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For: Kichaev G, Roytman M, Johnson R, Eskin E, Lindström S, Kraft P, Pasaniuc B. Improved methods for multi-trait fine mapping of pleiotropic risk loci. Bioinformatics 2016;33:248-255. [PMID: 27663501 DOI: 10.1093/bioinformatics/btw615] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/28/2016] [Accepted: 09/17/2016] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
1
Canida T, Ke H, Chen S, Ye Z, Ma T. Multivariate Bayesian variable selection for multi-trait genetic fine mapping. J R Stat Soc Ser C Appl Stat 2025;74:331-351. [PMID: 40092670 PMCID: PMC11905884 DOI: 10.1093/jrsssc/qlae055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/21/2024] [Accepted: 10/01/2024] [Indexed: 03/19/2025]
2
Kuksa PP, Ionita M, Carter L, Cifello J, Clark K, Valladares O, Leung YY, Wang LS. BTS: scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across omics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.10.30.621077. [PMID: 39975395 PMCID: PMC11838512 DOI: 10.1101/2024.10.30.621077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
3
Woodward DJ, Thorp JG, Middeldorp CM, Akóṣílè W, Derks EM, Gerring ZF. Leveraging pleiotropy for the improved treatment of psychiatric disorders. Mol Psychiatry 2025;30:705-721. [PMID: 39390223 PMCID: PMC11746150 DOI: 10.1038/s41380-024-02771-7] [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: 05/13/2024] [Revised: 09/23/2024] [Accepted: 09/25/2024] [Indexed: 10/12/2024]
4
Richard D, Muthuirulan P, Young M, Yengo L, Vedantam S, Marouli E, Bartell E, Hirschhorn J, Capellini TD. Functional genomics of human skeletal development and the patterning of height heritability. Cell 2025;188:15-32.e24. [PMID: 39549696 PMCID: PMC11724752 DOI: 10.1016/j.cell.2024.10.040] [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: 12/31/2023] [Revised: 08/01/2024] [Accepted: 10/21/2024] [Indexed: 11/18/2024]
5
Wang J, Ouyang L, You T, Yang N, Xu X, Zhang W, Yang H, Yi X, Huang D, Zhou W, Li M. CAUSALdb2: an updated database for causal variants of complex traits. Nucleic Acids Res 2025;53:D1295-D1301. [PMID: 39558176 PMCID: PMC11701604 DOI: 10.1093/nar/gkae1096] [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: 09/08/2024] [Revised: 10/16/2024] [Accepted: 10/25/2024] [Indexed: 11/20/2024]  Open
6
Li Y, Xiao J, Ming J, Zeng Y, Cai M. Funmap: integrating high-dimensional functional annotations to improve fine-mapping. Bioinformatics 2024;41:btaf017. [PMID: 39799513 PMCID: PMC11769679 DOI: 10.1093/bioinformatics/btaf017] [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: 06/23/2024] [Revised: 12/20/2024] [Accepted: 01/09/2025] [Indexed: 01/15/2025]  Open
7
Kontou PI, Bagos PG. The goldmine of GWAS summary statistics: a systematic review of methods and tools. BioData Min 2024;17:31. [PMID: 39238044 PMCID: PMC11375927 DOI: 10.1186/s13040-024-00385-x] [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: 02/09/2024] [Accepted: 08/27/2024] [Indexed: 09/07/2024]  Open
8
Zou Y, Carbonetto P, Xie D, Wang G, Stephens M. Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.14.536893. [PMID: 37425935 PMCID: PMC10327118 DOI: 10.1101/2023.04.14.536893] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
9
Tan MMX, Lawton MA, Pollard MI, Brown E, Real R, Carrasco AM, Bekadar S, Jabbari E, Reynolds RH, Iwaki H, Blauwendraat C, Kanavou S, Hubbard L, Malek N, Grosset KA, Bajaj N, Barker RA, Burn DJ, Bresner C, Foltynie T, Wood NW, Williams-Gray CH, Andreassen OA, Toft M, Elbaz A, Artaud F, Brice A, Corvol JC, Aasly J, Farrer MJ, Nalls MA, Singleton AB, Williams NM, Ben-Shlomo Y, Hardy J, Hu MTM, Grosset DG, Shoai M, Pihlstrøm L, Morris HR. Genome-wide determinants of mortality and motor progression in Parkinson's disease. NPJ Parkinsons Dis 2024;10:113. [PMID: 38849413 PMCID: PMC11161485 DOI: 10.1038/s41531-024-00729-8] [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: 02/05/2024] [Accepted: 05/24/2024] [Indexed: 06/09/2024]  Open
