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PUREE: accurate pan-cancer tumor purity estimation from gene expression data.
Revkov, Egor; Kulshrestha, Tanmay; Sung, Ken Wing-Kin; Skanderup, Anders Jacobsen.
Afiliação
  • Revkov E; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
  • Kulshrestha T; School of Computing, National University of Singapore, Computing 1, 13 Computing Drive, Singapore, 117417, Republic of Singapore.
  • Sung KW; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
  • Skanderup AJ; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
Commun Biol ; 6(1): 394, 2023 04 11.
Article em En | MEDLINE | ID: mdl-37041233
Tumors are complex masses composed of malignant and non-malignant cells. Variation in tumor purity (proportion of cancer cells in a sample) can both confound integrative analysis and enable studies of tumor heterogeneity. Here we developed PUREE, which uses a weakly supervised learning approach to infer tumor purity from a tumor gene expression profile. PUREE was trained on gene expression data and genomic consensus purity estimates from 7864 solid tumor samples. PUREE predicted purity with high accuracy across distinct solid tumor types and generalized to tumor samples from unseen tumor types and cohorts. Gene features of PUREE were further validated using single-cell RNA-seq data from distinct tumor types. In a comprehensive benchmark, PUREE outperformed existing transcriptome-based purity estimation approaches. Overall, PUREE is a highly accurate and versatile method for estimating tumor purity and interrogating tumor heterogeneity from bulk tumor gene expression data, which can complement genomics-based approaches or be used in settings where genomic data is unavailable.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Perfilação da Expressão Gênica / Neoplasias Limite: Humans Idioma: En Ano de publicação: 2023 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Perfilação da Expressão Gênica / Neoplasias Limite: Humans Idioma: En Ano de publicação: 2023 Tipo de documento: Article