Identification of a novel SNP mutation causing drop-out alleles in a paternity test using combined nest and touch-down PCR with Sanger sequencing
Background Short tandem repeat (STR) markers are widely used in forensic DNA analysis due to their ability to provide automated and standardised typing. However, incorrect STR typing can have a significant impact on forensic outcomes.Aim In this study, we detected drop-out alleles at the SE33 locus...
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Taylor & Francis Group
2024-12-01
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| Series: | Annals of Human Biology |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/03014460.2024.2418591 |
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| author | Hongbo Wang Botong Shi Liang Guo Yingnan Zou Bo Liu Jun Yao Baojie Wang Zhengdong Wang Xin Li Gang Mu Fu Ren |
| author_facet | Hongbo Wang Botong Shi Liang Guo Yingnan Zou Bo Liu Jun Yao Baojie Wang Zhengdong Wang Xin Li Gang Mu Fu Ren |
| author_sort | Hongbo Wang |
| collection | DOAJ |
| description | Background Short tandem repeat (STR) markers are widely used in forensic DNA analysis due to their ability to provide automated and standardised typing. However, incorrect STR typing can have a significant impact on forensic outcomes.Aim In this study, we detected drop-out alleles at the SE33 locus in a putative father-son pair using the Microreader™ 28 A ID System. This result could lead to a false conclusion of non-paternity.Subjects and methods To investigate the cause of the drop-out alleles, we developed a nest and touch-down PCR program for Sanger sequencing of the SE33 locus. Subsequently, we investigated the mutation frequency in 300 unrelated individuals and reviewed the results of 429 paternity tests.Results The results showed that the frequency of the G > T mutation at this locus was less than 0.01, which is a novel and rare mutation. Our analysis revealed a novel G > T mutation in the primer-binding region of both samples, which was a rare single-nucleotide mutation site in the Chinese population. This variation was found to be responsible for the drop-out alleles observed in the samples.Conclusion Our findings have important implications for optimising primer design and constructing DNA databases for forensic analysis. |
| format | Article |
| id | doaj-art-d751e67156de49028ecaaa43f8871363 |
| institution | OA Journals |
| issn | 0301-4460 1464-5033 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Annals of Human Biology |
| spelling | doaj-art-d751e67156de49028ecaaa43f88713632025-08-20T01:57:20ZengTaylor & Francis GroupAnnals of Human Biology0301-44601464-50332024-12-0151110.1080/03014460.2024.2418591Identification of a novel SNP mutation causing drop-out alleles in a paternity test using combined nest and touch-down PCR with Sanger sequencingHongbo Wang0Botong Shi1Liang Guo2Yingnan Zou3Bo Liu4Jun Yao5Baojie Wang6Zhengdong Wang7Xin Li8Gang Mu9Fu Ren10Department of Human Anatomy, School of Basic Medicine, Shenyang Medical College, Shenyang, P.R. ChinaCentral Hospital of Shenyang Sujiatun, Shenyang, P.R. ChinaCentral Hospital of Shenyang Sujiatun, Shenyang, P.R. ChinaCentral Hospital of Shenyang Sujiatun, Shenyang, P.R. ChinaCentral Hospital of Shenyang Sujiatun, Shenyang, P.R. ChinaSchool of Forensic Medicine, China Medical University, Shenyang, P.R. ChinaSchool of Forensic Medicine, China Medical University, Shenyang, P.R. ChinaDepartment of Human Anatomy, School of Basic Medicine, Shenyang Medical College, Shenyang, P.R. ChinaSchool of Stomatology, Shenyang Medical College, Shenyang, P.R. ChinaThe Fourth People’s Hospital of Shenyang, Shenyang, P.R. ChinaDepartment of Human Anatomy, School of Basic Medicine, Shenyang Medical College, Shenyang, P.R. ChinaBackground Short tandem repeat (STR) markers are widely used in forensic DNA analysis due to their ability to provide automated and standardised typing. However, incorrect STR typing can have a significant impact on forensic outcomes.Aim In this study, we detected drop-out alleles at the SE33 locus in a putative father-son pair using the Microreader™ 28 A ID System. This result could lead to a false conclusion of non-paternity.Subjects and methods To investigate the cause of the drop-out alleles, we developed a nest and touch-down PCR program for Sanger sequencing of the SE33 locus. Subsequently, we investigated the mutation frequency in 300 unrelated individuals and reviewed the results of 429 paternity tests.Results The results showed that the frequency of the G > T mutation at this locus was less than 0.01, which is a novel and rare mutation. Our analysis revealed a novel G > T mutation in the primer-binding region of both samples, which was a rare single-nucleotide mutation site in the Chinese population. This variation was found to be responsible for the drop-out alleles observed in the samples.Conclusion Our findings have important implications for optimising primer design and constructing DNA databases for forensic analysis.https://www.tandfonline.com/doi/10.1080/03014460.2024.2418591Forensic geneticsSE33 locusSNP mutationDrop-out alleles |
| spellingShingle | Hongbo Wang Botong Shi Liang Guo Yingnan Zou Bo Liu Jun Yao Baojie Wang Zhengdong Wang Xin Li Gang Mu Fu Ren Identification of a novel SNP mutation causing drop-out alleles in a paternity test using combined nest and touch-down PCR with Sanger sequencing Annals of Human Biology Forensic genetics SE33 locus SNP mutation Drop-out alleles |
| title | Identification of a novel SNP mutation causing drop-out alleles in a paternity test using combined nest and touch-down PCR with Sanger sequencing |
| title_full | Identification of a novel SNP mutation causing drop-out alleles in a paternity test using combined nest and touch-down PCR with Sanger sequencing |
| title_fullStr | Identification of a novel SNP mutation causing drop-out alleles in a paternity test using combined nest and touch-down PCR with Sanger sequencing |
| title_full_unstemmed | Identification of a novel SNP mutation causing drop-out alleles in a paternity test using combined nest and touch-down PCR with Sanger sequencing |
| title_short | Identification of a novel SNP mutation causing drop-out alleles in a paternity test using combined nest and touch-down PCR with Sanger sequencing |
| title_sort | identification of a novel snp mutation causing drop out alleles in a paternity test using combined nest and touch down pcr with sanger sequencing |
| topic | Forensic genetics SE33 locus SNP mutation Drop-out alleles |
| url | https://www.tandfonline.com/doi/10.1080/03014460.2024.2418591 |
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