10
Li X, Zhou Z, Ma Y, Ding K, Xiao H, Chen D, Liu N. Shared Genetic Architectures between Coronary Artery Disease and Type 2 Diabetes Mellitus in East Asian and European Populations. Biomedicines 2024;12:1243. [PMID: 38927450 PMCID: PMC11201280 DOI: 10.3390/biomedicines12061243] [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: 03/25/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024]  Open
11
Chin IM, Gardell ZA, Corces MR. Decoding polygenic diseases: advances in noncoding variant prioritization and validation. Trends Cell Biol 2024;34:465-483. [PMID: 38719704 DOI: 10.1016/j.tcb.2024.03.005] [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: 11/22/2023] [Revised: 03/12/2024] [Accepted: 03/21/2024] [Indexed: 06/09/2024]
12
Liao Y, Yu H, Zhang Y, Lu Z, Sun Y, Guo L, Guo J, Kang Z, Feng X, Sun Y, Wang G, Su Z, Lu T, Yang Y, Li W, Lv L, Yan H, Zhang D, Yue W. Genome-wide association study implicates lipid pathway dysfunction in antipsychotic-induced weight gain: multi-ancestry validation. Mol Psychiatry 2024;29:1857-1868. [PMID: 38336841 DOI: 10.1038/s41380-024-02447-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
13
Rossen J, Shi H, Strober BJ, Zhang MJ, Kanai M, McCaw ZR, Liang L, Weissbrod O, Price AL. MultiSuSiE improves multi-ancestry fine-mapping in All of Us whole-genome sequencing data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.13.24307291. [PMID: 38798542 PMCID: PMC11118590 DOI: 10.1101/2024.05.13.24307291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
14
Nizamuddin S, Timmers HTM. greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets. Bioinformatics 2024;40:btae307. [PMID: 38718209 PMCID: PMC11112040 DOI: 10.1093/bioinformatics/btae307] [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: 01/29/2024] [Revised: 03/28/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024]  Open
15
Chen H, Wang Z, Gong L, Wang Q, Chen W, Wang J, Ma X, Ding R, Li X, Zou X, Plass M, Lian C, Ni T, Wei GH, Li W, Deng L, Li L. A distinct class of pan-cancer susceptibility genes revealed by an alternative polyadenylation transcriptome-wide association study. Nat Commun 2024;15:1729. [PMID: 38409266 PMCID: PMC10897204 DOI: 10.1038/s41467-024-46064-7] [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: 08/09/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024]  Open
16
Hodonsky CJ, Turner AW, Khan MD, Barrientos NB, Methorst R, Ma L, Lopez NG, Mosquera JV, Auguste G, Farber E, Ma WF, Wong D, Onengut-Gumuscu S, Kavousi M, Peyser PA, van der Laan SW, Leeper NJ, Kovacic JC, Björkegren JLM, Miller CL. Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci. CELL GENOMICS 2024;4:100465. [PMID: 38190101 PMCID: PMC10794848 DOI: 10.1016/j.xgen.2023.100465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/07/2023] [Accepted: 11/19/2023] [Indexed: 01/09/2024]
17
Zhang X, Jiang W, Zhao H. Integration of expression QTLs with fine mapping via SuSiE. PLoS Genet 2024;20:e1010929. [PMID: 38271473 PMCID: PMC10846745 DOI: 10.1371/journal.pgen.1010929] [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: 08/22/2023] [Revised: 02/06/2024] [Accepted: 01/06/2024] [Indexed: 01/27/2024]  Open
18
