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MicroRNAs accurately identify cancer tissue origin

Abstract

MicroRNAs (miRNAs) belong to a class of noncoding, regulatory RNAs that is involved in oncogenesis and shows remarkable tissue specificity. Their potential for tumor classification suggests they may be used in identifying the tissue in which cancers of unknown primary origin arose, a major clinical problem. We measured miRNA expression levels in 400 paraffin-embedded and fresh-frozen samples from 22 different tumor tissues and metastases. We used miRNA microarray data of 253 samples to construct a transparent classifier based on 48 miRNAs. Two-thirds of samples were classified with high confidence, with accuracy >90%. In an independent blinded test-set of 83 samples, overall high-confidence accuracy reached 89%. Classification accuracy reached 100% for most tissue classes, including 131 metastatic samples. We further validated the utility of the miRNA biomarkers by quantitative RT-PCR using 65 additional blinded test samples. Our findings demonstrate the effectiveness of miRNAs as biomarkers for tracing the tissue of origin of cancers of unknown primary origin.

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Figure 1: Structure of the decision-tree classifier, with 24 nodes (numbered, Table 2) and 25 leaves.
Figure 2: Binary decisions at nodes of the decision tree.

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Acknowledgements

We thank Jung-Hwan Yoon of Seoul National University College of Medicine, Seoul, South Korea. N.R. dedicates this work to the memory of Yasha (Yaakov) Rosenfeld.

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Authors and Affiliations

Authors

Contributions

R.A., A.A., I. Bentwich, Z.B., D.C., A.C. and I. Barshack directed research; N.R., R.A., E.M., S.R., Y.S., S.G., A.C. and I. Barshack designed experiments; N.S.-V., A.T., M.F., O.K., O.N., D.N., M.P., A.Y., B.S., S.P.-C., E.F. and I. Barshack provided samples and performed pathological analysis; E.M., M.Z., N.S., S.T., D.L. and S.G. performed experiments; N.R., R.A., S.R., Y.G. and E.S. developed algorithms; N.R., S.R., H.B. and Y.G. analyzed data; Y.S., A.L., N.T. and A.B.-A. provided bioinformatic and database support; N.R., R.A., A.C. and I. Barschack wrote the paper.

Corresponding authors

Correspondence to Ranit Aharonov or Iris Barshack.

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Competing interests

All authors affiliated with Rosetta Genomics, except E.S., are full-time employees of Rosetta Genomics Ltd. and hold equity in the company, the value of which may be influenced by this publication. E.S. was engaged as an external consultant to Rosetta Genomics. O.N. is a paid consultant to Rosetta Genomics. All other authors declare that they have no competing interests.

Supplementary information

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Supplementary Table 1 (XLS 186 kb)

Supplementary Table

Supplementary Table 2 (XLS 25 kb)

Supplementary Table

Supplementary Table 3 (XLS 21 kb)

Supplementary Table

Supplementary Table 5 (XLS 29 kb)

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Rosenfeld, N., Aharonov, R., Meiri, E. et al. MicroRNAs accurately identify cancer tissue origin. Nat Biotechnol 26, 462–469 (2008). https://doi.org/10.1038/nbt1392

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