gr-hsa-prs

Germline GWAS + polygenic risk scoring for canine hemangiosarcoma (HSA) on the GRLS cohort (3,224 dogs, 913,984 SNPs). Part of the golden-retrievers effort to understand HSA.

Status

• GWAS (real, done): first hemangiosarcoma GWAS on GRLS Data Commons labels (306 cases / 1,329 cancer-free controls), GEMMA linear mixed model: lambda_GC = 0.955 (well-calibrated), SNP-h2 = 0.127 +/- 0.038, 0 genome-wide-significant at n=306; top signal is non-coding, consistent with the known shared HSA / B-cell-lymphoma risk on CFA5 (TRPC6/STX8).
• PRS: Clumping + Thresholding; held-out AUC 0.635 on a simulated polygenic trait (validation).

Aggregate statistics only (GRLS Data Commons DUA: no per-SNP summary statistics or individual-level data).

• Code: https://github.com/golden-retrievers/gr-hemangiosarcoma (scripts/run_gwas.py, scripts/prs.py)
• Experiments: https://wandb.ai/golden-retrievers/gr-hsa-gwas
• Data: https://huggingface.co/datasets/golden-retrievers/grls-genomics