Genetic Ancestry and Colorectal Cancer in the All of Us Dataset
Odysseas P. Chatzipanagiotou, Charalampos M. Charalampous, Adam Cordle, Abdulaziz Elemosho, Qaidar Alizai, Areesh Mevawalla, Lorenza Arena, Rida Ejaz, Timothy M. PawlikImportance
Genetic ancestry may complement biological, behavioral, and clinical factors in understanding colorectal cancer (CRC) disparities; yet, ancestry-informed analyses in CRC remain limited.
Objective
To characterize associations of genetic ancestry with CRC burden, age at diagnosis, and age-specific risk, and to develop a multiethnic CRC risk-prediction model.
Design, Setting, and Participants
This retrospective cohort study used All of Us data from July 1986 to October 2023, with follow-up through last visit or death (median [IQR], 133.1 [57.1-186.5] months); analyses were conducted from February to June 2026. All of Us is a US research cohort with linked electronic health record (EHR) and short-read whole-genome sequencing (srWGS) data. All of Us Research Program participants with srWGS and linked EHR data were included, except those with hereditary polyposis or Lynch syndrome.
Exposures
Genetically inferred ancestry categories and principal components.
Main Outcomes and Measures
Any CRC was the primary outcome. Associations were evaluated using Fisher exact tests, cumulative incidence functions with Gray tests, cause-specific and Fine-Gray subdistribution hazard models, and pooled multivariable logistic regression. Prediction models used penalized least absolute shrinkage and selection operator and extreme gradient boosting (XGBoost).
Results
Among 316 624 participants (median [IQR] age, 56.3 [40.2-68.2] years; 172 327 [54.4%] of European ancestry; 191 705 female [61.2%]; 121 585 male [38.8%]), 2914 (0.9%) developed CRC. European ancestry was associated with higher odds of CRC vs all other ancestries combined (odds ratio, 1.50; 95% CI, 1.39-1.62). The median age at CRC diagnosis was older in European (63.4 [53.9-71.2] years) than in American admixed-Latino, African, East Asian, and Other ancestry groups. In cause-specific hazard models on the attained-age scale, American admixed-Latino (hazard ratio, 1.30; 95% CI, 1.14-1.47) and East Asian (hazard ratio, 1.43; 95% CI, 1.06-1.94) ancestry had higher age-specific CRC hazard than European ancestry, with consistent findings on the subdistribution scale accounting for competing death. The multiethnic XGBoost model performed best (receiver operating characteristic area under the curve, 0.898; 95% CI, 0.882-0.912; precision-recall area under the curve, 0.338; 95% CI, 0.296-0.379) and was well calibrated.
Conclusions and Relevance
In this cohort study, genetic ancestry was associated with meaningful differences in CRC burden and age-specific risk. These findings suggest that a multiethnic XGBoost model may complement CRC screening as a risk-enrichment tool.