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Bick AG, Metcalf GA, Mayo KR, Lichtenstein L, Rura S, Carroll RJ, Musick A, Linder JE, Jordan IK, Nagar SD, Sharma S, Meller R, Basford M, Boerwinkle E, Cicek MS, Doheny KF, Eichler EE, Gabriel S, Gibbs RA, Glazer D, Harris PA, Jarvik GP, Philippakis A, Rehm HL, Roden DM, Thibodeau SN, Topper S, Blegen AL, Wirkus SJ, Wagner VA, Meyer JG, Cicek MS, Muzny DM, Venner E, Mawhinney MZ, Griffith SML, Hsu E, Ling H, Adams MK, Walker K, Hu J, Doddapaneni H, Kovar CL, Murugan M, Dugan S, Khan Z, Boerwinkle E, Lennon NJ, Austin-Tse C, Banks E, Gatzen M, Gupta N, Henricks E, Larsson K, McDonough S, Harrison SM, Kachulis C, Lebo MS, Neben CL, Steeves M, Zhou AY, Smith JD, Frazar CD, Davis CP, Patterson KE, Wheeler MM, McGee S, Lockwood CM, Shirts BH, Pritchard CC, Murray ML, Vasta V, Leistritz D, Richardson MA, Buchan JG, Radhakrishnan A, Krumm N, Ehmen BW, Schwartz S, Aster MMT, Cibulskis K, Haessly A, Asch R, Cremer A, Degatano K, Shergill A, Gauthier LD, Lee SK, Hatcher A, Grant GB, Brandt GR, Covarrubias M, Banks E, Able A, Green AE, Carroll RJ, Zhang J, Condon HR, Wang Y, Dillon MK, Albach CH, Baalawi W, Choi SH, Wang X, Rosenthal EA, Ramirez AH, Lim S, Nambiar S, Ozenberger B, Wise AL, Lunt C, Ginsburg GS, Denny JC. Genomic data in the All of Us Research Program. Nature 2024; 627:340-346. [PMID: 38374255 PMCID: PMC10937371 DOI: 10.1038/s41586-023-06957-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/08/2023] [Indexed: 02/21/2024]
Abstract
Comprehensively mapping the genetic basis of human disease across diverse individuals is a long-standing goal for the field of human genetics1-4. The All of Us Research Program is a longitudinal cohort study aiming to enrol a diverse group of at least one million individuals across the USA to accelerate biomedical research and improve human health5,6. Here we describe the programme's genomics data release of 245,388 clinical-grade genome sequences. This resource is unique in its diversity as 77% of participants are from communities that are historically under-represented in biomedical research and 46% are individuals from under-represented racial and ethnic minorities. All of Us identified more than 1 billion genetic variants, including more than 275 million previously unreported genetic variants, more than 3.9 million of which had coding consequences. Leveraging linkage between genomic data and the longitudinal electronic health record, we evaluated 3,724 genetic variants associated with 117 diseases and found high replication rates across both participants of European ancestry and participants of African ancestry. Summary-level data are publicly available, and individual-level data can be accessed by researchers through the All of Us Researcher Workbench using a unique data passport model with a median time from initial researcher registration to data access of 29 hours. We anticipate that this diverse dataset will advance the promise of genomic medicine for all.
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Venner E, Muzny D, Smith JD, Walker K, Neben CL, Lockwood CM, Empey PE, Metcalf GA, Kachulis C, Mian S, Musick A, Rehm HL, Harrison S, Gabriel S, Gibbs RA, Nickerson D, Zhou AY, Doheny K, Ozenberger B, Topper SE, Lennon NJ. Whole-genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program. Genome Med 2022; 14:34. [PMID: 35346344 PMCID: PMC8962531 DOI: 10.1186/s13073-022-01031-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 02/14/2022] [Indexed: 01/13/2023] Open
Abstract
Background The All of Us Research Program (AoURP, “the program”) is an initiative, sponsored by the National Institutes of Health (NIH), that aims to enroll one million people (or more) across the USA. Through repeated engagement of participants, a research resource is being created to enable a variety of future observational and interventional studies. The program has also committed to genomic data generation and returning important health-related information to participants. Methods Whole-genome sequencing (WGS), variant calling processes, data interpretation, and return-of-results procedures had to be created and receive an Investigational Device Exemption (IDE) from the United States Food and Drug Administration (FDA). The performance of the entire workflow was assessed through the largest known cross-center, WGS-based, validation activity that was refined iteratively through interactions with the FDA over many months. Results The accuracy and precision of the WGS process as a device for the return of certain health-related genomic results was determined to be sufficient, and an IDE was granted. Conclusions We present here both the process of navigating the IDE application process with the FDA and the results of the validation study as a guide to future projects which may need to follow a similar path. Changes to the program in the future will be covered in supplementary submissions to the IDE and will support additional variant classes, sample types, and any expansion to the reportable regions. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01031-z.
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Devarakonda SHK, Waqar SN, Guebert K, Maggi LB, Carpenter D, Ozenberger B, Govindan R, Morgensztern D. Characteristics of 1q amplification in adenocarcinoma of the lung (LUAD). J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.e22195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Saiama Naheed Waqar
- Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Kalin Guebert
- Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Leonard B. Maggi
- Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Danielle Carpenter
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Bradley Ozenberger
- The Genome Institute at Washington University in St.Louis, St. Louis, MO
| | - Ramaswamy Govindan
- Division of Oncology, Washington University School of Medicine, St. Louis, MO
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Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008; 455:1069-75. [PMID: 18948947 PMCID: PMC2694412 DOI: 10.1038/nature07423] [Citation(s) in RCA: 2027] [Impact Index Per Article: 126.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 09/10/2008] [Indexed: 02/08/2023]
Abstract
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.
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Affiliation(s)
- Li Ding
- The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
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Young K, Lin S, Sun L, Lee E, Modi M, Hellings S, Husbands M, Ozenberger B, Franco R. Identification of a calcium channel modulator using a high throughput yeast two-hybrid screen. Nat Biotechnol 1998; 16:946-50. [PMID: 9788351 DOI: 10.1038/nbt1098-946] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The interaction of the N-type calcium channel beta3 subunit with the alpha1B subunit alters the activation/inactivation kinetics and the maximal conductance of the channel. The defined protein-protein interaction of the human alpha1B and beta3 subunits provides a target for small-molecule modulation of N-type channel activity. We describe a high throughput screen based on a counterselection yeast two-hybrid assay, which was used to identify small molecules that disrupt alpha1B-beta3 subunit interactions and inhibit N-type calcium channel activity. These small molecules may be a new class of calcium channel antagonists with therapeutic potential.
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Affiliation(s)
- K Young
- Wyeth-Ayerst Research, CNS Disorders, Princeton, NJ 08543, USA
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