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To explore the reason for this difference we undertook a detailed technical comparison of the commonly used Europe Against Cancer (EAC)<jats:italic>BCR::ABL1<\/jats:italic>reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assay in European Treatment and Outcome Study (EUTOS) reference laboratories (<jats:italic>n<\/jats:italic>\u2009=\u200910). We found the amplification ratio of the e13a2 amplicon was 38% greater than e14a2 (<jats:italic>p<\/jats:italic>\u2009=\u20090.015), and the amplification efficiency was 2% greater (<jats:italic>P<\/jats:italic>\u2009=\u20090.17). This subtle difference led to measurable transcript-type dependent variation in estimates of residual disease which could be corrected by (i) taking the qPCR amplification efficiency into account, (ii) using alternative RT-qPCR approaches or (iii) droplet digital PCR (ddPCR), a technique which is relatively insensitive to differences in amplification kinetics. In CML patients, higher levels of<jats:italic>BCR<\/jats:italic>::<jats:italic>ABL1\/GUSB<\/jats:italic>were identified at diagnosis for patients expressing e13a2 (<jats:italic>n<\/jats:italic>\u2009=\u200967) compared to e14a2 (<jats:italic>n<\/jats:italic>\u2009=\u200978) when analysed by RT-qPCR (<jats:italic>P<\/jats:italic>\u2009=\u20090.0005) but not ddPCR (<jats:italic>P<\/jats:italic>\u2009=\u20090.5). These data indicate that widely used RT-qPCR assays result in subtly different estimates of disease depending on<jats:italic>BCR::ABL1<\/jats:italic>transcript type; these differences are small but may need to be considered for optimal patient management.<\/jats:p>","DOI":"10.1038\/s41375-022-01612-2","type":"journal-article","created":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T13:04:20Z","timestamp":1654693460000},"page":"1879-1886","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Impact of BCR::ABL1 transcript type on RT-qPCR amplification performance and molecular response to therapy"],"prefix":"10.1038","volume":"36","author":[{"given":"Matthew","family":"Salmon","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen 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Leukemia. 2020;34:1052\u201361.","journal-title":"Leukemia."}],"container-title":["Leukemia"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41375-022-01612-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41375-022-01612-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41375-022-01612-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,26]],"date-time":"2024-09-26T17:02:49Z","timestamp":1727370169000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41375-022-01612-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,8]]},"references-count":40,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2022,7]]}},"alternative-id":["1612"],"URL":"https:\/\/doi.org\/10.1038\/s41375-022-01612-2","relation":{},"ISSN":["0887-6924","1476-5551"],"issn-type":[{"value":"0887-6924","type":"print"},{"value":"1476-5551","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,8]]},"assertion":[{"value":"28 March 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 May 2022","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 May 2022","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 June 2022","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"HEW, MS, GNF, KMP, TE, NCPC and AH received support from Novartis through the European Treatment and Outcome Study (EUTOS) for CML. HW has received honoraria from Novartis. GNF has received honoraria from BMS, Novartis and Pfizer. TL has received honoraria from Incyte, Novartis, Pfizer, Angelini, Bristol Myers Squibb and research support from Incyte, Novartis and Pfizer. PV has received honoraria from Astra-Zeneca, Eli Lilly, Gilead; GlaxoSmithKline, Novartis, Pfizer, Roche, Teva and research support from Novartis and Pfizer. IR has received research support from Bristol-Myers Squibb and honoraria from Bristol Myers-Squibb and Janssen-Cilag. IG has received research support from Bristol-Myers Squibb. AH received research support from Novartis, BMS, Pfizer and Incyte. KMP has received honoraria from Angelini and Incyte. NCPC has received research support and honoraria from Novartis, and honoraria from Incyte and Astellas.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"This work involving patient samples and data was conducted in accordance with the principles of the Declaration of Helsinki and was approved by the Ethics Committees of the Institute of Haematology and Blood Transfusion, Prague and Faculty Hospital Brno. All patients provided written informed consent for the use of their samples for this research.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}]}}