Smart approach for cost-effective genotyping of single nucleotide polymorphisms
Single Nucleotide Polymorphisms (SNPs) are in prime focus of genomic studies for their probable roles in diagnostics and prognosis of diseases and forensic science. SNaPshot/minisequencing reaction based genotyping of targeted SNPs is a method of choice due to its fast and reliable detection assay....
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| Format: | Article |
| Language: | English |
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Elsevier
2021-04-01
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| Series: | Kuwait Journal of Science |
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| Online Access: | https://journalskuwait.org/kjs/index.php/KJS/article/view/8957 |
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| author | Muhammad Usman Ghani Muhammad Farooq Sabar Muhammad Akram |
| author_facet | Muhammad Usman Ghani Muhammad Farooq Sabar Muhammad Akram |
| author_sort | Muhammad Usman Ghani |
| collection | DOAJ |
| description | Single Nucleotide Polymorphisms (SNPs) are in prime focus of genomic studies for their probable roles in diagnostics and prognosis of diseases and forensic science. SNaPshot/minisequencing reaction based genotyping of targeted SNPs is a method of choice due to its fast and reliable detection assay. Here we described smart modifications in minisequencing reaction to make it cost effective assay for the detection of 15 SNPs in a single assay. The target SNPs were amplified in a multiplex PCR from genomic DNA and these multiplex PCR amplicons were utilized as a template in modified SNaPshot reaction for SNPs identification. Modified protocol was assessed for reproducibility on more than 50 human DNA samples and it was observed that this modified method is at least five times more productive than original protocol recommended by the manufacturer. The current smart modifications in SNaPshot reaction were successfully optimized for asthma susceptible SNPs. However, these can be applied for cost effective genotyping of any type of genomic Single Nucleotide Polymorphisms. |
| format | Article |
| id | doaj-art-1cb3fe9ab7da425cb861d9455fe16c46 |
| institution | OA Journals |
| issn | 2307-4108 2307-4116 |
| language | English |
| publishDate | 2021-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Kuwait Journal of Science |
| spelling | doaj-art-1cb3fe9ab7da425cb861d9455fe16c462025-08-20T02:30:28ZengElsevierKuwait Journal of Science2307-41082307-41162021-04-0148210.48129/kjs.v48i2.8957Smart approach for cost-effective genotyping of single nucleotide polymorphismsMuhammad Usman Ghani0Muhammad Farooq Sabar1Muhammad Akram2University of the PunjabUniversity of the PunjabUniversity of the PunjabSingle Nucleotide Polymorphisms (SNPs) are in prime focus of genomic studies for their probable roles in diagnostics and prognosis of diseases and forensic science. SNaPshot/minisequencing reaction based genotyping of targeted SNPs is a method of choice due to its fast and reliable detection assay. Here we described smart modifications in minisequencing reaction to make it cost effective assay for the detection of 15 SNPs in a single assay. The target SNPs were amplified in a multiplex PCR from genomic DNA and these multiplex PCR amplicons were utilized as a template in modified SNaPshot reaction for SNPs identification. Modified protocol was assessed for reproducibility on more than 50 human DNA samples and it was observed that this modified method is at least five times more productive than original protocol recommended by the manufacturer. The current smart modifications in SNaPshot reaction were successfully optimized for asthma susceptible SNPs. However, these can be applied for cost effective genotyping of any type of genomic Single Nucleotide Polymorphisms.https://journalskuwait.org/kjs/index.php/KJS/article/view/8957AssayGenotypingSingle Nucleotide PolymorphismSmart ApproachSNaPshot |
| spellingShingle | Muhammad Usman Ghani Muhammad Farooq Sabar Muhammad Akram Smart approach for cost-effective genotyping of single nucleotide polymorphisms Kuwait Journal of Science Assay Genotyping Single Nucleotide Polymorphism Smart Approach SNaPshot |
| title | Smart approach for cost-effective genotyping of single nucleotide polymorphisms |
| title_full | Smart approach for cost-effective genotyping of single nucleotide polymorphisms |
| title_fullStr | Smart approach for cost-effective genotyping of single nucleotide polymorphisms |
| title_full_unstemmed | Smart approach for cost-effective genotyping of single nucleotide polymorphisms |
| title_short | Smart approach for cost-effective genotyping of single nucleotide polymorphisms |
| title_sort | smart approach for cost effective genotyping of single nucleotide polymorphisms |
| topic | Assay Genotyping Single Nucleotide Polymorphism Smart Approach SNaPshot |
| url | https://journalskuwait.org/kjs/index.php/KJS/article/view/8957 |
| work_keys_str_mv | AT muhammadusmanghani smartapproachforcosteffectivegenotypingofsinglenucleotidepolymorphisms AT muhammadfarooqsabar smartapproachforcosteffectivegenotypingofsinglenucleotidepolymorphisms AT muhammadakram smartapproachforcosteffectivegenotypingofsinglenucleotidepolymorphisms |