clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers
| العنوان: | clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers |
|---|---|
| المؤلفون: | Samuel Aparicio, Kieran R Campbell, Beixi Wang, Emma Laks, Hossein Farahani, Andrew McPherson, Hans Zahn, David Lai, Sohrab P. Shah, Ciara H. O'Flanagan, Pascale Walters, Justina Biele, Alexandre Bouchard-Côté, Farhia Kabeer, Adi Steif, Jazmine Brimhall |
| المصدر: | Genome Biology, Vol 20, Iss 1, Pp 1-12 (2019) Genome Biology |
| بيانات النشر: | BMC, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | lcsh:QH426-470, Somatic cell, Cell, Method, Triple Negative Breast Neoplasms, Mice, SCID, Computational biology, Biology, DNA sequencing, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Mice, Inbred NOD, Gene expression, Biomarkers, Tumor, Tumor Cells, Cultured, medicine, Animals, Humans, lcsh:QH301-705.5, 030304 developmental biology, Ovarian Neoplasms, 0303 health sciences, Models, Statistical, High-Throughput Nucleotide Sequencing, RNA, Cancer, medicine.disease, Xenograft Model Antitumor Assays, Human genetics, Clone Cells, Cystadenocarcinoma, Serous, 3. Good health, lcsh:Genetics, medicine.anatomical_structure, chemistry, lcsh:Biology (General), Female, Single-Cell Analysis, Software, 030217 neurology & neurosurgery, DNA |
| الوصف: | 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. Electronic supplementary material The online version of this article (10.1186/s13059-019-1645-z) contains supplementary material, which is available to authorized users. |
| اللغة: | English |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5310cf61c009b92a4dfc8d68a4409dc7 http://link.springer.com/article/10.1186/s13059-019-1645-z |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....5310cf61c009b92a4dfc8d68a4409dc7 |
| قاعدة البيانات: | OpenAIRE |
| الوصف غير متاح. |