Quantitative evaluation of the molecular marker using droplet digital PCR
Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Korea Genome Organization
2020-03-01
|
| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gi-2020-18-1-e4.pdf |
| _version_ | 1818572532425424896 |
|---|---|
| author | Wonseok Shin Haneul Kim Dong-Yep Oh Dong Hee Kim Kyudong Han |
| author_facet | Wonseok Shin Haneul Kim Dong-Yep Oh Dong Hee Kim Kyudong Han |
| author_sort | Wonseok Shin |
| collection | DOAJ |
| description | Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE–association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers. |
| first_indexed | 2024-12-14T18:58:26Z |
| format | Article |
| id | doaj.art-a300b04bbb6348c59235d5164c0e4fa6 |
| institution | Directory Open Access Journal |
| issn | 2234-0742 |
| language | English |
| last_indexed | 2024-12-14T18:58:26Z |
| publishDate | 2020-03-01 |
| publisher | Korea Genome Organization |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj.art-a300b04bbb6348c59235d5164c0e4fa62022-12-21T22:51:01ZengKorea Genome OrganizationGenomics & Informatics2234-07422020-03-0118110.5808/GI.2020.18.1.e4592Quantitative evaluation of the molecular marker using droplet digital PCRWonseok Shin0Haneul Kim1Dong-Yep Oh2Dong Hee Kim3Kyudong Han4 Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea Livestock Research Institute, Yeongju 36052, Korea Department of Anesthesiology and Pain Management, Dankook University College of Medicine, Cheonan 31116, Korea Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, KoreaTransposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE–association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers.http://genominfo.org/upload/pdf/gi-2020-18-1-e4.pdfdroplet digital pcrhanwoo-specific markerstructure variation |
| spellingShingle | Wonseok Shin Haneul Kim Dong-Yep Oh Dong Hee Kim Kyudong Han Quantitative evaluation of the molecular marker using droplet digital PCR Genomics & Informatics droplet digital pcr hanwoo-specific marker structure variation |
| title | Quantitative evaluation of the molecular marker using droplet digital PCR |
| title_full | Quantitative evaluation of the molecular marker using droplet digital PCR |
| title_fullStr | Quantitative evaluation of the molecular marker using droplet digital PCR |
| title_full_unstemmed | Quantitative evaluation of the molecular marker using droplet digital PCR |
| title_short | Quantitative evaluation of the molecular marker using droplet digital PCR |
| title_sort | quantitative evaluation of the molecular marker using droplet digital pcr |
| topic | droplet digital pcr hanwoo-specific marker structure variation |
| url | http://genominfo.org/upload/pdf/gi-2020-18-1-e4.pdf |
| work_keys_str_mv | AT wonseokshin quantitativeevaluationofthemolecularmarkerusingdropletdigitalpcr AT haneulkim quantitativeevaluationofthemolecularmarkerusingdropletdigitalpcr AT dongyepoh quantitativeevaluationofthemolecularmarkerusingdropletdigitalpcr AT dongheekim quantitativeevaluationofthemolecularmarkerusingdropletdigitalpcr AT kyudonghan quantitativeevaluationofthemolecularmarkerusingdropletdigitalpcr |