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

Simple item page
dc.contributor"European Union (EU)" and "Horizon 2020"
dc.contributor.authorTeder, Hindrek
dc.contributor.authorKoel, Mariann
dc.contributor.authorPaluoja, Priit
dc.contributor.authorJatsenko, Tatjana
dc.contributor.authorRekker, Kadri
dc.contributor.authorLaisk-Podar, Triin
dc.contributor.authorKukuškina, Viktorija
dc.contributor.authorVelthut-Meikas, Agne
dc.contributor.authorFjodorova, Olga
dc.contributor.authorPeters, Maire
dc.contributor.authorKere, Juha
dc.contributor.authorSalumets, Andres
dc.contributor.authorPalta, Priit
dc.contributor.authorKrjutškov, Kaarel
dc.date.accessioned2019-02-27T09:43:23Z
dc.date.available2019-02-27T09:43:23Z
dc.date.issued2018
dc.description.abstractTargeted 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 × 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.et
dc.identifier.urihttps://doi.org/10.1038/s41525-018-0072-5
dc.identifier.urihttp://hdl.handle.net/10062/63433
dc.language.isoenget
dc.relationinfo:eu-repo/grantAgreement/EC/H2020/692065///WIDENLIFEet
dc.relation.ispartofseriesnpj Genomic Medicinevolume 3;Article number: 34 (2018)
dc.rightsinfo:eu-repo/semantics/openAccesset
dc.subjectTargeted resequencinget
dc.subjectDiagnostic markerset
dc.subjectNext-generation sequencinget
dc.titleTAC-seq: targeted DNA and RNA sequencing for precise biomarker molecule countinget
dc.typeinfo:eu-repo/semantics/articleet

Files

Original bundle
Now showing 1 - 2 of 2
Thumbnail Image
Name:
41525_2018_article_72.pdf
Size:
1.61 MB
Format:
Adobe Portable Document Format
Description:
Download
Thumbnail Image
Name:
41525_2018_72_moesm1_esm.pdf
Size:
2.38 MB
Format:
Adobe Portable Document Format
Description:
Supplementary Information
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

WIDENLIFE - Widening the Scientific Excellence for Studies on Women’s and Fetal Health and Wellbeing