RDAClone: Deciphering Tumor Heterozygosity through Single-Cell Genomics Data Analysis with Robust Deep Autoencoder.
Genes (Basel)
; 12(12)2021 11 23.
Article
in En
| MEDLINE
| ID: mdl-34946794
ABSTRACT
Rapid advances in single-cell genomics sequencing (SCGS) have allowed researchers to characterize tumor heterozygosity with unprecedented resolution and reveal the phylogenetic relationships between tumor cells or clones. However, high sequencing error rates of current SCGS data, i.e., false positives, false negatives, and missing bases, severely limit its application. Here, we present a deep learning framework, RDAClone, to recover genotype matrices from noisy data with an extended robust deep autoencoder, cluster cells into subclones by the Louvain-Jaccard method, and further infer evolutionary relationships between subclones by the minimum spanning tree. Studies on both simulated and real datasets demonstrate its robustness and superiority in data denoising, cell clustering, and evolutionary tree reconstruction, particularly for large datasets.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Genomics
/
Single-Cell Analysis
/
Neoplasms
Language:
En
Journal:
Genes (Basel)
Year:
2021
Document type:
Article
Affiliation country:
China