Tagging viral RNA with primer ID or immunoglobulin mRNA with UMI has been reported to overcome oversampling. Tagging DNA fragments with UIDs or duplex barcodes has been shown to reduce errors and improve sequencing accuracy. UID or UMI are introduced to targeted templates by ligation or through primers during PCR or reverse transcription. They are usually designed as a string of totally random nucleotides (such as NNNNNNN), partially degenerate nucleotides (such as NNNRNYN), or defined nucleotides (when template molecules are limited). The molecular barcodes or molecular indexes have been given various names, such as unique identifiers (UID), unique molecular identifiers (UMI), primer ID, duplex barcodes, etc. Tagging individual templates with a molecular barcode has been proposed and reported since 2007. Molecular indexing combined with deep sequencing holds great promise to break the limit imposed by PCR and sequencing errors, and enables the detection of rare and ultra-rare mutations. The potential of NGS deep sequencing, however, was hampered by systemic errors of PCR and sequencing methods. Advancements in next generation sequencing (NGS) has made it possible to detect low occurrence mutations in a heterogeneous population. For infectious diseases with a complex population of viral pathogens, the ability to detect low-abundant drug-resistant variants can significantly impact the treatment outcome. For body fluid carrying a few exfoliated or circulating tumor cells among a majority of normal cells, the ability to detect mutations specific to the tumor cells holds promise for non-invasive early diagnosis of new cases and painless follow-up of residual diseases. For a tumor made up of a heterogeneous cell population each with its own set of somatic mutations, the ability to detect a small population of tumor cells with characteristic driver mutations is important to predict prognosis and tailor with effective therapy. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: The deep sequencing data can be assessed at doi: 10.5061/dryad.n6068.įunding: The authors have no support or funding to report.Ĭompeting interests: The authors are all employed by a commercial company, GENEWIZ LLC, and this does not alter the authors’ adherence to PLOS ONE policies on sharing data and materials.Įarly diagnosis is often the key in disease management. Received: SeptemAccepted: DecemPublished: January 11, 2016Ĭopyright: © 2016 Kou et al. PLoS ONE 11(1):Įditor: Junwen Wang, The University of Hong Kong, HONG KONG (2016) Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations. Citation: Kou R, Lam H, Duan H, Ye L, Jongkam N, Chen W, et al.
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