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bioRxiv · 10.1101/2020.12.27.424506

Single cell gene fusion detection by scFusion

Jin, Z.·Huang, W.·Shen, N.·Li, J.·Wang, X.·Park, P. J.·Xi, R.
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Abstract

Gene fusions are widespread in tumor cells and can play important roles in tumor initiation and progression. Using full length single cell RNA sequencing (scRNA-seq), gene fusions can now be detected at single cell level. However, scRNA-seq data has a high noise level and contains various technical artefacts that can lead to spurous fusion discoveries. Here we present a computational tool, scFusion, for gene fusion detection based on scRNA-seq. scFusion can efficiently and sensitively detect fusions with a low false discovery rate. In a T cell data, scFusion detected the invariant TCR gene recombinations in Mucosal-associated invariant T cells that many methods developed for bulk-data failed to detect. In a multiple myeloma data, scFusion detected the known recurrent fusion IgH-WHSC1, which was associated with overexpression of the WHSC1 oncogene.

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Jin, Z., Huang, W., Shen, N., Li, J., Wang, X., Park, P. J., Xi, R.. 2020-12-28. Single cell gene fusion detection by scFusion. https://doi.org/10.1101/2020.12.27.424506

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