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For: He J, Wen W, Beeghly A, Chen Z, Cao C, Shu XO, Zheng W, Long Q, Guo X. Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers. Nat Commun 2022;13:7118. [PMID: 36402776 PMCID: PMC9675749 DOI: 10.1038/s41467-022-34888-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022]  Open
Number Cited by Other Article(s)
1
Wang G, Zhang H, Shao M, Tian M, Feng H, Li Q, Cao C. Optimal variable identification for accurate detection of causal expression Quantitative Trait Loci with applications in heart-related diseases. Comput Struct Biotechnol J 2024;23:2478-2486. [PMID: 38952424 PMCID: PMC11215961 DOI: 10.1016/j.csbj.2024.05.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 07/03/2024]  Open
2
He J, Perera D, Wen W, Ping J, Li Q, Lyu L, Chen Z, Shu X, Long J, Cai Q, Shu XO, Zheng W, Long Q, Guo X. Enhancing Disease Risk Gene Discovery by Integrating Transcription Factor-Linked Trans-located Variants into Transcriptome-Wide Association Analyses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.10.23295443. [PMID: 37873299 PMCID: PMC10593059 DOI: 10.1101/2023.10.10.23295443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
3
Li JL, McClellan JC, Zhang H, Gao G, Huo D. Multi-tissue transcriptome-wide association studies identified 235 genes for intrinsic subtypes of breast cancer. J Natl Cancer Inst 2024;116:1105-1115. [PMID: 38400758 PMCID: PMC11223833 DOI: 10.1093/jnci/djae041] [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: 09/22/2023] [Revised: 01/25/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]  Open
4
Gao G, McClellan J, Barbeira AN, Fiorica PN, Li JL, Mu Z, Olopade OI, Huo D, Im HK. A multi-tissue, splicing-based joint transcriptome-wide association study identifies susceptibility genes for breast cancer. Am J Hum Genet 2024;111:1100-1113. [PMID: 38733992 PMCID: PMC11179262 DOI: 10.1016/j.ajhg.2024.04.010] [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: 10/09/2023] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024]  Open
5
Li Q, Song Q, Chen Z, Choi J, Moreno V, Ping J, Wen W, Li C, Shu X, Yan J, Shu XO, Cai Q, Long J, Huyghe JR, Pai R, Gruber SB, Casey G, Wang X, Toriola AT, Li L, Singh B, Lau KS, Zhou L, Wu C, Peters U, Zheng W, Long Q, Yin Z, Guo X. Large-scale integration of omics and electronic health records to identify potential risk protein biomarkers and therapeutic drugs for cancer prevention and intervention. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.29.24308170. [PMID: 38853880 PMCID: PMC11160851 DOI: 10.1101/2024.05.29.24308170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
6
He J, Li Q, Zhang Q. rvTWAS: identifying gene-trait association using sequences by utilizing transcriptome-directed feature selection. Genetics 2024;226:iyad204. [PMID: 38001381 DOI: 10.1093/genetics/iyad204] [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: 10/20/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]  Open
7
Chen Z, Song W, Shu XO, Wen W, Devall M, Dampier C, Moratalla-Navarro F, Cai Q, Long J, Van Kaer L, Wu L, Huyghe JR, Thomas M, Hsu L, Woods MO, Albanes D, Buchanan DD, Gsur A, Hoffmeister M, Vodicka P, Wolk A, Marchand LL, Wu AH, Phipps AI, Moreno V, Ulrike P, Zheng W, Casey G, Guo X. Novel insights into genetic susceptibility for colorectal cancer from transcriptome-wide association and functional investigation. J Natl Cancer Inst 2024;116:127-137. [PMID: 37632791 PMCID: PMC10777674 DOI: 10.1093/jnci/djad178] [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: 03/29/2023] [Revised: 07/10/2023] [Accepted: 08/19/2023] [Indexed: 08/28/2023]  Open
8
He J, Antonyan L, Zhu H, Ardila K, Li Q, Enoma D, Zhang W, Liu A, Chekouo T, Cao B, MacDonald ME, Arnold PD, Long Q. A statistical method for image-mediated association studies discovers genes and pathways associated with four brain disorders. Am J Hum Genet 2024;111:48-69. [PMID: 38118447 PMCID: PMC10806749 DOI: 10.1016/j.ajhg.2023.11.006] [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: 07/03/2023] [Revised: 11/04/2023] [Accepted: 11/16/2023] [Indexed: 12/22/2023]  Open
9
Guo X, Ping J, Yang Y, Su X, Shu XO, Wen W, Chen Z, Zhang Y, Tao R, Jia G, He J, Cai Q, Zhang Q, Giles GG, Pearlman R, Rennert G, Vodicka P, Phipps A, Gruber SB, Casey G, Peters U, Long J, Lin W, Zheng W. Large-scale alternative polyadenylation (APA)-wide association studies to identify putative susceptibility genes in human common cancers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.05.23298125. [PMID: 37986797 PMCID: PMC10659493 DOI: 10.1101/2023.11.05.23298125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
10
Shao M, Zhang Z, Sun H, He J, Wang J, Zhang Q, Cao C. Editorial: Statistical methods for genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) and their applications. Front Genet 2023;14:1287673. [PMID: 37766879 PMCID: PMC10520498 DOI: 10.3389/fgene.2023.1287673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]  Open
11
Sun Y, Bae YE, Zhu J, Zhang Z, Zhong H, Cheng C, Deng Y, Wu C, Wu L. A Splicing Transcriptome-Wide Association Study Identifies Candidate Altered Splicing for Prostate Cancer Risk. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023;27:372-380. [PMID: 37486714 DOI: 10.1089/omi.2023.0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
12
Gao G, Fiorica PN, McClellan J, Barbeira AN, Li JL, Olopade OI, Im HK, Huo D. A joint transcriptome-wide association study across multiple tissues identifies candidate breast cancer susceptibility genes. Am J Hum Genet 2023;110:950-962. [PMID: 37164006 PMCID: PMC10257003 DOI: 10.1016/j.ajhg.2023.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/14/2023] [Indexed: 05/12/2023]  Open
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