Wasm-iCARE: a Portable and Privacy-preserving Web Module to Build, Validate, and Apply Absolute Risk Models

Overview

Journal ArXiv

Date 2023 Oct 24

PMID 37873020

Authors

Jeya Balaji Balasubramanian

Parichoy Pal Choudhury

Srijon Mukhopadhyay

Thomas Ahearn

Nilanjan Chatterjee

Montserrat Garcia-Closas

Jonas S Almeida

Affiliations

Soon will be listed here.

Abstract

Objective: Absolute risk models estimate an individual's future disease risk over a specified time interval. Applications utilizing server-side risk tooling, such as the R-based iCARE (R-iCARE), to build, validate, and apply absolute risk models, face serious limitations in portability and privacy due to their need for circulating user data in remote servers for operation. Our objective was to overcome these limitations.

Materials And Methods: We refactored R-iCARE into a Python package (Py-iCARE) then compiled it to WebAssembly (Wasm-iCARE): a portable web module, which operates entirely within the privacy of the user's device.

Results: We showcase the portability and privacy of Wasm-iCARE through two applications: for researchers to statistically validate risk models, and to deliver them to end-users. Both applications run entirely on the client-side, requiring no downloads or installations, and keeps user data on-device during risk calculation.

Conclusions: Wasm-iCARE fosters accessible and privacy-preserving risk tools, accelerating their validation and delivery.

References

Pal Choudhury P, Maas P, Wilcox A, Wheeler W, Brook M, Check D . iCARE: An R package to build, validate and apply absolute risk models. PLoS One. 2020; 15(2):e0228198. PMC: 7001949. DOI: 10.1371/journal.pone.0228198. View

Dikilitas O, Schaid D, Kosel M, Carroll R, Chute C, Denny J . Predictive Utility of Polygenic Risk Scores for Coronary Heart Disease in Three Major Racial and Ethnic Groups. Am J Hum Genet. 2020; 106(5):707-716. PMC: 7212267. DOI: 10.1016/j.ajhg.2020.04.002. View

Perkel J . Reactive, reproducible, collaborative: computational notebooks evolve. Nature. 2021; 593(7857):156-157. DOI: 10.1038/d41586-021-01174-w. View

Shi J, Kraft P, Rosner B, Benavente Y, Black A, Brinton L . Risk prediction models for endometrial cancer: development and validation in an international consortium. J Natl Cancer Inst. 2023; 115(5):552-559. PMC: 10165481. DOI: 10.1093/jnci/djad014. View

Kovalchik S, Ronckers C, Veiga L, Sigurdson A, Inskip P, De Vathaire F . Absolute risk prediction of second primary thyroid cancer among 5-year survivors of childhood cancer. J Clin Oncol. 2012; 31(1):119-27. PMC: 3530689. DOI: 10.1200/JCO.2012.41.8996. View

Minnier J, Rajeevan N, Gao L, Park B, Pyarajan S, Spellman P . Polygenic Breast Cancer Risk for Women Veterans in the Million Veteran Program. JCO Precis Oncol. 2021; 5. PMC: 8345920. DOI: 10.1200/PO.20.00541. View

Jee Y, Gao C, Kim J, Park S, Jee S, Kraft P . Validating Breast Cancer Risk Prediction Models in the Korean Cancer Prevention Study-II Biobank. Cancer Epidemiol Biomarkers Prev. 2020; 29(6):1271-1277. DOI: 10.1158/1055-9965.EPI-19-1478. View

He Y, Wang T, Ji M, Mai Z, Tang M, Wang R . A polygenic risk score for nasopharyngeal carcinoma shows potential for risk stratification and personalized screening. Nat Commun. 2022; 13(1):1966. PMC: 9005522. DOI: 10.1038/s41467-022-29570-4. View

Freedman A, Slattery M, Ballard-Barbash R, Willis G, Cann B, Pee D . Colorectal cancer risk prediction tool for white men and women without known susceptibility. J Clin Oncol. 2008; 27(5):686-93. PMC: 2645090. DOI: 10.1200/JCO.2008.17.4797. View

10.

