03962nas a2200733 4500008004100000022001400041245014300055210006900198260001600267520182100283100001602104700001602120700001502136700001802151700002202169700002102191700002002212700001802232700001602250700001302266700001902279700002302298700001702321700002002338700002602358700002002384700002302404700003102427700001902458700001902477700002502496700002502521700002002546700001702566700002202583700002102605700002002626700002002646700002402666700002702690700001902717700002102736700002402757700002102781700002202802700001702824700001902841700002002860700002002880700001902900700001902919700002502938700002302963700002602986700002403012700001703036700002503053700002403078700002003102700001903122700002103141710003003162856003603192 2022 eng d a1537-660500aPolygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program.0 aPolygenic transcriptome risk scores for COPD and lung function i c2022 Mar 313 a
While polygenic risk scores (PRSs) enable early identification of genetic risk for chronic obstructive pulmonary disease (COPD), predictive performance is limited when the discovery and target populations are not well matched. Hypothesizing that the biological mechanisms of disease are shared across ancestry groups, we introduce a PrediXcan-derived polygenic transcriptome risk score (PTRS) to improve cross-ethnic portability of risk prediction. We constructed the PTRS using summary statistics from application of PrediXcan on large-scale GWASs of lung function (forced expiratory volume in 1 s [FEV] and its ratio to forced vital capacity [FEV/FVC]) in the UK Biobank. We examined prediction performance and cross-ethnic portability of PTRS through smoking-stratified analyses both on 29,381 multi-ethnic participants from TOPMed population/family-based cohorts and on 11,771 multi-ethnic participants from TOPMed COPD-enriched studies. Analyses were carried out for two dichotomous COPD traits (moderate-to-severe and severe COPD) and two quantitative lung function traits (FEV and FEV/FVC). While the proposed PTRS showed weaker associations with disease than PRS for European ancestry, the PTRS showed stronger association with COPD than PRS for African Americans (e.g., odds ratio [OR] = 1.24 [95% confidence interval [CI]: 1.08-1.43] for PTRS versus 1.10 [0.96-1.26] for PRS among heavy smokers with ≥ 40 pack-years of smoking) for moderate-to-severe COPD. Cross-ethnic portability of the PTRS was significantly higher than the PRS (paired t test p < 2.2 × 10 with portability gains ranging from 5% to 28%) for both dichotomous COPD traits and across all smoking strata. Our study demonstrates the value of PTRS for improved cross-ethnic portability compared to PRS in predicting COPD risk.
1 aHu, Xiaowei1 aQiao, Dandi1 aKim, Wonji1 aMoll, Matthew1 aBalte, Pallavi, P1 aLange, Leslie, A1 aBartz, Traci, M1 aKumar, Rajesh1 aLi, Xingnan1 aYu, Bing1 aCade, Brian, E1 aLaurie, Cecelia, A1 aSofer, Tamar1 aRuczinski, Ingo1 aNickerson, Deborah, A1 aMuzny, Donna, M1 aMetcalf, Ginger, A1 aDoddapaneni, Harshavardhan1 aGabriel, Stacy1 aGupta, Namrata1 aDugan-Perez, Shannon1 aCupples, Adrienne, L1 aLoehr, Laura, R1 aJain, Deepti1 aRotter, Jerome, I1 aWilson, James, G1 aPsaty, Bruce, M1 aFornage, Myriam1 aMorrison, Alanna, C1 aVasan, Ramachandran, S1 aWashko, George1 aRich, Stephen, S1 aO'Connor, George, T1 aBleecker, Eugene1 aKaplan, Robert, C1 aKalhan, Ravi1 aRedline, Susan1 aGharib, Sina, A1 aMeyers, Deborah1 aOrtega, Victor1 aDupuis, Josée1 aLondon, Stephanie, J1 aLappalainen, Tuuli1 aOelsner, Elizabeth, C1 aSilverman, Edwin, K1 aBarr, Graham1 aThornton, Timothy, A1 aWheeler, Heather, E1 aCho, Michael, H1 aIm, Hae, Kyung1 aManichaikul, Ani1 aTOPMed Lung Working Group uhttps://chs-nhlbi.org/node/9037