Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries
We developed a targeted DNA sequencing method that is capable of detecting a comprehensive panel of DNA mutations including small DNA mutations and large DNA deletions with unknown/flexible boundaries. The method directly identifies the large DNA deletions (Cat-D) without relying on sequencing cover...
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| Format: | Journal Article |
| Language: | English |
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2018
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| Online Access: | https://hdl.handle.net/10356/89522 http://hdl.handle.net/10220/44982 |
| _version_ | 1811682512811851776 |
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| author | Hong, Ru Chandola, Udita Zhang, Li-Feng |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Hong, Ru Chandola, Udita Zhang, Li-Feng |
| author_sort | Hong, Ru |
| collection | NTU |
| description | We developed a targeted DNA sequencing method that is capable of detecting a comprehensive panel of DNA mutations including small DNA mutations and large DNA deletions with unknown/flexible boundaries. The method directly identifies the large DNA deletions (Cat-D) without relying on sequencing coverage to make the genotype calls. We performed the method to simultaneously detect 10 small DNA mutations in β-thalassemia and 2 large genomic deletions in α-thalassemia from 10 genomic DNA samples. Cat-D was performed on 8 genomic DNA samples in duplicate. The 18 Cat-D samples were combined in one sequencing run. In total, 216 genotype calls were made, and 215 of the genotype calls were accurate. No false negative genotype calls were made. One false positive genotype call was made on one target mutation in one experimental duplicate from a genomic DNA sample. In summary, Cat-D can be developed into a robust, high-throughput and cost-effective method suitable for population-based carrier screens. |
| first_indexed | 2024-10-01T03:58:01Z |
| format | Journal Article |
| id | ntu-10356/89522 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T03:58:01Z |
| publishDate | 2018 |
| record_format | dspace |
| spelling | ntu-10356/895222023-02-28T16:56:40Z Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries Hong, Ru Chandola, Udita Zhang, Li-Feng School of Biological Sciences Targeted DNA Sequencing Method DNA Mutations We developed a targeted DNA sequencing method that is capable of detecting a comprehensive panel of DNA mutations including small DNA mutations and large DNA deletions with unknown/flexible boundaries. The method directly identifies the large DNA deletions (Cat-D) without relying on sequencing coverage to make the genotype calls. We performed the method to simultaneously detect 10 small DNA mutations in β-thalassemia and 2 large genomic deletions in α-thalassemia from 10 genomic DNA samples. Cat-D was performed on 8 genomic DNA samples in duplicate. The 18 Cat-D samples were combined in one sequencing run. In total, 216 genotype calls were made, and 215 of the genotype calls were accurate. No false negative genotype calls were made. One false positive genotype call was made on one target mutation in one experimental duplicate from a genomic DNA sample. In summary, Cat-D can be developed into a robust, high-throughput and cost-effective method suitable for population-based carrier screens. NRF (Natl Research Foundation, S’pore) MOE (Min. of Education, S’pore) NMRC (Natl Medical Research Council, S’pore) MOH (Min. of Health, S’pore) Published version 2018-06-06T08:59:46Z 2019-12-06T17:27:34Z 2018-06-06T08:59:46Z 2019-12-06T17:27:34Z 2017 Journal Article Hong, R., Chandola, U.,& Zhang, L.-F. (2017). Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries. Scientific Reports, 7(1), 15701-. 2045-2322 https://hdl.handle.net/10356/89522 http://hdl.handle.net/10220/44982 10.1038/s41598-017-15764-0 en Scientific Reports © 2017 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. 8 p. application/pdf |
| spellingShingle | Targeted DNA Sequencing Method DNA Mutations Hong, Ru Chandola, Udita Zhang, Li-Feng Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries |
| title | Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries |
| title_full | Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries |
| title_fullStr | Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries |
| title_full_unstemmed | Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries |
| title_short | Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries |
| title_sort | cat d a targeted sequencing method for the simultaneous detection of small dna mutations and large dna deletions with flexible boundaries |
| topic | Targeted DNA Sequencing Method DNA Mutations |
| url | https://hdl.handle.net/10356/89522 http://hdl.handle.net/10220/44982 |
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