Thursday, August 15, 2013
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Assays & screens
In situ RNA sequencing in fixed cells and tissues
In situ RNA sequencing could help reveal genetic
heterogeneity in complex samples for clinical diagnostics. In fresh-frozen
cells or tissues, single-cell RNA sequence information was derived from
sequencing by ligation after padlock probing and rolling-circle
amplification. Control in situ experiments on the human b-actin
transcript showed an average accuracy of 98.6%. In sections of frozen tissue
from breast cancer biopsies, 39 probes, including 21 from a prognostic gene
panel, were combined in a single multiplex reaction, and the results were
validated by comparison to published RNA-sequencing data.
Next steps could include optimization of the workflow for handling large
numbers of samples and comparison of this method directly with bulk
expression profiling for prognostic evaluation.
Published online Aug. 15, 2013
Patent and licensing status
Ke, R. et al. Nat.
Methods; published online July 14, 2013;
Contact: Mats Nilsson, Stockholm University, Stockholm, Sweden
Contact: Carolina Wählby, Broad Institute of MIT and
Harvard, Cambridge, Mass.
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