The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia

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Kumar , A , Kankainen , M , Parsons , A , Kallioniemi , O , Mattila , P & Heckman , C A 2017 , ' The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia ' , BMC Genomics , vol. 18 , 629 . https://doi.org/10.1186/s12864-017-4039-1

Title: The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia
Author: Kumar, Ashwini; Kankainen, Matti; Parsons, Alun; Kallioniemi, Olli; Mattila, Pirkko; Heckman, Caroline A.
Contributor: University of Helsinki, Institute for Molecular Medicine Finland
University of Helsinki, Institute for Molecular Medicine Finland
University of Helsinki, Institute for Molecular Medicine Finland
University of Helsinki, Institute for Molecular Medicine Finland
University of Helsinki, Institute for Molecular Medicine Finland
University of Helsinki, Institute for Molecular Medicine Finland
Date: 2017-08-17
Language: eng
Number of pages: 13
Belongs to series: BMC Genomics
ISSN: 1471-2164
URI: http://hdl.handle.net/10138/224283
Abstract: Background: RNA sequencing (RNA-seq) has become an indispensable tool to identify disease associated transcriptional profiles and determine the molecular underpinnings of diseases. However, the broad adaptation of the methodology into the clinic is still hampered by inconsistent results from different RNA-seq protocols and involves further evaluation of its analytical reliability using patient samples. Here, we applied two commonly used RNA-seq library preparation protocols to samples from acute leukemia patients to understand how poly-A-tailed mRNA selection (PA) and ribo-depletion (RD) based RNA-seq library preparation protocols affect gene fusion detection, variant calling, and gene expression profiling. Results: Overall, the protocols produced similar results with consistent outcomes. Nevertheless, the PA protocol was more efficient in quantifying expression of leukemia marker genes and showed better performance in the expression-based classification of leukemia. Independent qRT-PCR experiments verified that the PA protocol better represented total RNA compared to the RD protocol. In contrast, the RD protocol detected a higher number of non-coding RNA features and had better alignment efficiency. The RD protocol also recovered more known fusion-gene events, although variability was seen in fusion gene predictions. Conclusion: The overall findings provide a framework for the use of RNA-seq in a precision medicine setting with limited number of samples and suggest that selection of the library preparation protocol should be based on the objectives of the analysis.
Subject: RNA-sequencing
Hematological malignancies
Library preparation
Ribo-depletion
Poly-A selection
ACUTE MYELOID-LEUKEMIA
ACUTE LYMPHOBLASTIC-LEUKEMIA
SOMATIC MUTATIONS
SEQ
EXPRESSION
MICROARRAY
MEDICINE
GENES
3111 Biomedicine
3122 Cancers
1184 Genetics, developmental biology, physiology
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