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Abstract: FR-PO924

Polygenic Risk Affects the Penetrance of Monogenic Kidney Disease

Session Information

Category: CKD (Non-Dialysis)

  • 2301 CKD (Non-Dialysis): Epidemiology, Risk Factors, and Prevention

Authors

  • Khan, Atlas, Columbia University, New York, New York, United States
  • Shang, Ning, Columbia University, New York, New York, United States
  • Nestor, Jordan Gabriela, Columbia University, New York, New York, United States
  • Weng, Chunhua, Columbia University, New York, New York, United States
  • Hripcsak, George, Columbia University, New York, New York, United States
  • Harris, Peter C., Mayo Foundation for Medical Education and Research, Rochester, Minnesota, United States
  • Gharavi, Ali G., Columbia University, New York, New York, United States
  • Kiryluk, Krzysztof, Columbia University, New York, New York, United States

Group or Team Name

  • Kiryluk Group.
Background

Chronic kidney disease (CKD) is a genetically complex disease determined by an interplay of monogenic, polygenic, and environmental risks. Most forms of monogenic kidney diseases have incomplete penetrance and variable expressivity. It is presently unknown if some of the variability in penetrance can be attributed to polygenic factors.

Methods

Using the UK Biobank (N=469,835) and the All of Us (N=98,622) datasets, we examined the two most common forms of monogenic kidney disorders, autosomal dominant polycystic kidney disease (ADPKD) caused by deleterious variants in the PKD1 or PKD2, and COL4A-associated nephropathy (COL4A-AN caused by deleterious variants in COL4A3, COL4A4, or COL4A5). We used the eMERGE-III electronic CKD phenotype to define cases (estimated glomerular filtration rate (eGFR) <60 or kidney failure) and controls (eGFR >90). The effects of the genome-wide polygenic score for CKD were tested in monogenic variant carriers and non-carriers using logistic regression controlling covariates.

Results

As expected, the carriers of known pathogenic and rare predicted loss-of-function variants in PKD1 or PKD2 had a high risk of CKD (ORmeta=17.1, 95% CI: 11.1-26.4, P=1.8E-37). The GPS was comparably predictive of CKD in both ADPKD variant carriers (ORmeta=2.28 per SD, 95%CI: 1.55-3.37, P=2.6E-05) and non-carriers (ORmeta=1.72 per SD, 95% CI=1.69-1.76, P< E-300) independent of age, sex, diabetes, and genetic ancestry. Compared to the middle tertile of the GPS distribution for non-carriers, ADPKD variant carriers in the top tertile had a 54-fold increased risk of CKD. In contrast, ADPKD variant carriers in the bottom tertile had only a 3-fold increased risk of CKD. Similarly, the GPS was predictive of CKD in both COL4-AN variant carriers (ORmeta=1.78, 95% CI=1.22-2.58, P=2.38E-03) and non-carriers (ORmeta=1.70, 95%CI: 1.68-1.73 P<E-300). The carriers in the top tertile of the GPS had a 2.5-fold higher risk of CKD, while the risk for carriers in the bottom tertile was similar to the middle tertile of non-carriers.

Conclusion

Variable penetrance of kidney disease in ADPKD and COL4-AN is partially explained by differences in polygenic risk profiles. Accounting for polygenic factors has the potential to improve risk stratification in monogenic kidney disease and may have implications for genetic counseling.

Funding

  • NIDDK Support