Prevalence of dental anomalies and genetic aberrations of nonsyndromic cleft-lip with or without cleft palate patients with hypodontia

Non-syndromic cleft lip and or without cleft palate (NSCL/P) with dental anomalies are a common craniofacial abnormality in humans and animals. NSCL/P is reported to have a higher prevalence of dental anomalies compared to non-cleft individuals. This study aims to determine the prevalence of dent...

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Main Author:	Ghazali, Norliana
Format:	Thesis
Language:	English
Published:	2022
Subjects:	RK Dentistry
Online Access:	http://eprints.usm.my/57762/1/NORLIANA%20BINTI%20GHAZALI-FINAL%20THESIS%20S-SGD000714%28R%29%20-24%20pages.pdf
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spelling	my-usm-ep.577622023-04-11T01:54:38Z Prevalence of dental anomalies and genetic aberrations of nonsyndromic cleft-lip with or without cleft palate patients with hypodontia 2022-09 Ghazali, Norliana RK Dentistry Non-syndromic cleft lip and or without cleft palate (NSCL/P) with dental anomalies are a common craniofacial abnormality in humans and animals. NSCL/P is reported to have a higher prevalence of dental anomalies compared to non-cleft individuals. This study aims to determine the prevalence of dental anomalies and to identify the genetic aberration among NSCL/P children using DNA microarray. A cross-sectional study was carried out at Hospital USM with a clinical oral examination followed by an orthopantomogram analysis among NSCL/P and non-cleft children between the ages of 7 to 13 years old. Saliva was collected from the subjects for genomic DNA extraction. Extracted genomic DNA from 61 NSCL/P and 20 non-cleft were subjected to the CytoScan 750K Array to identify genetic aberrations such as copy number variations (CNVs) and loss of heterozygosity (LOH). For CytoScan 750K Array, 250 ng of genomic DNA were digested with Nsp1, before being ligated to an adapter. Polymerase chain reaction (PCR) using a single pair of primers that recognised the adapter sequence was then performed. All four aliquots of PCR products were then combined and purified with magnetic beads followed by fragmentation with DNase 1 then subsequently end-labeled with biotin and hybridyzed into the CytoScan arrays. Next, the array was stained using GeneChips Fluidics Station 450 before scanning the arrays. The data was then analysed manually using the Chromosome Analysis Suite (ChAS) software to examine the genome. Statistical data analysis was performed using Mann-Whitney and Chi-Square test in the IBM SPSS software to confirm the significant results. The results showed that the prevalence (95% CI) of anomalies related to the number of teeth (67%:95% CI: 0.540,0.787) was higher than the morphology (8%;95% CI: 0.027, 0.181) in the NSCL/P children. The highest dental anomalies was hypodontia among NSCL/P and non-cleft children. Six significant CNVs were identified including gains (12q14.3, 15q26.3, 1p36.32, and 1p36.33) and losses (3p14.2 and 4q13.2) in the NSCL/P with hypodontia patients compared to the NSCL/P only. The genes encoded in these regions are LEMD3, IGF1R, TP73, SKI, FHIT, and UGT2β15. For LOH, the most recurrent regions were found at 1p33-1p32.3, 1q32.2-1q42.13, and 6p12.1-6p11.1 loci occurred in 13 (16%), 5 (6%) and 7 (9%) among NSCL/P and non-cleft with hypodontia children, respectively. Validation analysis revealed a significant copy number gain in TP73, SKI, IGF1R and LEMD3 and loss in FHIT and UGT2β15 in NSCL/P children with hypodontia (p < 0.005). Microsatellite markers analysis found a significant association between D1S197 (1p36.33-32.3) markers in NSCL/P with hypodontia. In conclusion, the present study has successfully determined the prevalence of dental anomalies and identified the genetic aberrations among NSCL/P. The current study shows a novel finding of copy number loss at 3p14.2 and 4q13.2 that includes FHIT and UGT2β15 which may contribute to the formation of NSCL/P with hypodontia. These results have an immerse prospect in the promising field of individualized preventive oral health care. 2022-09 Thesis http://eprints.usm.my/57762/ http://eprints.usm.my/57762/1/NORLIANA%20BINTI%20GHAZALI-FINAL%20THESIS%20S-SGD000714%28R%29%20-24%20pages.pdf application/pdf en public phd doctoral Universiti Sains Malaysia Pusat Pengajian Sains Pergigian
institution	Universiti Sains Malaysia
collection	USM Institutional Repository
language	English
topic	RK Dentistry
spellingShingle	RK Dentistry Ghazali, Norliana Prevalence of dental anomalies and genetic aberrations of nonsyndromic cleft-lip with or without cleft palate patients with hypodontia
