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For: Hukku A, Sampson MG, Luca F, Pique-Regi R, Wen X. Analyzing and reconciling colocalization and transcriptome-wide association studies from the perspective of inferential reproducibility. Am J Hum Genet 2022;109:825-837. [PMID: 35523146 PMCID: PMC9118134 DOI: 10.1016/j.ajhg.2022.04.005] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/04/2022] [Indexed: 11/29/2022]  Open
Number Cited by Other Article(s)
1
Chen DM, Dong R, Kachuri L, Hoffmann TJ, Jiang Y, Berndt SI, Shelley JP, Schaffer KR, Machiela MJ, Freedman ND, Huang WY, Li SA, Lilja H, Justice AC, Madduri RK, Rodriguez AA, Van Den Eeden SK, Chanock SJ, Haiman CA, Conti DV, Klein RJ, Mosley JD, Witte JS, Graff RE. Transcriptome-wide association analysis identifies candidate susceptibility genes for prostate-specific antigen levels in men without prostate cancer. HGG ADVANCES 2024;5:100315. [PMID: 38845201 DOI: 10.1016/j.xhgg.2024.100315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/18/2024]  Open
2
Keener R, Chhetri SB, Connelly CJ, Taub MA, Conomos MP, Weinstock J, Ni B, Strober B, Aslibekyan S, Auer PL, Barwick L, Becker LC, Blangero J, Bleecker ER, Brody JA, Cade BE, Celedon JC, Chang YC, Cupples LA, Custer B, Freedman BI, Gladwin MT, Heckbert SR, Hou L, Irvin MR, Isasi CR, Johnsen JM, Kenny EE, Kooperberg C, Minster RL, Naseri T, Viali S, Nekhai S, Pankratz N, Peyser PA, Taylor KD, Telen MJ, Wu B, Yanek LR, Yang IV, Albert C, Arnett DK, Ashley-Koch AE, Barnes KC, Bis JC, Blackwell TW, Boerwinkle E, Burchard EG, Carson AP, Chen Z, Chen YDI, Darbar D, de Andrade M, Ellinor PT, Fornage M, Gelb BD, Gilliland FD, He J, Islam T, Kaab S, Kardia SLR, Kelly S, Konkle BA, Kumar R, Loos RJF, Martinez FD, McGarvey ST, Meyers DA, Mitchell BD, Montgomery CG, North KE, Palmer ND, Peralta JM, Raby BA, Redline S, Rich SS, Roden D, Rotter JI, Ruczinski I, Schwartz D, Sciurba F, Shoemaker MB, Silverman EK, Sinner MF, Smith NL, Smith AV, Tiwari HK, Vasan RS, Weiss ST, Williams LK, Zhang Y, Ziv E, Raffield LM, Reiner AP, Arvanitis M, Greider CW, Mathias RA, Battle A. Validation of human telomere length multi-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as human telomere length regulation genes. Nat Commun 2024;15:4417. [PMID: 38789417 PMCID: PMC11126610 DOI: 10.1038/s41467-024-48394-y] [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: 07/13/2023] [Accepted: 04/26/2024] [Indexed: 05/26/2024]  Open
3
Eulalio T, Sun MW, Gevaert O, Greicius MD, Montine TJ, Nachun D, Montgomery SB. regionalpcs: improved discovery of DNA methylation associations with complex traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.590171. [PMID: 38746367 PMCID: PMC11092597 DOI: 10.1101/2024.05.01.590171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
4
De Almeida SD, Richter GM, de Coo A, Jepsen S, Kapferer-Seebacher I, Dommisch H, Berger K, Laudes M, Lieb W, Loos BG, van der Velde N, van Schoor N, de Groot L, Blanco J, Carracedo A, Cruz R, Schaefer AS. A genome-wide association study meta-analysis in a European sample of stage III/IV grade C periodontitis patients ≤35 years of age identifies new risk loci. J Clin Periodontol 2024;51:431-440. [PMID: 38140892 DOI: 10.1111/jcpe.13922] [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: 09/06/2023] [Revised: 11/07/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023]
5
