NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing
Xiaohui Zhang,1– 3 Da Zhen,4 Xuemei Li,1,2,5 Faling Yi,1,2,5 Zhanhao Zhang,1,2,5 Wei Yang,1,2,6 Xuguang Li,1,2,5 Yemeng Sheng,1,2,5 Xiaoli Liu,1,2,5 Tianbo Jin,1,2,5 Yongjun He1,2,5 1Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xia...
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Dove Medical Press
2023-04-01
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| Series: | Pharmacogenomics and Personalized Medicine |
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| Online Access: | https://www.dovepress.com/notch2-atic-mri1-slc6a13-atp13a2-genetic-variations-are-associated-wit-peer-reviewed-fulltext-article-PGPM |
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| author | Zhang X Zhen D Li X Yi F Zhang Z Yang W Li X Sheng Y Liu X Jin T He Y |
| author_facet | Zhang X Zhen D Li X Yi F Zhang Z Yang W Li X Sheng Y Liu X Jin T He Y |
| author_sort | Zhang X |
| collection | DOAJ |
| description | Xiaohui Zhang,1– 3 Da Zhen,4 Xuemei Li,1,2,5 Faling Yi,1,2,5 Zhanhao Zhang,1,2,5 Wei Yang,1,2,6 Xuguang Li,1,2,5 Yemeng Sheng,1,2,5 Xiaoli Liu,1,2,5 Tianbo Jin,1,2,5 Yongjun He1,2,5 1Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China; 2Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China; 3Department of Ultrasound, the Affiliated Hospital of Xizang Minzu University, Xianyang, People’s Republic of China; 4Department of Medical, Tibet Autonomous Region Maternity and Children’s Hospital, Lhasa, People’s Republic of China; 5School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China; 6Department of Emergency, the Affiliated Hospital of Xizang Minzu University, Xianyang, People’s Republic of ChinaCorrespondence: Tianbo Jin; Yongjun He, Xizang Minzu University, #6 East Wenhui Road, Xianyang, Shaanxi, 712082, People’s Republic of China, Email tianbo__jin@163.com; 545139647@qq.comBackground: Ventricular septal defect (VSD) is the most common congenital cardiac abnormality in children and the second most common in adults. This study aimed to explore the potentially causative genes in VSD patients in the Chinese Tibetan population, and to provide a theoretical basis for the genetic mechanism of VSD.Methods: Peripheral venous blood was collected from 20 VSD subjects, and whole-genome DNA was extracted. High-throughput sequencing was performed on qualified DNA samples using whole-exome sequencing (WES) technology. After filtering, detecting, and annotating qualified data, single nucleotide variations (SNVs) and insertion-deletion (InDel) markers were analyzed, and data processing software such as GATK, SIFT, Polyphen, and MutationTaster were used for comparative evaluation and prediction of pathogenic deleterious variants associated with VSD.Results: A total of 4793 variant loci, including 4168 SNVs, 557 InDels and 68 unknown loci and 2566 variant genes were obtained from 20 VSD subjects through bioinformatics analysis. According to the screening of the prediction software and database, the occurrence of VSD was predicted to be associated with five inherited pathogenic gene mutations, all of which were missense mutations, including NOTCH2 (c.1396C >A:p.Gln466Lys), ATIC (c.235C >T:p.Arg79Cys), MRI1 (c.629G >A:p.Arg210Gln), SLC6A13 (c.1138G >A:p.Gly380Arg), ATP13A2 (c.1363C >T:p.Arg455Trp).Conclusion: This study demonstrated that NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 gene variants were potentially associated with VSD in Chinese Tibetan population.Keywords: ventricular septal defect, genes, genetic variation, whole-exome sequencing |
| first_indexed | 2024-04-09T15:35:37Z |
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| id | doaj.art-8b69f2afcc434fb4ba240ceace53e229 |
| institution | Directory Open Access Journal |
| issn | 1178-7066 |
| language | English |
| last_indexed | 2024-04-09T15:35:37Z |
| publishDate | 2023-04-01 |
| publisher | Dove Medical Press |
| record_format | Article |
| series | Pharmacogenomics and Personalized Medicine |
