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In silico integration of thousands of epigenetic datasets into 707 cell type regulatory annotations improves the trans-ethnic portability of polygenic risk scores

By Tiffany Amariuta, Kazuyoshi Ishigaki, Hiroki Sugishita, Tazro Ohta, Koichi Matsuda, Yoshinori Murakami, Alkes L. Price, Eiryo Kawakami, Chikashi Terao, Soumya Raychaudhuri

Posted 25 Feb 2020
bioRxiv DOI: 10.1101/2020.02.21.959510

Poor trans-ethnic portability of polygenic risk score (PRS) models is a critical issue that may be partially due to limited knowledge of causal variants shared among populations. Hence, leveraging noncoding regulatory annotations that capture genetic variation across populations has the potential to enhance the trans-ethnic portability of PRS. To this end, we constructed a unique resource of 707 cell-type-specific IMPACT regulatory annotations by aggregating 5,345 public epigenetic datasets to predict binding patterns of 142 cell-type-regulating transcription factors across 245 cell types. With this resource, we partitioned the common SNP heritability of diverse polygenic traits and diseases from 111 GWAS summary statistics of European (EUR, average N=180K) and East Asian (EAS, average N=157K) origin. For 95 traits, we were able to identify a single IMPACT annotation most strongly enriched for trait heritability. Across traits, these annotations captured an average of 43.3% of heritability (se = 13.8%) with the top 5% of SNPs. Strikingly, we observed highly concordant polygenic trait regulation between populations: the same regulatory annotations captured statistically indistinguishable SNP heritability (fitted slope = 0.98, se = 0.04). Since IMPACT annotations capture both large and consistent proportions of heritability across populations, prioritizing variants in IMPACT regulatory elements may improve the trans-ethnic portability of PRS. Indeed, we observed that EUR PRS models more accurately predicted 21 tested phenotypes of EAS individuals when variants were prioritized by key IMPACT tracks (49.9% mean relative increase in R 2). Notably, the improvement afforded by IMPACT was greater in the trans-ethnic EUR-to-EAS PRS application than in the EAS-to-EAS application (47.3% vs 20.9%, P < 1.7e-4). Overall, our study identifies a crucial role for functional annotations such as IMPACT to improve the trans-ethnic portability of genetic data, and this has important implications for future risk prediction models that work across populations.

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