Mo C, Ye Z, Pan Y, Zhang Y, Wu Q, Bi C, Liu S, Mitchell B, Kochunov P, Hong LE, Ma T, Chen S. An in-depth association analysis of genetic variants within nicotine-related loci: Meeting in middle of GWAS and genetic fine-mapping. Mol Cell Neurosci 2023;127:103895. [PMID: 37634742 PMCID: PMC11128188 DOI: 10.1016/j.mcn.2023.103895] [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: 01/19/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]  Open
19
Zhou F, Soremekun O, Chikowore T, Fatumo S, Barroso I, Morris AP, Asimit JL. Leveraging information between multiple population groups and traits improves fine-mapping resolution. Nat Commun 2023;14:7279. [PMID: 37949886 PMCID: PMC10638399 DOI: 10.1038/s41467-023-43159-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]  Open
20
Chen H, Luo H, Tian T, Li S, Jiang Y. Integrated Analyses of Single-Cell Transcriptome and Mendelian Randomization Reveal the Protective Role of Resistin in Sepsis Survival in Intensive Care Unit. Int J Mol Sci 2023;24:14982. [PMID: 37834432 PMCID: PMC10573869 DOI: 10.3390/ijms241914982] [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: 09/03/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]  Open
21
Luo J, Huang H, Qiao H, Tan J, Chen W, Zhang M, Ruiz-Linares A, Wang J, Yang Y, Jin L, Headon DJ, Wang S. GWASs Identify Genetic Loci Associated with Human Scalp Hair Whorl Direction. J Invest Dermatol 2023;143:2065-2068.e10. [PMID: 37565938 DOI: 10.1016/j.jid.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/07/2023] [Accepted: 04/10/2023] [Indexed: 08/12/2023]
22
Als TD, Kurki MI, Grove J, Voloudakis G, Therrien K, Tasanko E, Nielsen TT, Naamanka J, Veerapen K, Levey DF, Bendl J, Bybjerg-Grauholm J, Zeng B, Demontis D, Rosengren A, Athanasiadis G, Bækved-Hansen M, Qvist P, Bragi Walters G, Thorgeirsson T, Stefánsson H, Musliner KL, Rajagopal VM, Farajzadeh L, Thirstrup J, Vilhjálmsson BJ, McGrath JJ, Mattheisen M, Meier S, Agerbo E, Stefánsson K, Nordentoft M, Werge T, Hougaard DM, Mortensen PB, Stein MB, Gelernter J, Hovatta I, Roussos P, Daly MJ, Mors O, Palotie A, Børglum AD. Depression pathophysiology, risk prediction of recurrence and comorbid psychiatric disorders using genome-wide analyses. Nat Med 2023;29:1832-1844. [PMID: 37464041 PMCID: PMC10839245 DOI: 10.1038/s41591-023-02352-1] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 04/17/2023] [Indexed: 07/20/2023]
23
Yang Z, Wang C, Liu L, Khan A, Lee A, Vardarajan B, Mayeux R, Kiryluk K, Ionita-Laza I. CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses. Nat Genet 2023;55:1057-1065. [PMID: 37169873 DOI: 10.1038/s41588-023-01392-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
24
Wang Z, Zhao G, Li B, Fang Z, Chen Q, Wang X, Luo T, Wang Y, Zhou Q, Li K, Xia L, Zhang Y, Zhou X, Pan H, Zhao Y, Wang Y, Wang L, Guo J, Tang B, Xia K, Li J. Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-coding Variants. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:649-661. [PMID: 35272052 PMCID: PMC10787016 DOI: 10.1016/j.gpb.2022.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 12/28/2021] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
25
McManus JN, Lovelett RJ, Lowengrub D, Christensen S. A unifying statistical framework to discover disease genes from GWASs. CELL GENOMICS 2023;3:100264. [PMID: 36950381 PMCID: PMC10025450 DOI: 10.1016/j.xgen.2023.100264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/07/2022] [Accepted: 01/19/2023] [Indexed: 03/10/2023]
26
