Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia
Abstract Background Nonsyndromic cleft lip and/or without cleft palate (NSCL/P) with or without hypodontia is a common developmental aberration in humans and animals. This study aimed to identify the loss of heterozygosity (LOH) involved in hypodontia and NSCL/P pathogenesis. Methods This is a cross...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-11-01
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| Series: | BMC Oral Health |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12903-023-03464-3 |
| _version_ | 1797413784073011200 |
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| author | Norliana Ghazali Normastura Abd Rahman Thirumulu Ponnuraj Kannan Azlina Ahmad Sarina Sulong |
| author_facet | Norliana Ghazali Normastura Abd Rahman Thirumulu Ponnuraj Kannan Azlina Ahmad Sarina Sulong |
| author_sort | Norliana Ghazali |
| collection | DOAJ |
| description | Abstract Background Nonsyndromic cleft lip and/or without cleft palate (NSCL/P) with or without hypodontia is a common developmental aberration in humans and animals. This study aimed to identify the loss of heterozygosity (LOH) involved in hypodontia and NSCL/P pathogenesis. Methods This is a cross-sectional study that conducted genome-wide copy number analysis using CytoScan 750K array on salivary samples from Malay subjects with NSCL/P with or without hypodontia aged 7–13 years. To confirm the significant results, simple logistic regression was employed to conduct statistical data analysis using SPSS software. Results The results indicated the most common recurrent copy neutral LOH (cnLOH) observed at 1p33-1p32.3, 1q32.2-1q42.13 and 6p12.1-6p11.1 loci in 8 (13%), 4 (7%), and 3 (5%) of the NSCL/P subjects, respectively. The cnLOHs at 1p33-1p32.3 (D1S197), 1q32.2-1q42.13 (D1S160), and 6p12.1-6p11.1 (D1S1661) were identified observed in NSCL/P and noncleft children using microsatellite analysis markers as a validation analysis. The regions affected by the cnLOHs at 1p33-1p32.3, 1q32.2-1q42.13, and 6p12.1-6p11.1 loci contained selected genes, namely FAF1, WNT3A and BMP5, respectively. There was a significant association between the D1S197 (1p33-32.3) markers containing the FAF1 gene among NSCL/P subjects with or without hypodontia compared with the noncleft subjects (p-value = 0.023). Conclusion The results supported the finding that the genetic aberration on 1p33-32.3 significantly contributed to the development of NSCL/P with or without hypodontia. These results have an exciting prospect in the promising field of individualized preventive oral health care. |
| first_indexed | 2024-03-09T05:23:41Z |
| format | Article |
| id | doaj.art-d00848ff469b406e8d8a7583c18f6260 |
| institution | Directory Open Access Journal |
| issn | 1472-6831 |
| language | English |
| last_indexed | 2024-03-09T05:23:41Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
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| series | BMC Oral Health |
| spelling | doaj.art-d00848ff469b406e8d8a7583c18f62602023-12-03T12:38:45ZengBMCBMC Oral Health1472-68312023-11-0123111310.1186/s12903-023-03464-3Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontiaNorliana Ghazali0Normastura Abd Rahman1Thirumulu Ponnuraj Kannan2Azlina Ahmad3Sarina Sulong4School of Dental Sciences, Universiti Sains Malaysia (USM)School of Dental Sciences, Universiti Sains Malaysia (USM)School of Dental Sciences, Universiti Sains Malaysia (USM)School of Dental Sciences, Universiti Sains Malaysia (USM)Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia (USM)Abstract Background Nonsyndromic cleft lip and/or without cleft palate (NSCL/P) with or without hypodontia is a common developmental aberration in humans and animals. This study aimed to identify the loss of heterozygosity (LOH) involved in hypodontia and NSCL/P pathogenesis. Methods This is a cross-sectional study that conducted genome-wide copy number analysis using CytoScan 750K array on salivary samples from Malay subjects with NSCL/P with or without hypodontia aged 7–13 years. To confirm the significant results, simple logistic regression was employed to conduct statistical data analysis using SPSS software. Results The results indicated the most common recurrent copy neutral LOH (cnLOH) observed at 1p33-1p32.3, 1q32.2-1q42.13 and 6p12.1-6p11.1 loci in 8 (13%), 4 (7%), and 3 (5%) of the NSCL/P subjects, respectively. The cnLOHs at 1p33-1p32.3 (D1S197), 1q32.2-1q42.13 (D1S160), and 6p12.1-6p11.1 (D1S1661) were identified observed in NSCL/P and noncleft children using microsatellite analysis markers as a validation analysis. The regions affected by the cnLOHs at 1p33-1p32.3, 1q32.2-1q42.13, and 6p12.1-6p11.1 loci contained selected genes, namely FAF1, WNT3A and BMP5, respectively. There was a significant association between the D1S197 (1p33-32.3) markers containing the FAF1 gene among NSCL/P subjects with or without hypodontia compared with the noncleft subjects (p-value = 0.023). Conclusion The results supported the finding that the genetic aberration on 1p33-32.3 significantly contributed to the development of NSCL/P with or without hypodontia. These results have an exciting prospect in the promising field of individualized preventive oral health care.https://doi.org/10.1186/s12903-023-03464-3Cleft lipCleft palateTooth lossLoss of heterozygosityOligonucleotide array sequence analysisMicrosatellite repeats |
| spellingShingle | Norliana Ghazali Normastura Abd Rahman Thirumulu Ponnuraj Kannan Azlina Ahmad Sarina Sulong Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia BMC Oral Health Cleft lip Cleft palate Tooth loss Loss of heterozygosity Oligonucleotide array sequence analysis Microsatellite repeats |
| title | Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia |
| title_full | Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia |
| title_fullStr | Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia |
| title_full_unstemmed | Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia |
| title_short | Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia |
| title_sort | identification of copy neutral loss of heterozygosity on chromosomes 1p 1q and 6p among nonsyndromic cleft lip and or without cleft palate with hypodontia |
| topic | Cleft lip Cleft palate Tooth loss Loss of heterozygosity Oligonucleotide array sequence analysis Microsatellite repeats |
| url | https://doi.org/10.1186/s12903-023-03464-3 |
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