Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4
Rs1948 A>G is a single nucleotide variation (SNV) in the 3’‐UTR of CHRNB4. Genotyping the synonymous CHRNB4 rs1948 may be useful in identifying a lung cancer susceptibility gene. The study aimed to develop a simple and easy tetra‐primer amplification refractory mutation system (ARMS PCR) for CHRN...
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| Format: | Article |
| Language: | English |
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Universitas Gadjah Mada, Research Center for Biotechnology
2022
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| Online Access: | https://repository.ugm.ac.id/284122/1/188.pdf |
| _version_ | 1797037801459417088 |
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| author | Dewi, Anggi Laksmita Paramita, Dewi Kartikawati Fachiroh, Jajah |
| author_facet | Dewi, Anggi Laksmita Paramita, Dewi Kartikawati Fachiroh, Jajah |
| author_sort | Dewi, Anggi Laksmita |
| collection | UGM |
| description | Rs1948 A>G is a single nucleotide variation (SNV) in the 3’‐UTR of CHRNB4. Genotyping the synonymous CHRNB4 rs1948 may be useful in identifying a lung cancer susceptibility gene. The study aimed to develop a simple and easy tetra‐primer amplification refractory mutation system (ARMS PCR) for CHRNB4 rs1948. The following steps were taken to optimize tetra‐primer ARMS PCR: 1) determining the gene sequence and position of a single mutation; 2) developing outer and inner primers; 3) amplification of target gene fragments via PCR using an outer primer; 4) genotyping PCR product using Sanger sequencing; 5) determining the optimal annealing temperature and PCR cycle; 6) determining optimal outer and inner primer ratio; and 7) testing the reproducibility of the PCR program and final validation with Sanger sequencing. Genotype (PCR result) was visualized with 3% agarose gel electrophoresis. Optimum condition was determined as annealing temperature of 64.8 ºC and 35 cycles, outer and inner primer ratio of 1:6, and DNA volume of 3 µL. Sanger sequencing confirmed the results of the tetra‐primer ARMS PCR and it was shown that ARMS PCR was able to identify three different variants of CHRNB4 rs1948. |
| first_indexed | 2024-03-14T00:09:31Z |
| format | Article |
| id | oai:generic.eprints.org:284122 |
| institution | Universiti Gadjah Mada |
| language | English |
| last_indexed | 2024-03-14T00:09:31Z |
| publishDate | 2022 |
| publisher | Universitas Gadjah Mada, Research Center for Biotechnology |
| record_format | dspace |
| spelling | oai:generic.eprints.org:2841222023-11-28T07:00:37Z https://repository.ugm.ac.id/284122/ Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4 Dewi, Anggi Laksmita Paramita, Dewi Kartikawati Fachiroh, Jajah Cell Physiology Rs1948 A>G is a single nucleotide variation (SNV) in the 3’‐UTR of CHRNB4. Genotyping the synonymous CHRNB4 rs1948 may be useful in identifying a lung cancer susceptibility gene. The study aimed to develop a simple and easy tetra‐primer amplification refractory mutation system (ARMS PCR) for CHRNB4 rs1948. The following steps were taken to optimize tetra‐primer ARMS PCR: 1) determining the gene sequence and position of a single mutation; 2) developing outer and inner primers; 3) amplification of target gene fragments via PCR using an outer primer; 4) genotyping PCR product using Sanger sequencing; 5) determining the optimal annealing temperature and PCR cycle; 6) determining optimal outer and inner primer ratio; and 7) testing the reproducibility of the PCR program and final validation with Sanger sequencing. Genotype (PCR result) was visualized with 3% agarose gel electrophoresis. Optimum condition was determined as annealing temperature of 64.8 ºC and 35 cycles, outer and inner primer ratio of 1:6, and DNA volume of 3 µL. Sanger sequencing confirmed the results of the tetra‐primer ARMS PCR and it was shown that ARMS PCR was able to identify three different variants of CHRNB4 rs1948. Universitas Gadjah Mada, Research Center for Biotechnology 2022-03 Article PeerReviewed application/pdf en https://repository.ugm.ac.id/284122/1/188.pdf Dewi, Anggi Laksmita and Paramita, Dewi Kartikawati and Fachiroh, Jajah (2022) Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4. Indonesian Journal of Biotechnology, 27 (1). pp. 1-7. ISSN 08538654 https://journal.ugm.ac.id/ijbiotech/article/view/64933 10.22146/ijbiotech.64933 |
| spellingShingle | Cell Physiology Dewi, Anggi Laksmita Paramita, Dewi Kartikawati Fachiroh, Jajah Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4 |
| title | Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4 |
| title_full | Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4 |
| title_fullStr | Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4 |
| title_full_unstemmed | Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4 |
| title_short | Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4 |
| title_sort | tetra primer amplification refractory mutation system arms pcr used to detect 3 utr rs1948 mutation in chrnb4 |
| topic | Cell Physiology |
| url | https://repository.ugm.ac.id/284122/1/188.pdf |
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