COSMIC-3D provides structural perspectives on cancer genetics for drug discovery

Nature GeNetics | VOL 50 | SEPTEMBER 2018 | 1198–1204 | www.nature.com/naturegenetics expression in each clone and cell), we find it misleading to describe clonal aRME as the “autosomal analog of X chromosome inactivation”1. Finally, Gimelbrant and colleagues suggest that single-cell RNA-seq may not be suitable (or may be underpowered) for allelic gene expression analyses. We would like to refer them to data from our study2, in which the significance of clonal aRME is reported per gene and chromosome. When XCI is used as an internal control in the cells, it is apparent that single-cell RNA-seq has sufficient power to identify essentially all genes on the X chromosome as having clonal monoallelic gene expression. Moreover, the single-cell RNA-seq in our study identified the same imprinted genes as bulk RNAseq performed on the same primary cells2, thus again confirming power and accuracy. The reference13 cited by Gimelbrant and colleagues regarding “challenges of singlecell RNA-seq, which make confident detection of less extreme bias difficult” simply reports that technical controls are needed to correctly adjust for the incomplete sensitivity of the libraries from each cell, procedures that we have advocated for and used in our studies2,9. Altogether, we agree with Gimelbrant and colleagues’ notion that clonal aRME occurs in mammalian cells beyond the classical cases such as antigen14 and olfactory15 receptors. However, it is now evident2 to us that this phenomenon is biologically much rarer than initially thought4–8,16, and it affects mostly genes that are weakly expressed, thus calling its functional role into question. Our study2 provided the first genome-wide insights into primary and in vivo cells, whereas previous bulk analyses on clonal aRME used immortalized cell lines4,5, which are notorious for genomic changes. (A full understanding of the clones used by Gimelbrant and colleagues in ref. 4, gained through modern methods such as RNA and DNA sequencing, has not been possible because of the authors’ unwillingness to share the cell clones.) In the future, we look forward to seeing more extensive in vivo datasets on clonal aRME, given that singlecell RNA-seq has become routine and can now be applied to resolve additional questions on monoallelic gene expression. ❐