Identification of Novel Genomic Variations in Susceptibility to Nonsyndromic Cleft Lip and Palate Patients
Background: Nonsyndromic cleft lip with or without palate (NSCL/P) is a multifactorial and common birth malformation caused by genetic and environmental factors, as well as by teratogens. Genome-wide association studies found genetic variations with modulatory effects of NSCL/P formation in Chinese...
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MDPI AG
2021-12-01
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| Series: | Pediatric Reports |
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| Online Access: | https://www.mdpi.com/2036-7503/13/4/77 |
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| author | Kapil Kumar Avasthi Srinivasan Muthuswamy Ambreen Asim Amit Agarwal Sarita Agarwal |
| author_facet | Kapil Kumar Avasthi Srinivasan Muthuswamy Ambreen Asim Amit Agarwal Sarita Agarwal |
| author_sort | Kapil Kumar Avasthi |
| collection | DOAJ |
| description | Background: Nonsyndromic cleft lip with or without palate (NSCL/P) is a multifactorial and common birth malformation caused by genetic and environmental factors, as well as by teratogens. Genome-wide association studies found genetic variations with modulatory effects of NSCL/P formation in Chinese and Iranian populations. We aimed to identify the susceptibility of single-nucleotide polymorphisms (SNPs) to nonsyndromic cleft lip with or without palate in the Indian population. Material and Methods: The present study was conducted on NSCL/P cases and controls. Genomic DNA was extracted from peripheral blood and Axiom- Precision Medicine Research Array (PMRA) was performed. The Axiom-PMRA covers 902,527 markers and several thousand novel risk variants. Quality control-passed samples were included for candidate genetic variation identification, gene functional enrichment, and pathway and network analysis. Results: The genome-wide association study identified fourteen novel candidate gene SNPs that showed the most significant association with the risk of NSCL/P, and eight were predicted to have regulatory sequences. Conclusion: The GWAS study showed novel candidate genetic variations in NSCL/P formations. These findings contribute to the understanding of genetic predisposition to nonsyndromic cleft lip with or without palate. |
| first_indexed | 2024-03-10T03:21:36Z |
| format | Article |
| id | doaj.art-8edc1be1c7e94c9b96bad2face94f9c3 |
| institution | Directory Open Access Journal |
| issn | 2036-7503 |
| language | English |
| last_indexed | 2024-03-10T03:21:36Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pediatric Reports |
| spelling | doaj.art-8edc1be1c7e94c9b96bad2face94f9c32023-11-23T10:02:24ZengMDPI AGPediatric Reports2036-75032021-12-0113465065710.3390/pediatric13040077Identification of Novel Genomic Variations in Susceptibility to Nonsyndromic Cleft Lip and Palate PatientsKapil Kumar Avasthi0Srinivasan Muthuswamy1Ambreen Asim2Amit Agarwal3Sarita Agarwal4Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, IndiaDepartment of Life Sciences, National Institute of Technology, Rourkela 769001, Odisha, IndiaDepartment of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, IndiaDepartment of Burn and Plastic Surgery, Vivekananda Polyclinic and Institute of Medical Sciences, Lucknow 226007, IndiaDepartment of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, IndiaBackground: Nonsyndromic cleft lip with or without palate (NSCL/P) is a multifactorial and common birth malformation caused by genetic and environmental factors, as well as by teratogens. Genome-wide association studies found genetic variations with modulatory effects of NSCL/P formation in Chinese and Iranian populations. We aimed to identify the susceptibility of single-nucleotide polymorphisms (SNPs) to nonsyndromic cleft lip with or without palate in the Indian population. Material and Methods: The present study was conducted on NSCL/P cases and controls. Genomic DNA was extracted from peripheral blood and Axiom- Precision Medicine Research Array (PMRA) was performed. The Axiom-PMRA covers 902,527 markers and several thousand novel risk variants. Quality control-passed samples were included for candidate genetic variation identification, gene functional enrichment, and pathway and network analysis. Results: The genome-wide association study identified fourteen novel candidate gene SNPs that showed the most significant association with the risk of NSCL/P, and eight were predicted to have regulatory sequences. Conclusion: The GWAS study showed novel candidate genetic variations in NSCL/P formations. These findings contribute to the understanding of genetic predisposition to nonsyndromic cleft lip with or without palate.https://www.mdpi.com/2036-7503/13/4/77NSCL/Pnonsyndromic cleft lip and/or palateCLPPMRAgenome-wide associationSNPs |
| spellingShingle | Kapil Kumar Avasthi Srinivasan Muthuswamy Ambreen Asim Amit Agarwal Sarita Agarwal Identification of Novel Genomic Variations in Susceptibility to Nonsyndromic Cleft Lip and Palate Patients Pediatric Reports NSCL/P nonsyndromic cleft lip and/or palate CLP PMRA genome-wide association SNPs |
| title | Identification of Novel Genomic Variations in Susceptibility to Nonsyndromic Cleft Lip and Palate Patients |
| title_full | Identification of Novel Genomic Variations in Susceptibility to Nonsyndromic Cleft Lip and Palate Patients |
| title_fullStr | Identification of Novel Genomic Variations in Susceptibility to Nonsyndromic Cleft Lip and Palate Patients |
| title_full_unstemmed | Identification of Novel Genomic Variations in Susceptibility to Nonsyndromic Cleft Lip and Palate Patients |
| title_short | Identification of Novel Genomic Variations in Susceptibility to Nonsyndromic Cleft Lip and Palate Patients |
| title_sort | identification of novel genomic variations in susceptibility to nonsyndromic cleft lip and palate patients |
| topic | NSCL/P nonsyndromic cleft lip and/or palate CLP PMRA genome-wide association SNPs |
| url | https://www.mdpi.com/2036-7503/13/4/77 |
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