| spelling | doaj.art-8b69f2afcc434fb4ba240ceace53e2292023-04-27T19:02:47ZengDove Medical PressPharmacogenomics and Personalized Medicine1178-70662023-04-01Volume 1638940083363NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome SequencingZhang XZhen DLi XYi FZhang ZYang WLi XSheng YLiu XJin THe YXiaohui Zhang,1– 3 Da Zhen,4 Xuemei Li,1,2,5 Faling Yi,1,2,5 Zhanhao Zhang,1,2,5 Wei Yang,1,2,6 Xuguang Li,1,2,5 Yemeng Sheng,1,2,5 Xiaoli Liu,1,2,5 Tianbo Jin,1,2,5 Yongjun He1,2,5 1Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China; 2Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China; 3Department of Ultrasound, the Affiliated Hospital of Xizang Minzu University, Xianyang, People’s Republic of China; 4Department of Medical, Tibet Autonomous Region Maternity and Children’s Hospital, Lhasa, People’s Republic of China; 5School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China; 6Department of Emergency, the Affiliated Hospital of Xizang Minzu University, Xianyang, People’s Republic of ChinaCorrespondence: Tianbo Jin; Yongjun He, Xizang Minzu University, #6 East Wenhui Road, Xianyang, Shaanxi, 712082, People’s Republic of China, Email tianbo__jin@163.com; 545139647@qq.comBackground: Ventricular septal defect (VSD) is the most common congenital cardiac abnormality in children and the second most common in adults. This study aimed to explore the potentially causative genes in VSD patients in the Chinese Tibetan population, and to provide a theoretical basis for the genetic mechanism of VSD.Methods: Peripheral venous blood was collected from 20 VSD subjects, and whole-genome DNA was extracted. High-throughput sequencing was performed on qualified DNA samples using whole-exome sequencing (WES) technology. After filtering, detecting, and annotating qualified data, single nucleotide variations (SNVs) and insertion-deletion (InDel) markers were analyzed, and data processing software such as GATK, SIFT, Polyphen, and MutationTaster were used for comparative evaluation and prediction of pathogenic deleterious variants associated with VSD.Results: A total of 4793 variant loci, including 4168 SNVs, 557 InDels and 68 unknown loci and 2566 variant genes were obtained from 20 VSD subjects through bioinformatics analysis. According to the screening of the prediction software and database, the occurrence of VSD was predicted to be associated with five inherited pathogenic gene mutations, all of which were missense mutations, including NOTCH2 (c.1396C >A:p.Gln466Lys), ATIC (c.235C >T:p.Arg79Cys), MRI1 (c.629G >A:p.Arg210Gln), SLC6A13 (c.1138G >A:p.Gly380Arg), ATP13A2 (c.1363C >T:p.Arg455Trp).Conclusion: This study demonstrated that NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 gene variants were potentially associated with VSD in Chinese Tibetan population.Keywords: ventricular septal defect, genes, genetic variation, whole-exome sequencinghttps://www.dovepress.com/notch2-atic-mri1-slc6a13-atp13a2-genetic-variations-are-associated-wit-peer-reviewed-fulltext-article-PGPMventricular septal defectgenesgenetic variationwhole-exome sequencing |
| spellingShingle | Zhang X Zhen D Li X Yi F Zhang Z Yang W Li X Sheng Y Liu X Jin T He Y NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing Pharmacogenomics and Personalized Medicine ventricular septal defect genes genetic variation whole-exome sequencing |
| title | NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing |
| title_full | NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing |
| title_fullStr | NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing |
| title_full_unstemmed | NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing |
| title_short | NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing |
| title_sort | notch2 atic mri1 slc6a13 atp13a2 genetic variations are associated with ventricular septal defect in the chinese tibetan population through whole exome sequencing |
| topic | ventricular septal defect genes genetic variation whole-exome sequencing |
| url | https://www.dovepress.com/notch2-atic-mri1-slc6a13-atp13a2-genetic-variations-are-associated-wit-peer-reviewed-fulltext-article-PGPM |
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