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For: Geoffroy E, Gregga I, Wheeler HE. Population-Matched Transcriptome Prediction Increases TWAS Discovery and Replication Rate. iScience 2020;23:101850. [PMID: 33313492 DOI: 10.1016/j.isci.2020.101850] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Petty LE, Chen HH, Frankel EG, Zhu W, Downie CG, Graff M, Lin P, Sharma P, Zhang X, Scartozzi AC, Roshani R, Landman JM, Boehnke M, Bowden DW, Chambers JC, Mahajan A, McCarthy MI, Ng MCY, Sim X, Spracklen CN, Zhang W, Preuss M, Bottinger EP, Nadkarni GN, Loos RJF, Chen YDI, Tan J, Ipp E, Genter P, Emery LS, Louie T, Sofer T, Stilp AM, Taylor KD, Xiang AH, Buchanan TA, Roll K, Gao C, Palmer ND, Norris JM, Wagenknecht LE, Nousome D, Varma R, McKean-Cowdin R, Guo X, Hai Y, Hsueh W, Sandow K, Parra EJ, Cruz M, Valladares-Salgado A, Wacher-Rodarte N, Rotter JI, Goodarzi MO, Rich SS, Bertoni A, Raffel LJ, Nadler JL, Kandeel FR, Duggirala R, Blangero J, Lehman DM, DeFronzo RA, Thameem F, Wang Y, Gahagan S, Blanco E, Burrows R, Huerta-Chagoya A, Florez JC, Tusie-Luna T, González-Villalpando C, Orozco L, Haiman CA, Hanis CL, Rohde R, Whitsel EA, Reiner AP, Kooperberg C, Li Y, Duan Q, Lee M, Correa-Burrows P, Fried SK, North KE, McCormick JB, Fisher-Hoch SP, Gamazon ER, Morris AP, Mercader JM, Highland HM, Below JE. Large-scale multi-omics analyses in Hispanic/Latino populations identify genes for cardiometabolic traits. Nat Commun 2025;16:3438. [PMID: 40210677 PMCID: PMC11985957 DOI: 10.1038/s41467-025-58574-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 03/21/2025] [Indexed: 04/12/2025]  Open
2
Xu X, Wang S, Zhou H, Tan Q, Lang Z, Zhu Y, Yuan H, Wu Z, Zhu L, Hu K, Li W, Zhou D, Wu M, Wu X. Transcriptome-wide association study of alternative polyadenylation identifies susceptibility genes in non-small cell lung cancer. Oncogene 2025:10.1038/s41388-025-03338-8. [PMID: 40205015 DOI: 10.1038/s41388-025-03338-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 02/09/2025] [Accepted: 02/28/2025] [Indexed: 04/11/2025]
3
Yang H, Huang H, Pu K. A cross-tissue transcriptome-wide association study identified susceptibility genes for age-related macular degeneration. Sci Rep 2025;15:4788. [PMID: 39922885 PMCID: PMC11807202 DOI: 10.1038/s41598-025-89246-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Accepted: 02/04/2025] [Indexed: 02/10/2025]  Open
4
Slack SD, Esquinca E, Arehart CH, Boorgula MP, Szczesny B, Romero A, Campbell M, Chavan S, Rafaels N, Watson H, Landis RC, Hansel NN, Rotimi CN, Olopade CO, Figueiredo CA, Ober C, Liu AH, Kenny EE, Kammers K, Ruczinski I, Taub MA, Daya M, Gignoux CR, Kechris K, Barnes KC, Mathias RA, Johnson RK. Prediction and Characterization of Genetically Regulated Expression of Target Tissues in Asthma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.02.06.25321273. [PMID: 39974046 PMCID: PMC11838648 DOI: 10.1101/2025.02.06.25321273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
5
Pagnuco I, Eyre S, Rattray M, Morris AP. Transferability of Single- and Cross-Tissue Transcriptome Imputation Models Across Ancestry Groups. Genet Epidemiol 2025;49:e22611. [PMID: 39812501 PMCID: PMC11734644 DOI: 10.1002/gepi.22611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 10/02/2024] [Accepted: 12/19/2024] [Indexed: 01/16/2025]
6
