Differential mRNA expression between ancestry groups can be explained by both genetic and environmental factors. We outline a computational workflow to determine the extent to which germline genetic variation explains cancer-specific molecular differences across ancestry groups. Using multi-omics datasets from The Cancer Genome Atlas (TCGA), we enumerate ancestry-informative markers colocalized with cancer-type-specific expression quantitative trait loci (e-QTLs) at ancestry-associated genes. This approach is generalizable to other settings with paired germline genotyping and mRNA expression data for a multi-ethnic cohort. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020), Robertson et al. (2021), and Sayaman et al. (2021).
Analysis of germline-driven ancestry-associated gene expression in cancers / Chambwe, N., Sayaman, R.W., Hu, D., Huntsman, S., Kemal, A., Caesar-Johnson, S., Zenklusen, J.C., Ziv, E., Beroukhim, R., Cherniack, A.D., Carrot-Zhang, J., Berger, A.C., Han, S., Meyerson, M., Damrauer, J.S., Hoadley, K.A., Felau, I., Demchok, J.A., Mensah, M.K.A., Tarnuzzer, R., et al.. - In: STAR PROTOCOLS. - ISSN 2666-1667. - 3:3(2022), pp. 10158601-10158618. [10.1016/j.xpro.2022.101586]
Analysis of germline-driven ancestry-associated gene expression in cancers
Romanel, Alessandro;Demichelis, Francesca;
2022-01-01
Abstract
Differential mRNA expression between ancestry groups can be explained by both genetic and environmental factors. We outline a computational workflow to determine the extent to which germline genetic variation explains cancer-specific molecular differences across ancestry groups. Using multi-omics datasets from The Cancer Genome Atlas (TCGA), we enumerate ancestry-informative markers colocalized with cancer-type-specific expression quantitative trait loci (e-QTLs) at ancestry-associated genes. This approach is generalizable to other settings with paired germline genotyping and mRNA expression data for a multi-ethnic cohort. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020), Robertson et al. (2021), and Sayaman et al. (2021).| File | Dimensione | Formato | |
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