Systematic replication of smoking disease associations using survey responses and EHR data in the All of Us Research Program Article Swipe
YOU?
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· 2023
· Open Access
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· DOI: https://doi.org/10.1093/jamia/ocad205
Objective The All of Us Research Program (All of Us) aims to recruit over a million participants to further precision medicine. Essential to the verification of biobanks is a replication of known associations to establish validity. Here, we evaluated how well All of Us data replicated known cigarette smoking associations. Materials and Methods We defined smoking exposure as follows: (1) an EHR Smoking exposure that used International Classification of Disease codes; (2) participant provided information (PPI) Ever Smoking; and, (3) PPI Current Smoking, both from the lifestyle survey. We performed a phenome-wide association study (PheWAS) for each smoking exposure measurement type. For each, we compared the effect sizes derived from the PheWAS to published meta-analyses that studied cigarette smoking from PubMed. We defined two levels of replication of meta-analyses: (1) nominally replicated: which required agreement of direction of effect size, and (2) fully replicated: which required overlap of confidence intervals. Results PheWASes with EHR Smoking, PPI Ever Smoking, and PPI Current Smoking revealed 736, 492, and 639 phenome-wide significant associations, respectively. We identified 165 meta-analyses representing 99 distinct phenotypes that could be matched to EHR phenotypes. At P < .05, 74 were nominally replicated and 55 were fully replicated. At P < 2.68 × 10−5 (Bonferroni threshold), 58 were nominally replicated and 40 were fully replicated. Discussion Most phenotypes found in published meta-analyses associated with smoking were nominally replicated in All of Us. Both survey and EHR definitions for smoking produced similar results. Conclusion This study demonstrated the feasibility of studying common exposures using All of Us data.
Related Topics
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/jamia/ocad205
- https://academic.oup.com/jamia/advance-article-pdf/doi/10.1093/jamia/ocad205/52603616/ocad205.pdf
- OA Status
- hybrid
- Cited By
- 6
- References
- 191
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4387963398
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4387963398Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/jamia/ocad205Digital Object Identifier
- Title
-
Systematic replication of smoking disease associations using survey responses and EHR data in the All of Us Research ProgramWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-10-26Full publication date if available
- Authors
-
David J. Schlueter, Lina Sulieman, Huan Mo, Jacob M. Keaton, Tracey M. Ferrara, Ariel Williams, Jun Qian, Onajia Stubblefield, Chenjie Zeng, Tam C. Tran, Lisa Bastarache, Jian Dai, Anav Babbar, Andrea H. Ramirez, Slavina B. Goleva, Joshua C. DennyList of authors in order
- Landing page
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https://doi.org/10.1093/jamia/ocad205Publisher landing page
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https://academic.oup.com/jamia/advance-article-pdf/doi/10.1093/jamia/ocad205/52603616/ocad205.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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hybridOpen access status per OpenAlex
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https://academic.oup.com/jamia/advance-article-pdf/doi/10.1093/jamia/ocad205/52603616/ocad205.pdfDirect OA link when available
- Concepts
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Phenome, Bonferroni correction, Biobank, Replication (statistics), Meta-analysis, Medicine, MEDLINE, Disease, Bioinformatics, Phenotype, Internal medicine, Biology, Genetics, Statistics, Virology, Gene, Mathematics, BiochemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
6Total citation count in OpenAlex
- Citations by year (recent)
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2024: 6Per-year citation counts (last 5 years)
- References (count)
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191Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.International | 67 |
| abstract_inverted_index.associations, | 170 |
| abstract_inverted_index.associations. | 50 |
| abstract_inverted_index.meta-analyses | 115, 175, 223 |
| abstract_inverted_index.respectively. | 171 |
| abstract_inverted_index.Classification | 68 |
| abstract_inverted_index.meta-analyses: | 129 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 97 |
| corresponding_author_ids | https://openalex.org/A5090809993 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 16 |
| corresponding_institution_ids | https://openalex.org/I1299303238, https://openalex.org/I185261750, https://openalex.org/I2799376586, https://openalex.org/I4210090236 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.8799999952316284 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.88961587 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |