clonealign: Statistical integration of independent single-cell RNA and DNA sequencing data from human cancers Journal Article
| Authors: | Campbell, K. R.; Steif, A.; Laks, E.; Zahn, H.; Lai, D.; McPherson, A.; Farahani, H.; Kabeer, F.; O'Flanagan, C.; Biele, J.; Brimhall, J.; Wang, B.; Walters, P.; IMAXT Consortium; Bouchard-Côté, A.; Aparicio, S.; Shah, S. P. |
| Article Title: | clonealign: Statistical integration of independent single-cell RNA and DNA sequencing data from human cancers |
| Abstract: | Measuring gene expression of tumor clones at single-cell resolution links functional consequences to somatic alterations. Without scalable methods to simultaneously assay DNA and RNA from the same single cell, parallel single-cell DNA and RNA measurements from independent cell populations must be mapped for genome-transcriptome association. We present clonealign, which assigns gene expression states to cancer clones using single-cell RNA and DNA sequencing independently sampled from a heterogeneous population. We apply clonealign to triple-negative breast cancer patient-derived xenografts and high-grade serous ovarian cancer cell lines and discover clone-specific dysregulated biological pathways not visible using either sequencing method alone. © 2019 The Author(s). |
| Journal Title: | Genome Biology |
| Volume: | 20 |
| ISSN: | 1465-6906 |
| Publisher: | Biomed Central Ltd |
| Date Published: | 2019-03-12 |
| Start Page: | 54 |
| Language: | English |
| DOI: | 10.1186/s13059-019-1645-z |
| PUBMED: | 30866997 |
| PROVIDER: | scopus |
| PMCID: | PMC6417140 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 April 2019 -- Source: Scopus |
