Analysis of germline-driven ancestry-associated gene expression in cancers
| Title: | Analysis of germline-driven ancestry-associated gene expression in cancers |
|---|---|
| Authors: | Chambwe, Nyasha; Sayaman, Rosalyn W.; Hu, Donglei; Huntsman, Scott; Kemal, Anab; Caesar-Johnson, Samantha; Zenklusen, Jean C.; Ziv, Elad; Beroukhim, Rameen; Cherniack, Andrew D.; Carrot-Zhang, Jian; Berger, Ashton C.; Han, Seunghun; Meyerson, Matthew; Damrauer, Jeffrey S.; Hoadley, Katherine A.; Felau, Ina; Demchok, John A.; Mensah, Michael K. A.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Knijnenburg, Theo A.; Robertson, A. Gordon; Yau, Christina; Benz, Christopher; Huang, Kuan-lin; Newberg, Justin Y.; Frampton, Garrett M.; Mashl, R. Jay; Ding, Li; Romanel, Alessandro; Demichelis, Francesca; Zhou, Wanding; Laird, Peter W.; Shen, Hui; Wong, Christopher K.; Stuart, Joshua M.; Lazar, Alexander J.; Le, Xiuning; Oak, Ninad |
| Contributors: | Chambwe, Nyasha; Sayaman, Rosalyn W.; Hu, Donglei; Huntsman, Scott; Kemal, Anab; Caesar-Johnson, Samantha; Zenklusen, Jean C.; Ziv, Elad; Beroukhim, Rameen; Cherniack, Andrew D.; Carrot-Zhang, Jian; Berger, Ashton C.; Han, Seunghun; Meyerson, Matthew; Damrauer, Jeffrey S.; Hoadley, Katherine A.; Felau, Ina; Demchok, John A.; Mensah, Michael K. A.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Knijnenburg, Theo A.; Robertson, A. Gordon; Yau, Christina; Benz, Christopher; Huang, Kuan-lin; Newberg, Justin Y.; Frampton, Garrett M.; Mashl, R. Jay; Ding, Li; Romanel, Alessandro; Demichelis, Francesca; Zhou, Wanding; Laird, Peter W.; Shen, Hui; Wong, Christopher K.; Stuart, Joshua M.; Lazar, Alexander J.; Le, Xiuning; Oak, Ninad |
| Publication Year: | 2022 |
| Collection: | Università degli Studi di Trento: CINECA IRIS |
| Subject Terms: | Bioinformatic; Cancer; Computer science; Gene Expression; Genomic; RNAseq; Sequence analysis |
| 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 etal. (2020), Robertson etal. (2021), and Sayaman etal. (2021). |
| Document Type: | article in journal/newspaper |
| Language: | English |
| Relation: | info:eu-repo/semantics/altIdentifier/pmid/35942349; info:eu-repo/semantics/altIdentifier/wos/WOS:001060918800008; volume:3; issue:3; firstpage:10158601; lastpage:10158618; numberofpages:18; journal:STAR PROTOCOLS; https://hdl.handle.net/11572/406370; https://www.sciencedirect.com/science/article/pii/S266616672200466X?via=ihub |
| DOI: | 10.1016/j.xpro.2022.101586 |
| Availability: | https://hdl.handle.net/11572/406370; https://doi.org/10.1016/j.xpro.2022.101586; https://www.sciencedirect.com/science/article/pii/S266616672200466X?via=ihub |
| Rights: | info:eu-repo/semantics/openAccess ; license:Creative commons ; license uri:http://creativecommons.org/licenses/by-nc-nd/4.0/ |
| Accession Number: | edsbas.E2D2014B |
| Database: | BASE |