Ahearn T, Pal Choudhury P, Derkach A, Wiafe-Addai B, Awuah B, Yarney J . Breast Cancer Risk in Women from Ghana Carrying Rare Germline Pathogenic Mutations. Cancer Epidemiol Biomarkers Prev. 2022; 31(8):1593-1601. PMC: 11284919. DOI: 10.1158/1055-9965.EPI-21-1397. View

11.

Garcia-Closas M, Ahearn T, Gaudet M, Hurson A, Balasubramanian J, Pal Choudhury P . Moving Toward Findable, Accessible, Interoperable, Reusable Practices in Epidemiologic Research. Am J Epidemiol. 2023; 192(6):995-1005. PMC: 10505418. DOI: 10.1093/aje/kwad040. View

12.

Pal Choudhury P, Brook M, Hurson A, Lee A, Mulder C, Coulson P . Comparative validation of the BOADICEA and Tyrer-Cuzick breast cancer risk models incorporating classical risk factors and polygenic risk in a population-based prospective cohort of women of European ancestry. Breast Cancer Res. 2021; 23(1):22. PMC: 7885342. DOI: 10.1186/s13058-021-01399-7. View

13.

Chien L, Chen T, Chen C, Chen K, Hsiao C, Chang G . Recalibrating Risk Prediction Models by Synthesizing Data Sources: Adapting the Lung Cancer PLCO Model for Taiwan. Cancer Epidemiol Biomarkers Prev. 2022; 31(12):2208-2218. PMC: 9720426. DOI: 10.1158/1055-9965.EPI-22-0281. View

14.

Carver T, Hartley S, Lee A, Cunningham A, Archer S, de Villiers C . CanRisk Tool-A Web Interface for the Prediction of Breast and Ovarian Cancer Risk and the Likelihood of Carrying Genetic Pathogenic Variants. Cancer Epidemiol Biomarkers Prev. 2020; 30(3):469-473. PMC: 7611188. DOI: 10.1158/1055-9965.EPI-20-1319. View

15.

Eriksson M, Destounis S, Czene K, Zeiberg A, Day R, Conant E . A risk model for digital breast tomosynthesis to predict breast cancer and guide clinical care. Sci Transl Med. 2022; 14(644):eabn3971. DOI: 10.1126/scitranslmed.abn3971. View

16.

Jee Y, Ho W, Park S, Easton D, Teo S, Jung K . Polygenic risk scores for prediction of breast cancer in Korean women. Int J Epidemiol. 2022; 52(3):796-805. PMC: 10244045. DOI: 10.1093/ije/dyac206. View

17.

Hartz S, Mozersky J, Schindler S, Linnenbringer E, Wang J, Gordon B . A flexible modeling approach for biomarker-based computation of absolute risk of Alzheimer's disease dementia. Alzheimers Dement. 2022; 19(4):1452-1465. PMC: 10060442. DOI: 10.1002/alz.12781. View

18.

Maas P, Barrdahl M, Joshi A, Auer P, Gaudet M, Milne R . Breast Cancer Risk From Modifiable and Nonmodifiable Risk Factors Among White Women in the United States. JAMA Oncol. 2016; 2(10):1295-1302. PMC: 5719876. DOI: 10.1001/jamaoncol.2016.1025. View

19.

Robbins H, Ferreiro-Iglesias A, Waterboer T, Brenner N, Nygard M, Bender N . Absolute Risk of Oropharyngeal Cancer After an HPV16-E6 Serology Test and Potential Implications for Screening: Results From the Human Papillomavirus Cancer Cohort Consortium. J Clin Oncol. 2022; 40(31):3613-3622. PMC: 9622695. DOI: 10.1200/JCO.21.01785. View

20.

Hurson A, Pal Choudhury P, Gao C, Husing A, Eriksson M, Shi M . Prospective evaluation of a breast-cancer risk model integrating classical risk factors and polygenic risk in 15 cohorts from six countries. Int J Epidemiol. 2022; 50(6):1897-1911. PMC: 8743128. DOI: 10.1093/ije/dyab036. View