Abstract: SA-PO232
Preliminary Results from a Genome-Wide Association Study (GWAS) in Bladder Cancer: Toward a Multi-Omics Approach
Session Information
- Onconephrology: Immunological Cross-Talk
November 04, 2023 | Location: Exhibit Hall, Pennsylvania Convention Center
Abstract Time: 10:00 AM - 12:00 PM
Category: Onconephrology
- 1700 Onconephrology
Authors
- Lim, Tze Yin, Universita degli Studi di Torino, Torino, Piemonte, Italy
- Allione, Alessandra, Universita degli Studi di Torino, Torino, Piemonte, Italy
- Debernardi, Carla, Universita degli Studi di Torino, Torino, Piemonte, Italy
- Di Primio, Cecilia, Universita degli Studi di Torino, Torino, Piemonte, Italy
- Sacerdote, Carlotta, CPO-Piemonte, Torino, Piemonte, Italy
- Sanna-Cherchi, Simone, Columbia University, New York, New York, United States
- Matullo, Giuseppe, Universita degli Studi di Torino, Torino, Piemonte, Italy
Background
Bladder cancer is one of the most prevalent cancers, and its heterogeneity in clinical outcomes necessitates further investigation into the molecular mechanisms contributing to the disease to improve risk stratification, treatment, and prognosis. Here, we present the preliminary results of a GWAS in bladder cancer in an Italian cohort (N = 581) with paired genotyping and multi-omics data.
Methods
594 individuals were genotyped with the Infinium OmniExpressExome-8 kit. PLINK2 was used for standard GWAS QC. The resulting dataset of 581 unrelated individuals consisting of 148 cases and 433 controls were imputed with the ToPMed panel (R2, GRC38). Logistic regression was performed on dosages under the additive model adjusting for age, sex, and principal components. Polygenic Risk Score (PRS) was calculated with PRSice-2 v2.3.5.
Results
581 individuals (148 cases and 433 controls) and 594,108 SNPs remained after QC. Post-imputation QCs requiring SNP call rate (>95%), MAF (>1%) and Hardy-Weinberg (P <1 x 10-6) within the cohort yielded a final set of 7,660,056 SNPs for GWAS. We identified three loci with suggestive association: chr10p15.3 (rs2605905, OR=3.06, P = 1.53 x 10-6; DIP2C), chr5p13.3 (rs5026245; OR = 2.14; P = 3.83 x 10-6; ADAMTS12), and chr15q21.3 (rs17543144; OR = 2.03; P = 4.46 x 10-6; nearest gene FAM214A).The quantile-quantile plot showed no evidence of inflation (λ = 0.969) suggesting no residual population stratification. An interim assessment of the portability of existing PRS(PGS000782) on this cohort showed significant differences in means between cases and controls (P = 2.17 x 10-4).
Conclusion
An initial comparison of summary statistics between our cohort and larger bladder cancer cohorts deposited in the GWAS catalog showed consistent directionality in effect sizes at previously reported significant loci. Our GWAS may be underpowered for new discoveries but, leveraging on paired epigenomic and transcriptomic data available in our cohorts, we are well positioned for constructing multi-omics genetic correlations to dissect known and novel bladder cancer loci and provide insights into the pathobiology of disease. Finally, an interim assessment of PGS000782 showed portability in distinguishing cases from controls in this cohort.
Funding
- Government Support – Non-U.S.