Hodonsky CJ, Turner AW, Khan MD, Barrientos NB, Methorst R, Ma L, Lopez NG, Mosquera JV, Auguste G, Farber E, Ma WF, Wong D, Onengut-Gumuscu S, Kavousi M, Peyser PA, van der Laan SW, Leeper NJ, Kovacic JC, Björkegren JLM, Miller CL. Integrative multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.09.23285622. [PMID: 36824883 PMCID: PMC9949190 DOI: 10.1101/2023.02.09.23285622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
27
Zhou H, Arapoglou T, Li X, Li Z, Zheng X, Moore J, Asok A, Kumar S, Blue E, Buyske S, Cox N, Felsenfeld A, Gerstein M, Kenny E, Li B, Matise T, Philippakis A, Rehm HL, Sofia HJ, Snyder G, NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Weng Z, Neale B, Sunyaev S, Lin X. FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Res 2023;51:D1300-D1311. [PMID: 36350676 PMCID: PMC9825437 DOI: 10.1093/nar/gkac966] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/25/2022] [Accepted: 10/14/2022] [Indexed: 11/11/2022]  Open
28
McDonald MLN, Lakshman Kumar P, Srinivasasainagendra V, Nair A, Rocco AP, Wilson AC, Chiles JW, Richman JS, Pinson SA, Dennis RA, Jagadale V, Brown CJ, Pyarajan S, Tiwari HK, Bamman MM, Singh JA. Novel genetic loci associated with osteoarthritis in multi-ancestry analyses in the Million Veteran Program and UK Biobank. Nat Genet 2022;54:1816-1826. [PMID: 36411363 DOI: 10.1038/s41588-022-01221-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/05/2022] [Indexed: 11/22/2022]
29
Chen J, Wang L, De Jager PL, Bennett DA, Buchman AS, Yang J. A scalable Bayesian functional GWAS method accounting for multivariate quantitative functional annotations with applications for studying Alzheimer disease. HGG ADVANCES 2022;3:100143. [PMID: 36204489 PMCID: PMC9530673 DOI: 10.1016/j.xhgg.2022.100143] [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: 01/28/2022] [Accepted: 09/14/2022] [Indexed: 11/30/2022]  Open
30
Dubé M, Chazara O, Lemaçon A, Asselin G, Provost S, Barhdadi A, Lemieux Perreault L, Mongrain I, Wang Q, Carss K, Paul DS, Cunningham JW, Rouleau J, Solomon SD, McMurray JJ, Yusuf S, Granger CB, Haefliger C, de Denus S, Tardif J. Pharmacogenomic study of heart failure and candesartan response from the CHARM programme. ESC Heart Fail 2022;9:2997-3008. [PMID: 35736394 PMCID: PMC9715825 DOI: 10.1002/ehf2.14026] [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: 09/23/2021] [Revised: 03/21/2022] [Accepted: 06/03/2022] [Indexed: 11/07/2022]  Open
31
Piras IS, Raju A, Don J, Schork NJ, Gerhard GS, DiStefano JK. Hepatic PEMT Expression Decreases with Increasing NAFLD Severity. Int J Mol Sci 2022;23:ijms23169296. [PMID: 36012560 PMCID: PMC9409182 DOI: 10.3390/ijms23169296] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022]  Open
32
Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, Han L, Morley T, Niestroj LM, Ulirsch J, Everett S, Howrigan DP, Boone PM, Fu J, Karczewski KJ, Kellaris G, Lowther C, Lucente D, Mohajeri K, Nõukas M, Nuttle X, Samocha KE, Trinh M, Ullah F, Võsa U, Hurles ME, Aradhya S, Davis EE, Finucane H, Gusella JF, Janze A, Katsanis N, Matyakhina L, Neale BM, Sanders D, Warren S, Hodge JC, Lal D, Ruderfer DM, Meck J, Mägi R, Esko T, Reymond A, Kutalik Z, Hakonarson H, Sunyaev S, Brand H, Talkowski ME. A cross-disorder dosage sensitivity map of the human genome. Cell 2022;185:3041-3055.e25. [PMID: 35917817 PMCID: PMC9742861 DOI: 10.1016/j.cell.2022.06.036] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/17/2022] [Accepted: 06/20/2022] [Indexed: 02/06/2023]
33
Dey KK, Gazal S, van de Geijn B, Kim SS, Nasser J, Engreitz JM, Price AL. SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease. CELL GENOMICS 2022;2:100145. [PMID: 35873673 PMCID: PMC9306342 DOI: 10.1016/j.xgen.2022.100145] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 04/03/2021] [Accepted: 05/27/2022] [Indexed: 12/11/2022]
