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Schlueter DJ, Sulieman L, Mo H, Keaton JM, Ferrara TM, Williams A, Qian J, Stubblefield O, Zeng C, Tran TC, Bastarache L, Dai J, Babbar A, Ramirez A, Goleva SB, Denny JC. Systematic replication of smoking disease associations using survey responses and EHR data in the All of Us Research Program. J Am Med Inform Assoc 2023; 31:139-153. [PMID: 37885303 PMCID: PMC10746325 DOI: 10.1093/jamia/ocad205] [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: 01/06/2023] [Revised: 05/04/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
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.
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Affiliation(s)
- David J Schlueter
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
- Department of Health and Society, University of Toronto, Scarborough, Toronto, ON, Canada
| | - Lina Sulieman
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Huan Mo
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
- The Cohort Analytics Core (CAC), Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - Jacob M Keaton
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Tracey M Ferrara
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ariel Williams
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jun Qian
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Onajia Stubblefield
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Chenjie Zeng
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Tam C Tran
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
- The Cohort Analytics Core (CAC), Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jian Dai
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Anav Babbar
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Andrea Ramirez
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Slavina B Goleva
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Joshua C Denny
- Precision Health Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
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Wang M, Gong WW, Lu F, He QF, Hu RY, Zhong JM, Yu M. Associations of intensity, duration, cumulative dose, and age at start of smoking, with thyroid cancer in Chinese males: A hospital-based case-control study in Zhejiang Province. Tob Induc Dis 2020; 18:97. [PMID: 33281531 PMCID: PMC7713696 DOI: 10.18332/tid/130350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/25/2020] [Accepted: 11/10/2020] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION There has been considerable research on the association between smoking status and thyroid cancer risk in males, yet the findings are inconsistent. In this study, we investigated the associations of intensity, duration, cumulative dose, and age at start of smoking, with thyroid cancer in Chinese males. METHODS From a 1:1 matched case–control study conducted between 2015 and 2017 in Zhejiang Province, China, 676 pairs of male subjects were included in the analysis. The associations between smoking characteristics and thyroid cancer were evaluated in logistic regression models by odds ratios (ORs) with 95% confidence intervals (CIs). RESULTS Compared with never smokers, the former smokers were 0.096 times (95% CI: 0.012–0.778) less likely to have thyroid cancer. The significant inverse association was not observed in current smokers (OR=0.333; 95% CI: 0.084–1.322). Among both former and current smokers, higher smoking intensity (>10 cigarettes/day), duration (>15 years), and cumulative dose of smoking (>10 packyears) were significantly associated with reduced occurrence of thyroid cancer. CONCLUSIONS Our findings indicate that former smoking is inversely associated with thyroid cancer occurrence in Chinese males. The reduction in the occurrence of thyroid cancer was also confirmed for both former and current smokers with higher smoking intensity, duration, and cumulative dose.
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Affiliation(s)
- Meng Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Wei W Gong
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Feng Lu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Qing F He
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Ru Y Hu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jie M Zhong
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Min Yu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
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