Ultra-precise quantification of mRNA targets across a broad dynamic range with nanoreactor beads

Precise quantification of molecular targets in a biological sample across a wide dynamic range is a key requirement in many diagnostic procedures, such as monitoring response to therapy or detection of measurable residual disease. State of the art digital PCR assays provide for a dynamic range of fo...

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Bibliographic Details
Published in:PloS one 2021-03, Vol.16 (3), p.e0242529-e0242529
Main Authors: Loncarevic, Ivan Francisco, Toepfer, Susanne, Hubold, Stephan, Klingner, Susanne, Kanitz, Lea, Ellinger, Thomas, Steinmetzer, Katrin, Ernst, Thomas, Hochhaus, Andreas, Ermantraut, Eugen
Format: Article
Language:English
Subjects:
Beads
Biochemical assays
Biology and Life Sciences
Chambers
CMOS
Engineering and Technology
Fluorescence
Genetic aspects
Hydrogels
Methods
mRNA
Nucleic acids
Physical Sciences
Polymerase chain reaction
Polymers
Reagents
Research and Analysis Methods
Temperature
Temperature control
Thermal cycling
Workflow
Yttrium
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Summary:Precise quantification of molecular targets in a biological sample across a wide dynamic range is a key requirement in many diagnostic procedures, such as monitoring response to therapy or detection of measurable residual disease. State of the art digital PCR assays provide for a dynamic range of four orders of magnitude. However digital assays are complex and require sophisticated microfluidic tools. Here we present an assay format that enables ultra-precise quantification of RNA targets in a single measurement across a dynamic range of more than six orders of magnitude. The approach is based on hydrogel beads that provide for microfluidic free compartmentalization of the sample as they are used as nanoreactors for reverse transcription, PCR amplification and combined real time and digital detection of gene transcripts. We have applied these nanoreactor beads for establishing an assay for the detection and quantification of BCR-ABL1 fusion transcripts. The assay has been characterized for its precision and linear dynamic range. A comparison of the new method against conventional real time RT-PCR analysis (reference method) with clinical samples from patients with chronic myeloid leukemia (CML) revealed excellent concordance with Pearsons correlation coefficient of 0.983 and slope of 1.08.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0242529