomaly with multifactorial etiology. Many high-risk markers at different loci were reported to be involved in its etiology. Advanced genetic research led to the discovery of evidence of a new linkage on 13q33.1-34 region at marker rs1830756 in two multigenerational Indian families. However, no further study was reported to confirm or validate this linkage in other families. Hence, the present study was designed.

METHODS: Twenty multigenerational families affected by non-syndromic cleft lip palate were selected for the study. Polymorphisms, rs1830756, rs1323672, rs1935135 of FAM155A gene; rs1961495, rs953386, rs1411040 of COL4A1 gene; and rs726449, rs984300 of MYO16 gene were selected. Genomic DNA was isolated and sent for genetic analysis by single nucleotide polymorphism (SNP) genotyping using the MassArray method. Statistical analysis of the genomic data was done by PLINK. Bonferroni correction was applied and haplotype analysis was done using Haploview software.

RESULTS: Polymorphisms followed the Hardy Weinberg Equilibrium. In the allelic association, all the polymorphisms analysed showed no statistical significance. Hence, there was no significant difference in the allelic frequencies between non-syndromic cleft lip palate patients and healthy controls. The odds ratio was not more than 1.6 for all the SNPs. Haplotype analysis showed that haplotypes were not significantly higher in non-syndromic cleft patients than in control subjects.

CONCLUSION: There is no association between SNPs analysed in the locus 13q33.1-34 with cleft lip palate.

KEYWORDS: cleft lip palate, chromosome, polymorphism


Full Text:

PDF

References


Mossey P. Global strategies to reduce the healthcare burden of craniofacial anomalies. Br Dent J. 2003; 195(10): 613, CrossRef.

Reddy SG, Reddy RR, Bronkhorst EM, Prasad R, Ettema AM, Sailer HF, et al. Incidence of cleft lip and palate in the state of Andhra Pradesh, South India. Indian J Plast Surg. 2010; 43: 184-9, CrossRef.

Neela PK, Reddy SG, Husain A, Mohan V. Association of cleft lip and/or palate in people born to consanguineous parents: A 13-year retrospective study from a very high-volume cleft center. J Cleft Lip Palate Craniofac Anomal. 2019; 6: 33-7, CrossRef.

Mossey P, Little J. Addressing the challenges of cleft lip and palate research in India. Indian J Plast Surg. 2009; 42(Suppl): S9-S18, CrossRef.

Leslie EJ, Taub MA, Liu H, Steinberg KM, Koboldt DC, Zhang Q, et al. Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. Am J Hum Genet. 2015; 96: 397-411, CrossRef.

Mohamad Shah NS, Salahshourifar I, Sulong S, Wan-Sulaiman WA, Halim AS. Discovery of candidate genes for nonsyndromic cleft lip palate through genome-wide linkage analysis of large extended families in the Malay population. BMC Genetics. 2016; 17: 39, CrossRef.

Mehrotra D. Genomic expression in non-syndromic cleft lip and palate patients: A review. J Oral Biol Craniofac Res. 2015; 5: 86-91, CrossRef.

Vieira AR. Unraveling human cleft lip and palate research. J Dent Res. 2008; 87: 119-25, CrossRef.

Sull JW, Liang KY, Hetmanski JB, Fallin MD, Ingersoll RG, Park J, et al. Differential parental transmission of markers in RUNX2 among cleft case-parent trios from four populations. Genet Epidemiol. 2008; 32: 505-12, CrossRef.

Funato N, Nakamura M. Identification of shared and unique gene families associated with oral clefts. Int J Oral Sci. 2017; 9: 104-9, CrossRef.

Radhakrishna U, Ratnamala U, Gaines M, Beiraghi S, Hutchings D, Golla J, 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, CrossRef.

Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 1988; 16: 1215, CrossRef.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81: 559-75, CrossRef.

Mitra AK, Stessman HAF, Schaefer RJ, Wang W, Myers CL, Van Ness, et al. Fine-mapping of 18q21.1 locus identifies single nucleotide polymorphisms associated with non-syndromic cleft lip with or without cleft palate. Front Genet. 2016; 7: 88, CrossRef.

Lin JY, Chen YJ, Huang YL, Tang GP, Zhang L, Deng B, et al. Association of bone morphogenetic protein 4 gene polymorphisms with non-syndromic cleft lip with or without cleft palate in Chinese children. DNA Cell Biol. 2008; 27: 601-5, CrossRef.

Hao J, Gao R, Wu W, Hua L, Chen Y, Li F, et al. Association between BMP4 gene polymorphisms and cleft lip with or without cleft palate in a population from South China. Arch Oral Biol. 2018; 93: 95-9, CrossRef.

Rafighdoost H, Hashemi M, Danesh H, Bizhani F, Bahari G, Taheri M. Association of single nucleotide polymorphisms in AXIN2, BMP4, and IRF6 with non-syndromic cleft lip with or without cleft palate in a sample of the southeast Iranian population. J Appl Oral Sci. 2017; 25: 650-6, CrossRef.

Savitha S, Sharma S M, Veena S, Rekha R. Single nucleotide polymorphism of bone morphogenetic protein 4 gene: A risk factor of non-syndromic cleft lip with or without palate. Indian J Plast Surg. 2015; 48: 159-64, CrossRef.

Lang D, Powell SK, Plummer RS, Young KP, Ruggeri, BA. PAX genes: Roles in development, pathophysiology, and cancer. Biochem Pharmacol. 2007; 73: 1-14, CrossRef.

Wang Q, Fang WH, Krupinski J, Kumar S, Slevin M, Kumar P. Pax genes in embryogenesis and oncogenesis. J Cell Mol Med. 2008; 12: 2281-94, CrossRef.

Gaczkowska A, Biedziak B, Budner M, Zadurska M, Lasota A, Hozyasz KK. PAX7 nucleotide variants and the risk of non‐syndromic orofacial clefts in the Polish population. Oral Diseases. 2019; 25: 1608-18, CrossRef.




DOI: https://doi.org/10.18585/inabj.v13i1.1239

Indexed by:

                 

                  

               

     

 

The Prodia Education and Research Institute