COOBoostR: An Extreme Gradient Boosting-Based Tool for Robust Tissue or Cell-of-Origin Prediction of Tumors.
Life (Basel)
; 13(1)2022 Dec 27.
Article
em En
| MEDLINE
| ID: mdl-36676020
ABSTRACT
We present here COOBoostR, a computational method designed for the putative prediction of the tissue- or cell-of-origin of various cancer types. COOBoostR leverages regional somatic mutation density information and chromatin mark features to be applied to an extreme gradient boosting-based machine-learning algorithm. COOBoostR ranks chromatin marks from various tissue and cell types, which best explain the somatic mutation density landscape of any sample of interest. A specific tissue or cell type matching the chromatin mark feature with highest explanatory power is designated as a potential tissue- or cell-of-origin. Through integrating either ChIP-seq based chromatin data, along with regional somatic mutation density data derived from normal cells/tissue, precancerous lesions, and cancer types, we show that COOBoostR outperforms existing random forest-based methods in prediction speed, with comparable or better tissue or cell-of-origin prediction performance (prediction accuracy-normal cells/tissue 76.99%, precancerous lesions 95.65%, cancer cells 89.39%). In addition, our results suggest a dynamic somatic mutation accumulation at the normal tissue or cell stage which could be intertwined with the changes in open chromatin marks and enhancer sites. These results further represent chromatin marks shaping the somatic mutation landscape at the early stage of mutation accumulation, possibly even before the initiation of precancerous lesions or neoplasia.
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Base de dados:
MEDLINE
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Ano de publicação:
2022
Tipo de documento:
Article