Evans P, Nagai T, Konkashbaev A, Zhou D, Knapik EW, Gamazon ER. Transcriptome-Wide Association Studies (TWAS): Methodologies, Applications, and Challenges. Curr Protoc 2024;4:e981. [PMID: 38314955 PMCID: PMC10846672 DOI: 10.1002/cpz1.981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
7
Araujo DS, Nguyen C, Hu X, Mikhaylova AV, Gignoux C, Ardlie K, Taylor KD, Durda P, Liu Y, Papanicolaou G, Cho MH, Rich SS, Rotter JI, NHLBI TOPMed Consortium, Im HK, Manichaikul A, Wheeler HE. Multivariate adaptive shrinkage improves cross-population transcriptome prediction and association studies in underrepresented populations. HGG ADVANCES 2023;4:100216. [PMID: 37869564 PMCID: PMC10589725 DOI: 10.1016/j.xhgg.2023.100216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 10/24/2023]  Open
8
Ghaffar A, Nyholt DR. Integrating eQTL and GWAS data characterises established and identifies novel migraine risk loci. Hum Genet 2023;142:1113-1137. [PMID: 37245199 PMCID: PMC10449685 DOI: 10.1007/s00439-023-02568-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/02/2023] [Indexed: 05/29/2023]
9
Kachuri L, Mak ACY, Hu D, Eng C, Huntsman S, Elhawary JR, Gupta N, Gabriel S, Xiao S, Keys KL, Oni-Orisan A, Rodríguez-Santana JR, LeNoir MA, Borrell LN, Zaitlen NA, Williams LK, Gignoux CR, Burchard EG, Ziv E. Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture. Nat Genet 2023;55:952-963. [PMID: 37231098 PMCID: PMC10260401 DOI: 10.1038/s41588-023-01377-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/21/2023] [Indexed: 05/27/2023]
10
Araujo DS, Nguyen C, Hu X, Mikhaylova AV, Gignoux C, Ardlie K, Taylor KD, Durda P, Liu Y, Papanicolaou G, Cho MH, Rich SS, Rotter JI, NHLBI TOPMed Consortium, Im HK, Manichaikul A, Wheeler HE. Multivariate adaptive shrinkage improves cross-population transcriptome prediction for transcriptome-wide association studies in underrepresented populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527747. [PMID: 36798214 PMCID: PMC9934635 DOI: 10.1101/2023.02.09.527747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
11
Bhattacharya A, Hirbo JB, Zhou D, Zhou W, Zheng J, Kanai M, the Global Biobank Meta-analysis Initiative, Pasaniuc B, Gamazon ER, Cox NJ. Best practices for multi-ancestry, meta-analytic transcriptome-wide association studies: Lessons from the Global Biobank Meta-analysis Initiative. CELL GENOMICS 2022;2:100180. [PMID: 36341024 PMCID: PMC9631681 DOI: 10.1016/j.xgen.2022.100180] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 08/09/2022] [Accepted: 09/01/2022] [Indexed: 12/13/2022]
12
Yin X, Kim K, Suetsugu H, Bang SY, Wen L, Koido M, Ha E, Liu L, Sakamoto Y, Jo S, Leng RX, Otomo N, Kwon YC, Sheng Y, Sugano N, Hwang MY, Li W, Mukai M, Yoon K, Cai M, Ishigaki K, Chung WT, Huang H, Takahashi D, Lee SS, Wang M, Karino K, Shim SC, Zheng X, Miyamura T, Kang YM, Ye D, Nakamura J, Suh CH, Tang Y, Motomura G, Park YB, Ding H, Kuroda T, Choe JY, Li C, Niiro H, Park Y, Shen C, Miyamoto T, Ahn GY, Fei W, Takeuchi T, Shin JM, Li K, Kawaguchi Y, Lee YK, Wang YF, Amano K, Park DJ, Yang W, Tada Y, Lau YL, Yamaji K, Zhu Z, Shimizu M, Atsumi T, Suzuki A, Sumida T, Okada Y, Matsuda K, Matsuo K, Kochi Y, Yamamoto K, Ohmura K, Kim TH, Yang S, Yamamoto T, Kim BJ, Shen N, Ikegawa S, Lee HS, Zhang X, Terao C, Cui Y, Bae SC. Biological insights into systemic lupus erythematosus through an immune cell-specific transcriptome-wide association study. Ann Rheum Dis 2022;81:1273-1280. [PMID: 35609976 PMCID: PMC9380500 DOI: 10.1136/annrheumdis-2022-222345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/11/2022] [Indexed: 11/04/2022]
