{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T09:00:34Z","timestamp":1765184434427,"version":"3.46.0"},"reference-count":29,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T00:00:00Z","timestamp":1765152000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001411","name":"Indian Council of Medical Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001411","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Pharmacol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Thiopurines such as 6-mercaptopurine (6-MP) are central to maintenance therapy for pediatric acute lymphoblastic leukemia (ALL), yet their narrow therapeutic index frequently causes dose-limiting myelosuppression in genetically susceptible patients. Variants in\n                      <jats:italic>NUDT15<\/jats:italic>\n                      and\n                      <jats:italic>TPMT<\/jats:italic>\n                      are major pharmacogenetic determinants of thiopurine intolerance, particularly in Asian populations. Despite CPIC recommendations for pre-emptive genotyping, routine pharmacogenetic testing is seldom implemented in India due to high costs and limited access to sequencing-based platforms.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Aim<\/jats:title>\n                    <jats:p>\n                      To develop, standardize, and validate a rapid, low-cost tetra-primer ARMS-PCR assay for simultaneous detection of the most clinically relevant variants\u2014\n                      <jats:italic>NUDT15<\/jats:italic>\n                      c.415C&amp;gt;T and\n                      <jats:italic>TPMT 3C<\/jats:italic>\n                      (c.719A&amp;gt;G)\u2014prioritized through comprehensive\n                      <jats:italic>in silico<\/jats:italic>\n                      analysis.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Missense SNPs in\n                      <jats:italic>NUDT15<\/jats:italic>\n                      and\n                      <jats:italic>TPMT<\/jats:italic>\n                      were screened using SIFT, PolyPhen-2, PROVEAN, Meta-SNP, and SNPs&amp;amp;GO to identify high-impact variants. A multiplex ARMS-PCR assay was optimized and applied to 61 pediatric ALL samples. Genotyping results were validated by Sanger sequencing. Clinical correlations included hematologic toxicity, 6-MP dose intensity, and blast-percentage dynamics.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      In-silico prioritization consistently identified\n                      <jats:italic>NUDT15<\/jats:italic>\n                      c.415C&amp;gt;T and\n                      <jats:italic>TPMT 3C<\/jats:italic>\n                      as the most deleterious and clinically actionable variants. Among 60 successfully genotyped patients,\n                      <jats:italic>NUDT15<\/jats:italic>\n                      variants were detected in 16.7% (9\u00a0C\/T and 1\u00a0T\/T), while\n                      <jats:italic>TPMT 3C<\/jats:italic>\n                      heterozygosity was observed in 3.3%; no double-mutants were identified. ARMS-PCR showed 98.4% overall diagnostic accuracy relative to Sanger sequencing (sensitivity 90.9%, specificity 100%).\n                      <jats:italic>NUDT15<\/jats:italic>\n                      -variant carriers exhibited significantly reduced 6-MP dose intensity (median 0.50 vs. 0.79; p &amp;lt; 0.0001). Blast-percentage analysis demonstrated marked reduction from baseline to follow-up (median 75%\u201315%; p = 0.0001), consistent with expected treatment response.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      The validated ARMS-PCR assay provides a reliable, rapid, and cost-effective platform for simultaneous\n                      <jats:italic>NUDT15<\/jats:italic>\n                      and\n                      <jats:italic>TPMT 3C<\/jats:italic>\n                      genotyping, demonstrating strong concordance with sequencing and clear clinical relevance. Its affordability and minimal infrastructure requirements make it suitable for integration into routine pre-treatment workflows in India, enabling genotype-guided thiopurine dosing and reducing the risk of treatment-related toxicity. This assay supports a scalable path toward equitable implementation of pharmacogenomics in resource-limited pediatric oncology settings.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fphar.2025.1714797","type":"journal-article","created":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T08:57:31Z","timestamp":1765184251000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Validation of diagnostic screening test for pharmacogenomic targets for thiopurine drugs in indian pediatric acute lymphoblastic leukemia patients"],"prefix":"10.3389","volume":"16","author":[{"given":"Gratial Theres","family":"Joseph","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandeep Kumar","family":"Swain","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tejas","family":"Somwanshi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aarishi","family":"Singh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manpreet","family":"Kaur","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raj","family":"Kamal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Himanshu","family":"Dhanda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Prashant","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Upasana","family":"Kaushik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Baseer","family":"Noor","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saurabh","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pranay","family":"Tanwar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sufian","family":"Zaheer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sumita","family":"Chaudhry","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Prashant","family":"Prabhakar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amitabh","family":"Singh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bhavika","family":"Rishi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aroonima","family":"Misra","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,12,8]]},"reference":[{"key":"B32","doi-asserted-by":"publisher","DOI":"10.38079\/igusabder.1196511","article-title":"Determination of deleterious snps in nudt15 generelated to acute lymphoblastic leukemia by using bioinformatics tools deniz A\u015flar \u00d6ner","author":"A\u015flar \u00d6ner","year":"2024","journal-title":"\u0130stanbul Geli\u015fim \u00dcniversitesi Sa\u011fl\u0131k Bilimleri Dergisi"},{"key":"B29","doi-asserted-by":"publisher","first-page":"1785","DOI":"10.1182\/blood.2021012328","article-title":"Remission, treatment failure, and relapse in pediatric ALL: an international consensus of the Ponte-di-Legno Consortium","volume":"139","author":"Buchmann","year":"2022","journal-title":"Blood"},{"key":"B1","doi-asserted-by":"publisher","first-page":"1352","DOI":"10.1111\/cts.13539","article-title":"Comparison of variants in TPMT and NUDT15 between sequencing and genotyping methods in a multistate pediatric institution","volume":"16","author":"Cook","year":"2023","journal-title":"Clin. 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