TAC-seq : targeted DNA and RNA sequencing for precise biomarker molecule counting

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dc.contributor University of Helsinki, Juha Kere / Principal Investigator en
dc.contributor University of Helsinki, Clinicum en
dc.contributor University of Helsinki, Institute for Molecular Medicine Finland en
dc.contributor University of Helsinki, Research Programme for Molecular Neurology en
dc.contributor.author Teder, Hindrek
dc.contributor.author Koel, Mariann
dc.contributor.author Paluoja, Priit
dc.contributor.author Jatsenko, Tatjana
dc.contributor.author Rekker, Kadri
dc.contributor.author Laisk-Podar, Triin
dc.contributor.author Kukuskina, Viktorija
dc.contributor.author Velthut-Meikas, Agne
dc.contributor.author Fjodorova, Olga
dc.contributor.author Peters, Maire
dc.contributor.author Kere, Juha
dc.contributor.author Salumets, Andres
dc.contributor.author Palta, Priit
dc.contributor.author Krjutskov, Kaarel
dc.date.accessioned 2019-01-09T10:47:01Z
dc.date.available 2019-01-09T10:47:01Z
dc.date.issued 2018-12-18
dc.identifier.citation Teder , H , Koel , M , Paluoja , P , Jatsenko , T , Rekker , K , Laisk-Podar , T , Kukuskina , V , Velthut-Meikas , A , Fjodorova , O , Peters , M , Kere , J , Salumets , A , Palta , P & Krjutskov , K 2018 , ' TAC-seq : targeted DNA and RNA sequencing for precise biomarker molecule counting ' , Npj genomic medicine , vol. 3 , 34 . https://doi.org/10.1038/s41525-018-0072-5 en
dc.identifier.issn 2056-7944
dc.identifier.other PURE: 120893473
dc.identifier.other PURE UUID: d4bc4c87-2e3e-4f73-ad18-1c7257cfd4d0
dc.identifier.other WOS: 000454051200001
dc.identifier.other Scopus: 85058842481
dc.identifier.other ORCID: /0000-0001-9320-7008/work/52695920
dc.identifier.uri http://hdl.handle.net/10138/288721
dc.description.abstract Targeted next-generation sequencing (NGS) methods have become essential in medical research and diagnostics. In addition to NGS sensitivity and high-throughput capacity, precise biomolecule counting based on unique molecular identifier (UMI) has potential to increase biomolecule detection accuracy. Although UMIs are widely used in basic research its introduction to clinical assays is still in progress. Here, we present a robust and cost-effective TAC-seq (Targeted Allele Counting by sequencing) method that uses UMIs to estimate the original molecule counts of mRNAs, microRNAs, and cell-free DNA. We applied TAC-seq in three different clinical applications and compared the results with standard NGS. RNA samples extracted from human endometrial biopsies were analyzed using previously described 57 mRNA-based receptivity biomarkers and 49 selected microRNAs at different expression levels. Cell-free DNA aneuploidy testing was based on cell line (47,XX, +21) genomic DNA. TAC-seq mRNA profiling showed identical clustering results to transcriptome RNA sequencing, and microRNA detection demonstrated significant reduction in amplification bias, allowing to determine minor expression changes between different samples that remained undetermined by standard NGS. The mimicking experiment for cell-free DNA fetal aneuploidy analysis showed that TAC-seq can be applied to count highly fragmented DNA, detecting significant (p = 7.6 x 10(-4)) excess of chromosome 21 molecules at 10% fetal fraction level. Based on three proof-of-principle applications we demonstrate that TAC-seq is an accurate and highly potential biomarker profiling method for advanced medical research and diagnostics. en
dc.format.extent 8
dc.language.iso eng
dc.relation.ispartof Npj genomic medicine
dc.rights en
dc.subject CELL-FREE DNA en
dc.subject QUANTIFICATION en
dc.subject MUTATIONS en
dc.subject AMPLIFICATION en
dc.subject LIGATION en
dc.subject 3111 Biomedicine en
dc.subject 1184 Genetics, developmental biology, physiology en
dc.title TAC-seq : targeted DNA and RNA sequencing for precise biomarker molecule counting en
dc.type Article
dc.description.version Peer reviewed
dc.identifier.doi https://doi.org/10.1038/s41525-018-0072-5
dc.type.uri info:eu-repo/semantics/other
dc.type.uri info:eu-repo/semantics/publishedVersion
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