Lappalainen T, Li YI, Ramachandran S, Gusev A. Genetic and molecular architecture of complex traits. Cell 2024;187:1059-1075. [PMID: 38428388 DOI: 10.1016/j.cell.2024.01.023] [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: 10/03/2023] [Revised: 12/20/2023] [Accepted: 01/16/2024] [Indexed: 03/03/2024]
6
Jia K, Shen J. Transcriptome-wide association studies associated with Crohn's disease: challenges and perspectives. Cell Biosci 2024;14:29. [PMID: 38403629 PMCID: PMC10895848 DOI: 10.1186/s13578-024-01204-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/04/2024] [Indexed: 02/27/2024]  Open
7
Zhao S, Crouse W, Qian S, Luo K, Stephens M, He X. Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits. Nat Genet 2024;56:336-347. [PMID: 38279041 PMCID: PMC10864181 DOI: 10.1038/s41588-023-01648-9] [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: 12/20/2022] [Accepted: 12/14/2023] [Indexed: 01/28/2024]
8
Cabana-Domínguez J, Llonga N, Arribas L, Alemany S, Vilar-Ribó L, Demontis D, Fadeuilhe C, Corrales M, Richarte V, Børglum AD, Ramos-Quiroga JA, Soler Artigas M, Ribasés M. Transcriptomic risk scores for attention deficit/hyperactivity disorder. Mol Psychiatry 2023;28:3493-3502. [PMID: 37537283 PMCID: PMC10618083 DOI: 10.1038/s41380-023-02200-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023]
9
Ursini G, Di Carlo P, Mukherjee S, Chen Q, Han S, Kim J, Deyssenroth M, Marsit CJ, Chen J, Hao K, Punzi G, Weinberger DR. Prioritization of potential causative genes for schizophrenia in placenta. Nat Commun 2023;14:2613. [PMID: 37188697 PMCID: PMC10185564 DOI: 10.1038/s41467-023-38140-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/17/2023] [Indexed: 05/17/2023]  Open
10
Chen DM, Dong R, Kachuri L, Hoffmann T, Jiang Y, Berndt SI, Shelley JP, Schaffer KR, Machiela MJ, Freedman ND, Huang WY, Li SA, Lilja H, Van Den Eeden SK, Chanock S, Haiman CA, Conti DV, Klein RJ, Mosley JD, Witte JS, Graff RE. Transcriptome-Wide Association Analysis Identifies Novel Candidate Susceptibility Genes for Prostate-Specific Antigen Levels in Men Without Prostate Cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.04.23289526. [PMID: 37205487 PMCID: PMC10187439 DOI: 10.1101/2023.05.04.23289526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
11
Okamoto J, Wang L, Yin X, Luca F, Pique-Regi R, Helms A, Im HK, Morrison J, Wen X. Probabilistic integration of transcriptome-wide association studies and colocalization analysis identifies key molecular pathways of complex traits. Am J Hum Genet 2023;110:44-57. [PMID: 36608684 PMCID: PMC9892769 DOI: 10.1016/j.ajhg.2022.12.002] [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: 09/01/2022] [Accepted: 12/06/2022] [Indexed: 01/07/2023]  Open
12
Yin X, Bose D, Kwon A, Hanks SC, Jackson AU, Stringham HM, Welch R, Oravilahti A, Fernandes Silva L, Locke AE, Fuchsberger C, Service SK, Erdos MR, Bonnycastle LL, Kuusisto J, Stitziel NO, Hall IM, Morrison J, Ripatti S, Palotie A, Freimer NB, Collins FS, Mohlke KL, Scott LJ, Fauman EB, Burant C, Boehnke M, Laakso M, Wen X. Integrating transcriptomics, metabolomics, and GWAS helps reveal molecular mechanisms for metabolite levels and disease risk. Am J Hum Genet 2022;109:1727-1741. [PMID: 36055244 PMCID: PMC9606383 DOI: 10.1016/j.ajhg.2022.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023]  Open
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