34
Zhou F, Butterworth AS, Asimit JL. Flashfm-ivis: interactive visualization for fine-mapping of multiple quantitative traits. Bioinformatics 2022;38:4238-4242. [PMID: 35792838 PMCID: PMC9438951 DOI: 10.1093/bioinformatics/btac453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/31/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022]  Open
35
Song YQ, Hu SD, Lin X, Meng XH, Wang X, Zhang YH, Peng C, Gong R, Xu T, Zhang T, Li CZ, Pan DY, Yang JY, Greenbaum J, Shen J, Deng HW. Identification of PDXDC1 as a novel pleiotropic susceptibility locus shared between lumbar spine bone mineral density and birth weight. J Mol Med (Berl) 2022;100:723-734. [PMID: 35314877 PMCID: PMC9110509 DOI: 10.1007/s00109-021-02165-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/13/2021] [Accepted: 11/04/2021] [Indexed: 02/04/2023]
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Yuan Z, Liu L, Guo P, Yan R, Xue F, Zhou X. Likelihood-based Mendelian randomization analysis with automated instrument selection and horizontal pleiotropic modeling. SCIENCE ADVANCES 2022;8:eabl5744. [PMID: 35235357 PMCID: PMC8890724 DOI: 10.1126/sciadv.abl5744] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/05/2022] [Indexed: 05/03/2023]
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Network-Based Approach to Repurpose Approved Drugs for COVID-19 by Integrating GWAS and Text Mining Data. Processes (Basel) 2022. [DOI: 10.3390/pr10020326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
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Zhang X, Li TY, Xiao HM, Ehrlich KC, Shen H, Deng HW, Ehrlich M. Epigenomic and Transcriptomic Prioritization of Candidate Obesity-Risk Regulatory GWAS SNPs. Int J Mol Sci 2022;23:1271. [PMID: 35163195 PMCID: PMC8836216 DOI: 10.3390/ijms23031271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 02/06/2023]  Open
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Schilder BM, Humphrey J, Raj T. echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline. Bioinformatics 2022;38:536-539. [PMID: 34529038 PMCID: PMC10060715 DOI: 10.1093/bioinformatics/btab658] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 02/03/2023]  Open
40
Wang QS, Huang H. Methods for statistical fine-mapping and their applications to auto-immune diseases. Semin Immunopathol 2022;44:101-113. [PMID: 35041074 PMCID: PMC8837575 DOI: 10.1007/s00281-021-00902-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/22/2021] [Indexed: 01/07/2023]
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Schilder BM, Navarro E, Raj T. Multi-omic insights into Parkinson's Disease: From genetic associations to functional mechanisms. Neurobiol Dis 2021;163:105580. [PMID: 34871738 PMCID: PMC10101343 DOI: 10.1016/j.nbd.2021.105580] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023]  Open
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Srinivasan C, Phan BN, Lawler AJ, Ramamurthy E, Kleyman M, Brown AR, Kaplow IM, Wirthlin ME, Pfenning AR. Addiction-Associated Genetic Variants Implicate Brain Cell Type- and Region-Specific Cis-Regulatory Elements in Addiction Neurobiology. J Neurosci 2021;41:9008-9030. [PMID: 34462306 PMCID: PMC8549541 DOI: 10.1523/jneurosci.2534-20.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 06/18/2021] [Accepted: 07/10/2021] [Indexed: 12/14/2022]  Open
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Hernández N, Soenksen J, Newcombe P, Sandhu M, Barroso I, Wallace C, Asimit JL. The flashfm approach for fine-mapping multiple quantitative traits. Nat Commun 2021;12:6147. [PMID: 34686674 PMCID: PMC8536717 DOI: 10.1038/s41467-021-26364-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022]  Open
