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To develop and evaluate dPCR for SNP detection using DNA, RNA, and clinical samples, an influenza virus model of resistance to oseltamivir (Tamiflu) was used. First, this study was able to recognize and reduce off-target amplification in dPCR quantification, thereby enabling technical sensitivities down to 0.1% SNP abundance at a range of template concentrations, a 50-fold improvement on the qPCR assay used routinely in the clinic. Second, a method was developed for determining the false-positive rate (background) signal. Finally, comparison of dPCR with qPCR results on clinical samples demonstrated the potential impact dPCR could have on clinical research and patient management by earlier (trace) detection of rare drug-resistant sequence variants. Ultimately this could reduce the quantity of ineffective drugs taken and facilitate early switching to alternative medication when available. In the short term such methods could advance our understanding of microbial dynamics and therapeutic responses in a range of infectious diseases such as HIV, viral hepatitis, and tuberculosis. Furthermore, the findings presented here are directly relevant to other diagnostic areas, such as the detection of rare SNPs in malignancy, monitoring of graft rejection, and fetal screening.<\/jats:p>","DOI":"10.1128\/jcm.02611-15","type":"journal-article","created":{"date-parts":[[2015,12,11]],"date-time":"2015-12-11T12:53:55Z","timestamp":1449838435000},"page":"392-400","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":59,"title":["Detection of Rare Drug Resistance Mutations by Digital PCR in a Human Influenza A Virus Model System and Clinical Samples"],"prefix":"10.1128","volume":"54","author":[{"given":"Alexandra S.","family":"Whale","sequence":"first","affiliation":[{"name":"Molecular and Cell Biology Team, LGC, Teddington, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire A.","family":"Bushell","sequence":"additional","affiliation":[{"name":"Molecular and Cell Biology Team, LGC, Teddington, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul R.","family":"Grant","sequence":"additional","affiliation":[{"name":"Virology Laboratory, Clinical Microbiology and Virology, University College London Hospital NHS Foundation Trust, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Cowen","sequence":"additional","affiliation":[{"name":"Statistics Team, LGC, Teddington, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ion","family":"Gutierrez-Aguirre","sequence":"additional","affiliation":[{"name":"National Institute of Biology, Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denise M.","family":"O'Sullivan","sequence":"additional","affiliation":[{"name":"Molecular and Cell Biology Team, LGC, Teddington, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"\u017del","sequence":"additional","affiliation":[{"name":"National Institute of Biology, Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mojca","family":"Milavec","sequence":"additional","affiliation":[{"name":"National Institute of Biology, Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carole A.","family":"Foy","sequence":"additional","affiliation":[{"name":"Molecular and Cell Biology Team, LGC, Teddington, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleni","family":"Nastouli","sequence":"additional","affiliation":[{"name":"Virology Laboratory, Clinical Microbiology and Virology, University College London Hospital NHS Foundation Trust, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy A.","family":"Garson","sequence":"additional","affiliation":[{"name":"Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jim F.","family":"Huggett","sequence":"additional","affiliation":[{"name":"Molecular and Cell Biology Team, LGC, Teddington, United Kingdom"},{"name":"Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","volume-title":"WHO global strategy for containment of antimicrobial resistance","author":"WHO","year":"2001","unstructured":"WHO. 2001. 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