Analysis of germline-driven ancestry-associated gene expression in cancers
© 2022 The Author(s)..
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).
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:3 |
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| Enthalten in: |
STAR protocols - 3(2022), 3 vom: 16. Sept., Seite 101586 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Chambwe, Nyasha [VerfasserIn] |
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| Links: |
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| Themen: |
Bioinformatics |
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| Anmerkungen: |
Date Completed 10.08.2022 Date Revised 19.05.2023 published: Electronic-eCollection Citation Status MEDLINE |
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| doi: |
10.1016/j.xpro.2022.101586 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 245 | 1 | 0 | |a Analysis of germline-driven ancestry-associated gene expression in cancers |
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| 500 | |a Date Completed 10.08.2022 | ||
| 500 | |a Date Revised 19.05.2023 | ||
| 500 | |a published: Electronic-eCollection | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2022 The Author(s). | ||
| 520 | |a 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) | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Research Support, N.I.H., Extramural | |
| 650 | 4 | |a Bioinformatics | |
| 650 | 4 | |a Cancer | |
| 650 | 4 | |a Computer sciences | |
| 650 | 4 | |a Gene Expression | |
| 650 | 4 | |a Genomics | |
| 650 | 4 | |a RNAseq | |
| 650 | 4 | |a Sequence analysis | |
| 650 | 7 | |a RNA, Messenger |2 NLM | |
| 700 | 1 | |a Sayaman, Rosalyn W |e verfasserin |4 aut | |
| 700 | 1 | |a Hu, Donglei |e verfasserin |4 aut | |
| 700 | 1 | |a Huntsman, Scott |e verfasserin |4 aut | |
| 700 | 0 | |a Cancer Genome Analysis Network |e verfasserin |4 aut | |
| 700 | 1 | |a Kemal, Anab |e verfasserin |4 aut | |
| 700 | 1 | |a Caesar-Johnson, Samantha |e verfasserin |4 aut | |
| 700 | 1 | |a Zenklusen, Jean C |e verfasserin |4 aut | |
| 700 | 1 | |a Ziv, Elad |e verfasserin |4 aut | |
| 700 | 1 | |a Beroukhim, Rameen |e verfasserin |4 aut | |
| 700 | 1 | |a Cherniack, Andrew D |e verfasserin |4 aut | |
| 700 | 1 | |a Carrot-Zhang, Jian |e investigator |4 oth | |
| 700 | 1 | |a Berger, Ashton C |e investigator |4 oth | |
| 700 | 1 | |a Han, Seunghun |e investigator |4 oth | |
| 700 | 1 | |a Meyerson, Matthew |e investigator |4 oth | |
| 700 | 1 | |a Damrauer, Jeffrey S |e investigator |4 oth | |
| 700 | 1 | |a Hoadley, Katherine A |e investigator |4 oth | |
| 700 | 1 | |a Felau, Ina |e investigator |4 oth | |
| 700 | 1 | |a Demchok, John A |e investigator |4 oth | |
| 700 | 1 | |a Mensah, Michael K A |e investigator |4 oth | |
| 700 | 1 | |a Tarnuzzer, Roy |e investigator |4 oth | |
| 700 | 1 | |a Wang, Zhining |e investigator |4 oth | |
| 700 | 1 | |a Yang, Liming |e investigator |4 oth | |
| 700 | 1 | |a Knijnenburg, Theo A |e investigator |4 oth | |
| 700 | 1 | |a Robertson, A Gordon |e investigator |4 oth | |
| 700 | 1 | |a Yau, Christina |e investigator |4 oth | |
| 700 | 1 | |a Benz, Christopher |e investigator |4 oth | |
| 700 | 1 | |a Huang, Kuan-Lin |e investigator |4 oth | |
| 700 | 1 | |a Newberg, Justin Y |e investigator |4 oth | |
| 700 | 1 | |a Frampton, Garrett M |e investigator |4 oth | |
| 700 | 1 | |a Mashl, R Jay |e investigator |4 oth | |
| 700 | 1 | |a Ding, Li |e investigator |4 oth | |
| 700 | 1 | |a Romanel, Alessandro |e investigator |4 oth | |
| 700 | 1 | |a Demichelis, Francesca |e investigator |4 oth | |
| 700 | 1 | |a Zhou, Wanding |e investigator |4 oth | |
| 700 | 1 | |a Laird, Peter W |e investigator |4 oth | |
| 700 | 1 | |a Shen, Hui |e investigator |4 oth | |
| 700 | 1 | |a Wong, Christopher K |e investigator |4 oth | |
| 700 | 1 | |a Stuart, Joshua M |e investigator |4 oth | |
| 700 | 1 | |a Lazar, Alexander J |e investigator |4 oth | |
| 700 | 1 | |a Le, Xiuning |e investigator |4 oth | |
| 700 | 1 | |a Oak, Ninad |e investigator |4 oth | |
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