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The distribution of common-variant effect sizes. Nat Genet 2021;53:1243-1249. [PMID: 34326547 DOI: 10.1038/s41588-021-00901-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 06/23/2021] [Indexed: 01/08/2023]
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Althouse AD, Below JE, Claggett BL, Cox NJ, de Lemos JA, Deo RC, Duval S, Hachamovitch R, Kaul S, Keith SW, Secemsky E, Teixeira-Pinto A, Roger VL. Recommendations for Statistical Reporting in Cardiovascular Medicine: A Special Report From the American Heart Association. Circulation 2021;144:e70-e91. [PMID: 34032474 DOI: 10.1161/circulationaha.121.055393] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Fisher V, Sebastiani P, Cupples LA, Liu CT. ANNORE: Genetic fine mapping with functional annotation. Hum Mol Genet 2021;31:32-40. [PMID: 34302344 DOI: 10.1093/hmg/ddab210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022]  Open
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Pluta J, Pyle LC, Nead KT, Wilf R, Li M, Mitra N, Weathers B, D'Andrea K, Almstrup K, Anson-Cartwright L, Benitez J, Brown CD, Chanock S, Chen C, Cortessis VK, Ferlin A, Foresta C, Gamulin M, Gietema JA, Grasso C, Greene MH, Grotmol T, Hamilton RJ, Haugen TB, Hauser R, Hildebrandt MAT, Johnson ME, Karlsson R, Kiemeney LA, Lessel D, Lothe RA, Loud JT, Loveday C, Martin-Gimeno P, Meijer C, Nsengimana J, Quinn DI, Rafnar T, Ramdas S, Richiardi L, Skotheim RI, Stefansson K, Turnbull C, Vaughn DJ, Wiklund F, Wu X, Yang D, Zheng T, Wells AD, Grant SFA, Rajpert-De Meyts E, Schwartz SM, Bishop DT, McGlynn KA, Kanetsky PA, Nathanson KL. Identification of 22 susceptibility loci associated with testicular germ cell tumors. Nat Commun 2021;12:4487. [PMID: 34301922 PMCID: PMC8302763 DOI: 10.1038/s41467-021-24334-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 06/01/2021] [Indexed: 02/07/2023]  Open
48
Boocock J, Leask M, Okada Y, Matsuo H, Kawamura Y, Shi Y, Li C, Mount DB, Mandal AK, Wang W, Cadzow M, Gosling AL, Major TJ, Horsfield JA, Choi HK, Fadason T, O'Sullivan J, Stahl EA, Merriman TR. Genomic dissection of 43 serum urate-associated loci provides multiple insights into molecular mechanisms of urate control. Hum Mol Genet 2021;29:923-943. [PMID: 31985003 DOI: 10.1093/hmg/ddaa013] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/23/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022]  Open
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Liu YQ, Liu Y, Zhang Q, Xiao T, Deng HW. Identification of Novel Pleiotropic SNPs Associated with Osteoporosis and Rheumatoid Arthritis. Calcif Tissue Int 2021;109:17-31. [PMID: 33740106 PMCID: PMC8238865 DOI: 10.1007/s00223-021-00817-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/28/2021] [Indexed: 01/21/2023]
50
Dubé MP, Lemaçon A, Barhdadi A, Lemieux Perreault LP, Oussaïd E, Asselin G, Provost S, Sun M, Sandoval J, Legault MA, Mongrain I, Dubois A, Valois D, Dedelis E, Lousky J, Choi J, Goulet E, Savard C, Chicoine LM, Cossette M, Chabot-Blanchet M, Guertin MC, de Denus S, Bouabdallaoui N, Marchand R, Bassevitch Z, Nozza A, Gaudet D, L'Allier PL, Hussin J, Boivin G, Busseuil D, Tardif JC. Genetics of symptom remission in outpatients with COVID-19. Sci Rep 2021;11:10847. [PMID: 34035401 PMCID: PMC8149390 DOI: 10.1038/s41598-021-90365-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/11/2021] [Indexed: 01/09/2023]  Open
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