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RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
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Number of Authors: 112018 (English)In: Communications biology, E-ISSN 2399-3642, Vol. 1, article id 209Article in journal (Refereed) Published
Abstract [en]

Single-molecule RNA fluorescence in situ hybridization (smFISH) represents a promising approach to quantify the expression of clinically useful biomarkers in tumor samples. However, routine application of smFISH to formalin-fixed, paraffin-embedded (FFPE) samples is challenging due to the low signal intensity and high background noise. Here we present RollFISH, a method combining the specificity of smFISH with the signal boosting of rolling circle amplification. We apply RollFISH to quantify widely used breast cancer biomarkers in cell lines and FFPE samples. Thanks to the high signal-to-noise ratio, we can visualize selected biomarkers at low magnification (20 x) across entire tissue sections, and thus assess their spatial heterogeneity. Lastly, we apply RollFISH to quantify HER2 mRNA in 150 samples on a single tissue microarray, achieving a sensitivity and specificity of detection of HER2-positive samples of similar to 90%. RollFISH is a robust method for quantifying the expression and intratumor heterogeneity of biomarkers in FFPE tissues.

Place, publisher, year, edition, pages
2018. Vol. 1, article id 209
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Biological Sciences Other Natural Sciences
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URN: urn:nbn:se:su:diva-167708DOI: 10.1038/s42003-018-0218-0ISI: 000461126500208PubMedID: 30511022OAI: oai:DiVA.org:su-167708DiVA, id: diva2:1301315
Available from: 2019-04-01 Created: 2019-04-01 Last updated: 2019-04-01Bibliographically approved

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Wu, ChenglinMignardi, MarcoAnnaratone, LauraSapino, AnnaBienko, MagdaNilsson, Mats
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Department of Biochemistry and BiophysicsScience for Life Laboratory (SciLifeLab)
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