description	Non-syndromic cleft lip and or without cleft palate (NSCL/P) with dental anomalies are a common craniofacial abnormality in humans and animals. NSCL/P is reported to have a higher prevalence of dental anomalies compared to non-cleft individuals. This study aims to determine the prevalence of dental anomalies and to identify the genetic aberration among NSCL/P children using DNA microarray. A cross-sectional study was carried out at Hospital USM with a clinical oral examination followed by an orthopantomogram analysis among NSCL/P and non-cleft children between the ages of 7 to 13 years old. Saliva was collected from the subjects for genomic DNA extraction. Extracted genomic DNA from 61 NSCL/P and 20 non-cleft were subjected to the CytoScan 750K Array to identify genetic aberrations such as copy number variations (CNVs) and loss of heterozygosity (LOH). For CytoScan 750K Array, 250 ng of genomic DNA were digested with Nsp1, before being ligated to an adapter. Polymerase chain reaction (PCR) using a single pair of primers that recognised the adapter sequence was then performed. All four aliquots of PCR products were then combined and purified with magnetic beads followed by fragmentation with DNase 1 then subsequently end-labeled with biotin and hybridyzed into the CytoScan arrays. Next, the array was stained using GeneChips Fluidics Station 450 before scanning the arrays. The data was then analysed manually using the Chromosome Analysis Suite (ChAS) software to examine the genome. Statistical data analysis was performed using Mann-Whitney and Chi-Square test in the IBM SPSS software to confirm the significant results. The results showed that the prevalence (95% CI) of anomalies related to the number of teeth (67%:95% CI: 0.540,0.787) was higher than the morphology (8%;95% CI: 0.027, 0.181) in the NSCL/P children. The highest dental anomalies was hypodontia among NSCL/P and non-cleft children. Six significant CNVs were identified including gains (12q14.3, 15q26.3, 1p36.32, and 1p36.33) and losses (3p14.2 and 4q13.2) in the NSCL/P with hypodontia patients compared to the NSCL/P only. The genes encoded in these regions are LEMD3, IGF1R, TP73, SKI, FHIT, and UGT2β15. For LOH, the most recurrent regions were found at 1p33-1p32.3, 1q32.2-1q42.13, and 6p12.1-6p11.1 loci occurred in 13 (16%), 5 (6%) and 7 (9%) among NSCL/P and non-cleft with hypodontia children, respectively. Validation analysis revealed a significant copy number gain in TP73, SKI, IGF1R and LEMD3 and loss in FHIT and UGT2β15 in NSCL/P children with hypodontia (p < 0.005). Microsatellite markers analysis found a significant association between D1S197 (1p36.33-32.3) markers in NSCL/P with hypodontia. In conclusion, the present study has successfully determined the prevalence of dental anomalies and identified the genetic aberrations among NSCL/P. The current study shows a novel finding of copy number loss at 3p14.2 and 4q13.2 that includes FHIT and UGT2β15 which may contribute to the formation of NSCL/P with hypodontia. These results have an immerse prospect in the promising field of individualized preventive oral health care.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Ghazali, Norliana
author_facet	Ghazali, Norliana
author_sort	Ghazali, Norliana
title	Prevalence of dental anomalies and genetic aberrations of nonsyndromic cleft-lip with or without cleft palate patients with hypodontia
title_short	Prevalence of dental anomalies and genetic aberrations of nonsyndromic cleft-lip with or without cleft palate patients with hypodontia
title_full	Prevalence of dental anomalies and genetic aberrations of nonsyndromic cleft-lip with or without cleft palate patients with hypodontia
title_fullStr	Prevalence of dental anomalies and genetic aberrations of nonsyndromic cleft-lip with or without cleft palate patients with hypodontia
title_full_unstemmed	Prevalence of dental anomalies and genetic aberrations of nonsyndromic cleft-lip with or without cleft palate patients with hypodontia
title_sort	prevalence of dental anomalies and genetic aberrations of nonsyndromic cleft-lip with or without cleft palate patients with hypodontia
granting_institution	Universiti Sains Malaysia
granting_department	Pusat Pengajian Sains Pergigian
publishDate	2022
url	http://eprints.usm.my/57762/1/NORLIANA%20BINTI%20GHAZALI-FINAL%20THESIS%20S-SGD000714%28R%29%20-24%20pages.pdf
_version_	1776101209363447808

Prevalence of dental anomalies and genetic aberrations of nonsyndromic cleft-lip with or without cleft palate patients with hypodontia

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