13
Dai Y, Jia P, Zhao Z, Gottlieb A. A Method for Bridging Population-Specific Genotypes to Detect Gene Modules Associated with Alzheimer's Disease. Cells 2022;11:2219. [PMID: 35883662 PMCID: PMC9319087 DOI: 10.3390/cells11142219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023]  Open
14
Highland HM, Wojcik GL, Graff M, Nishimura KK, Hodonsky CJ, Baldassari AR, Cote AC, Cheng I, Gignoux CR, Tao R, Li Y, Boerwinkle E, Fornage M, Haessler J, Hindorff LA, Hu Y, Justice AE, Lin BM, Lin D, Stram DO, Haiman CA, Kooperberg C, Le Marchand L, Matise TC, Kenny EE, Carlson CS, Stahl EA, Avery CL, North KE, Ambite JL, Buyske S, Loos RJ, Peters U, Young KL, Bien SA, Huckins LM. Predicted gene expression in ancestrally diverse populations leads to discovery of susceptibility loci for lifestyle and cardiometabolic traits. Am J Hum Genet 2022;109:669-679. [PMID: 35263625 PMCID: PMC9069067 DOI: 10.1016/j.ajhg.2022.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/15/2022] [Indexed: 02/06/2023]  Open
15
Schubert R, Geoffroy E, Gregga I, Mulford AJ, Aguet F, Ardlie K, Gerszten R, Clish C, Van Den Berg D, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy R, Conomos M, Blackwell T, Papanicolaou G, Lappalainen T, Mikhaylova AV, Thornton TA, Cho MH, Gignoux CR, Lange L, Lange E, Rich SS, Rotter JI, NHLBI TOPMed Consortium, Manichaikul A, Im HK, Wheeler HE. Protein prediction for trait mapping in diverse populations. PLoS One 2022;17:e0264341. [PMID: 35202437 PMCID: PMC8870552 DOI: 10.1371/journal.pone.0264341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022]  Open
16
Soumboundou M, Dossou J, Kalaga Y, Nkengurutse I, Faye I, Guingani A, Gadji M, Yameogo KJ, Zongo H, Mbaye G, Dem A, Diarra M, Adjibade R, Djebou C, Junker S, Oudrhiri N, Hempel WM, Dieterlen A, Jeandidier E, Carde P, El Maalouf E, Colicchio B, Bennaceur-Griscelli A, Fenech M, Voisin P, Rodriguez-Lafrasse C, M'Kacher R. Is Response to Genotoxic Stress Similar in Populations of African and European Ancestry? A Study of Dose-Response After in vitro Irradiation. Front Genet 2021;12:657999. [PMID: 34868192 PMCID: PMC8632650 DOI: 10.3389/fgene.2021.657999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 05/13/2021] [Indexed: 11/17/2022]  Open
17
Wen J, Xie M, Rowland B, Rosen JD, Sun Q, Chen J, Tapia AL, Qian H, Kowalski MH, Shan Y, Young KL, Graff M, Argos M, Avery CL, Bien SA, Buyske S, Yin J, Choquet H, Fornage M, Hodonsky CJ, Jorgenson E, Kooperberg C, Loos RJF, Liu Y, Moon JY, North KE, Rich SS, Rotter JI, Smith JA, Zhao W, Shang L, Wang T, Zhou X, Reiner AP, Raffield LM, Li Y. Transcriptome-Wide Association Study of Blood Cell Traits in African Ancestry and Hispanic/Latino Populations. Genes (Basel) 2021;12:1049. [PMID: 34356065 PMCID: PMC8307403 DOI: 10.3390/genes12071049] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/21/2023]  Open
18
Feng H, Mancuso N, Pasaniuc B, Kraft P. Multitrait transcriptome-wide association study (TWAS) tests. Genet Epidemiol 2021;45:563-576. [PMID: 34082479 DOI: 10.1002/gepi.22391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 12/19/2022]
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