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

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http://hdl.handle.net/10138/288721

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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

Title: TAC-seq : targeted DNA and RNA sequencing for precise biomarker molecule counting
Author: Teder, Hindrek; Koel, Mariann; Paluoja, Priit; Jatsenko, Tatjana; Rekker, Kadri; Laisk-Podar, Triin; Kukuskina, Viktorija; Velthut-Meikas, Agne; Fjodorova, Olga; Peters, Maire; Kere, Juha; Salumets, Andres; Palta, Priit; Krjutskov, Kaarel
Contributor: University of Helsinki, Juha Kere / Principal Investigator
University of Helsinki, Clinicum
University of Helsinki, Institute for Molecular Medicine Finland
University of Helsinki, Research Programme for Molecular Neurology
Date: 2018-12-18
Language: eng
Number of pages: 8
Belongs to series: Npj genomic medicine
ISSN: 2056-7944
URI: http://hdl.handle.net/10138/288721
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.
Subject: CELL-FREE DNA
QUANTIFICATION
MUTATIONS
AMPLIFICATION
LIGATION
3111 Biomedicine
1184 Genetics, developmental biology, physiology
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