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Analysis of germline-driven ancestry-associated gene expression in cancers
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 da...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9356164/ https://www.ncbi.nlm.nih.gov/pubmed/35942349 http://dx.doi.org/10.1016/j.xpro.2022.101586 |
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author | Chambwe, Nyasha Sayaman, Rosalyn W. Hu, Donglei Huntsman, Scott Kemal, Anab Caesar-Johnson, Samantha Zenklusen, Jean C. Ziv, Elad Beroukhim, Rameen Cherniack, Andrew D. |
author_facet | Chambwe, Nyasha Sayaman, Rosalyn W. Hu, Donglei Huntsman, Scott Kemal, Anab Caesar-Johnson, Samantha Zenklusen, Jean C. Ziv, Elad Beroukhim, Rameen Cherniack, Andrew D. |
author_sort | Chambwe, Nyasha |
collection | PubMed |
description | 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). |
format | Online Article Text |
id | pubmed-9356164 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-93561642022-08-07 Analysis of germline-driven ancestry-associated gene expression in cancers Chambwe, Nyasha Sayaman, Rosalyn W. Hu, Donglei Huntsman, Scott Kemal, Anab Caesar-Johnson, Samantha Zenklusen, Jean C. Ziv, Elad Beroukhim, Rameen Cherniack, Andrew D. STAR Protoc Protocol 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). Elsevier 2022-07-31 /pmc/articles/PMC9356164/ /pubmed/35942349 http://dx.doi.org/10.1016/j.xpro.2022.101586 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Protocol Chambwe, Nyasha Sayaman, Rosalyn W. Hu, Donglei Huntsman, Scott Kemal, Anab Caesar-Johnson, Samantha Zenklusen, Jean C. Ziv, Elad Beroukhim, Rameen Cherniack, Andrew D. Analysis of germline-driven ancestry-associated gene expression in cancers |
title | Analysis of germline-driven ancestry-associated gene expression in cancers |
title_full | Analysis of germline-driven ancestry-associated gene expression in cancers |
title_fullStr | Analysis of germline-driven ancestry-associated gene expression in cancers |
title_full_unstemmed | Analysis of germline-driven ancestry-associated gene expression in cancers |
title_short | Analysis of germline-driven ancestry-associated gene expression in cancers |
title_sort | analysis of germline-driven ancestry-associated gene expression in cancers |
topic | Protocol |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9356164/ https://www.ncbi.nlm.nih.gov/pubmed/35942349 http://dx.doi.org/10.1016/j.xpro.2022.101586 |
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