A direct sequencing assay for pharmacogenetic testing of thiopurine-intolerant NUDT15 alleles in an Asian population
Abstract Objective The nucleoside diphosphate linked moiety X (Nudix)-Type motif 15 (NUDT15) enzyme is involved in thiopurine metabolism. Genetic variants in the NUDT15 gene result in decreased NUDT15 activity, which in addition to decreased thiopurine S-methyltransferase (TPMT) activity, contribute...
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | BMC Research Notes |
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| Online Access: | https://doi.org/10.1186/s13104-021-05821-3 |
| _version_ | 1811289210002341888 |
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| author | Kok-Siong Poon Izz Irfan B. Imran Silvester Kheng-Han Chew Patrice Tan Karen Mei-Ling Tan |
| author_facet | Kok-Siong Poon Izz Irfan B. Imran Silvester Kheng-Han Chew Patrice Tan Karen Mei-Ling Tan |
| author_sort | Kok-Siong Poon |
| collection | DOAJ |
| description | Abstract Objective The nucleoside diphosphate linked moiety X (Nudix)-Type motif 15 (NUDT15) enzyme is involved in thiopurine metabolism. Genetic variants in the NUDT15 gene result in decreased NUDT15 activity, which in addition to decreased thiopurine S-methyltransferase (TPMT) activity, contributes to thiopurine toxicity. Current standard approaches of NUDT15 genetic analysis have mainly been targeting several common variants. We aimed to develop a clinical-grade DNA-based assay for genetic analysis of the NUDT15 gene using Sanger di-deoxy sequencing. Results Sanger sequencing results were fully concordant with the expected NUDT15 genotype in all 17 cell line samples with known NUDT15 variants (accuracy = 100%; 95% CI 80.49 to 100.00%). Precision studies showed 100% intra-run repeatability and 100% inter-run reproducibility, respectively. Genetic analysis of the NUDT15 gene was performed for 80 patients of Asian ethnicity with wildtype TPMT. 76% (N = 61) of the studied individuals had NUDT15 *1/*1 diplotype. 25% (N = 14) of Chinese and 36% (N = 5) of Malays were found to carry at least 1 non-functional NUDT15 allele. Our study confirmed a high frequency of NUDT15 c.415C>T and c.55_56insGAGTCG variants in the Chinese and Malay ethnic groups in Singapore, highlighting the importance of determining NUDT15 genotype prior to thiopurine dosing. |
| first_indexed | 2024-04-13T03:50:54Z |
| format | Article |
| id | doaj.art-208e61217ede40d2b6b0dcb24f92ece9 |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-04-13T03:50:54Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-208e61217ede40d2b6b0dcb24f92ece92022-12-22T03:03:49ZengBMCBMC Research Notes1756-05002022-04-011511610.1186/s13104-021-05821-3A direct sequencing assay for pharmacogenetic testing of thiopurine-intolerant NUDT15 alleles in an Asian populationKok-Siong Poon0Izz Irfan B. Imran1Silvester Kheng-Han Chew2Patrice Tan3Karen Mei-Ling Tan4Department of Laboratory Medicine, National University Hospital, NUH Main BuildingSchool of Life Sciences and Chemical Technology, Ngee Ann PolytechnicSchool of Life Sciences and Chemical Technology, Ngee Ann PolytechnicDepartment of Laboratory Medicine, National University Hospital, NUH Main BuildingDepartment of Laboratory Medicine, National University Hospital, NUH Main BuildingAbstract Objective The nucleoside diphosphate linked moiety X (Nudix)-Type motif 15 (NUDT15) enzyme is involved in thiopurine metabolism. Genetic variants in the NUDT15 gene result in decreased NUDT15 activity, which in addition to decreased thiopurine S-methyltransferase (TPMT) activity, contributes to thiopurine toxicity. Current standard approaches of NUDT15 genetic analysis have mainly been targeting several common variants. We aimed to develop a clinical-grade DNA-based assay for genetic analysis of the NUDT15 gene using Sanger di-deoxy sequencing. Results Sanger sequencing results were fully concordant with the expected NUDT15 genotype in all 17 cell line samples with known NUDT15 variants (accuracy = 100%; 95% CI 80.49 to 100.00%). Precision studies showed 100% intra-run repeatability and 100% inter-run reproducibility, respectively. Genetic analysis of the NUDT15 gene was performed for 80 patients of Asian ethnicity with wildtype TPMT. 76% (N = 61) of the studied individuals had NUDT15 *1/*1 diplotype. 25% (N = 14) of Chinese and 36% (N = 5) of Malays were found to carry at least 1 non-functional NUDT15 allele. Our study confirmed a high frequency of NUDT15 c.415C>T and c.55_56insGAGTCG variants in the Chinese and Malay ethnic groups in Singapore, highlighting the importance of determining NUDT15 genotype prior to thiopurine dosing.https://doi.org/10.1186/s13104-021-05821-3NUDT15ThiopurinePharmacogeneticsDirect sequencing |
| spellingShingle | Kok-Siong Poon Izz Irfan B. Imran Silvester Kheng-Han Chew Patrice Tan Karen Mei-Ling Tan A direct sequencing assay for pharmacogenetic testing of thiopurine-intolerant NUDT15 alleles in an Asian population BMC Research Notes NUDT15 Thiopurine Pharmacogenetics Direct sequencing |
| title | A direct sequencing assay for pharmacogenetic testing of thiopurine-intolerant NUDT15 alleles in an Asian population |
| title_full | A direct sequencing assay for pharmacogenetic testing of thiopurine-intolerant NUDT15 alleles in an Asian population |
| title_fullStr | A direct sequencing assay for pharmacogenetic testing of thiopurine-intolerant NUDT15 alleles in an Asian population |
| title_full_unstemmed | A direct sequencing assay for pharmacogenetic testing of thiopurine-intolerant NUDT15 alleles in an Asian population |
| title_short | A direct sequencing assay for pharmacogenetic testing of thiopurine-intolerant NUDT15 alleles in an Asian population |
| title_sort | direct sequencing assay for pharmacogenetic testing of thiopurine intolerant nudt15 alleles in an asian population |
| topic | NUDT15 Thiopurine Pharmacogenetics Direct sequencing |
| url | https://doi.org/10.1186/s13104-021-05821-3 |
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