clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers.
Genome Biol
; 20(1): 54, 2019 03 12.
Article
in En
| MEDLINE
| ID: mdl-30866997
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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Ovarian Neoplasms
/
Software
/
Biomarkers, Tumor
/
Models, Statistical
/
Cystadenocarcinoma, Serous
/
Single-Cell Analysis
/
High-Throughput Nucleotide Sequencing
/
Triple Negative Breast Neoplasms
Type of study:
Risk_factors_studies
Limits:
Animals
/
Female
/
Humans
Language:
En
Journal:
Genome Biol
Journal subject:
BIOLOGIA MOLECULAR
/
GENETICA
Year:
2019
Document type:
Article
Affiliation country:
Canada