Norland, Kristján

BACKGROUND: Performance and transferability of contemporary polygenic risk scores (PRS) for atherosclerotic cardiovascular disease phenotypes may vary across PRS methods, training data, and trait ascertainment. METHODS: We aimed to investigate the performance and transferability of contemporary PRS for atherosclerotic cardiovascular disease subtypes: coronary heart disease (CHD), abdominal aortic aneurysm (AAA), ischemic stroke (IS), and peripheral artery disease (PAD), using the All of Us Workbench, which consists of a large, diverse cohort with whole-genome sequence data. We also developed and evaluated a multi-trait PRS for each subtype. Performance of PRS for 4 atherosclerotic cardiovascular disease subtypes was compared across genetic similarity groups in 245 388 All of Us participants. Groups genetically similar to European, African, admixed American, and remaining groups (combined as other) were used to assess PRS for CHD, IS, AAA, PAD, and multi-trait. RESULTS: PRS for CHD and AAA performed better than IS and PAD. For CHD, CHD PGS003725 performed the best (hazard ratio per SD increase [95% CI]), across genetic ancestry groups, European, and African (1.72 [1.67–1.78], 1.23 [1.17–1.29]), with CHD PGS004696 being best for admixed American (1.91 [1.70–2.15]), and CHD PGS003356 for other (1.75 [1.58–1.95]). The best performing PRS for AAA was AAA Multi for European, other, and admixed American (1.71 [1.52–1.92], 1.59 [1.07–2.37], 1.50 [0.90–2.52]) and AAA PGS003972 for African (1.39 [1.19–1.63]). For IS, IS Multi performed best for other and European (1.49 [1.17–1.89], 1.33 [1.25–1.42]), and IS PGS000039 performed best in admixed American and African (1.17 [1.07–1.27], 1.09 [1.04–1.15]). For PAD, PAD Multi performed best for all groups (other, 1.51 [1.19–1.92]; European, 1.32 [1.24–1.41]; admixed American, 1.23 [1.05–1.45]; and African, 1.18 [1.04–1.34]). CONCLUSIONS: Multi-trait and multi-ancestry PRS performed better than individual trait and/or single ancestry PRS for each atherosclerotic cardiovascular disease phenotype across ancestrally diverse and admixed individuals, with minimal change including adjustment for conventional risk factors.

Abstract Background Contemporary prevalence and penetrance of familial hypercholesterolemia (FH) and the associated coronary heart disease (CHD) risk across diverse genetic ancestries in the United States are unclear. Purpose To estimate prevalence of individuals harboring pathogenic/likely pathogenic (P/LP) variants in LDLR, APOB, and PCSK9, distribution of low-density-lipoprotein cholesterol (LDL-C) levels, and associated CHD risk for carriers in an ancestrally diverse cohort. Methods In 242,167 All of Us (AoU) participants with available whole-genome sequencing data, we obtained LDL-C measurements, statin prescriptions, and ascertained P/LP variants in FH-related genes and presence of CHD based on electronic-health record data. P/LP variants in LDLR, APOB, and PCSK9 were identified in AoU data by filtering for high-impact (frameshift, canonical splice site, indels, and stop gain) and predicted-deleterious missense variants, then selecting those classified as P/LP in ClinVar. Untreated LDL-C levels were estimated assuming a 30% reduction if there was a record of a statin prescription in the preceding 12 months and the highest value among multiple measurements for each individual were selected. Penetrance was defined as LDL-C>155 mg/dl. CHD was determined using a validated phenotyping algorithm based on diagnostic and procedural billing codes. Logistic regression models were used to obtain prevalence and penetrance estimates and odds ratios for CHD, along with associated 95% confidence intervals (95% CI). Results We identified 221 FH-related P/LP variants (LDLR=169, APOB=50, PCSK9=2) in the study cohort. Of 125,841 European (EUR), 53,367 African (AFR), 40,189 admixed American (AMR), and 22,770 other ancestry individuals, 1:218 (0.46%, 95% CI 0.42%-0.50%), 1:307 (0.33%,0.28%-0.38%), 1:350 (0.29%, 0.24%-0.34%), and 1:201 (0.50%, 0.41%-0.59%) were carriers of a P/LP variant. In 92,616 individuals with at least one LDL-C measurement, carriers of a P/LP variant had a higher distribution of LDL-C across all ancestries with similarly high penetrance (Figure 1). Harboring a P/LP variant in LDLR, APOB, and PCSK9 was associated with similarly increased odds of CHD across all the different ancestry groups (Figure 2). Conclusions Monogenic FH was prevalent, penetrant, and significantly associated with CHD similarly across diverse ancestry groups in the AoU cohort. These findings support a ‘genotype first’ approach to detection of FH to enable early intervention across diverse ancestry groups.Figure 1 Figure 2

BACKGROUND: In the Myocardial Infarction Genes clinical trial (URL: https://www.clinicaltrials.gov ; Unique identifier: NCT01936675), participants at intermediate risk of coronary heart disease (CHD) were randomized to receive a Framingham risk score (Framingham risk score group, n=103) or an integrated risk score (integrated risk score group [IRS g ], n=104) that additionally included a polygenic risk score. After 6 months, IRS g participants had higher statin initiation and lower low-density lipoprotein cholesterol. We conducted a post hoc 10-year follow-up analysis to investigate whether disclosure of a polygenic risk score for CHD was associated with a reduction in major adverse cardiovascular events (MACE). METHODS: Participants were followed from randomization in October 2013 to September 2023 to ascertain MACE, testing for CHD, and changes in risk factors. The primary outcome was time to first MACE, defined as cardiovascular death, nonfatal myocardial infarction, coronary revascularization, and nonfatal stroke. Statistical analyses included Cox proportional hazards regression and linear mixed-effects models. RESULTS: We followed all participants who completed the trial, 100 in Framingham risk score group and 103 in IRS g (mean age at the end of follow-up, 68.2±5.2; 48% male). During a median follow-up of 9.5 years, 9 MACEs occurred in Framingham risk score group and 2 in IRS g (hazard ratio, 0.20 [95% CI, 0.04–0.94]; P =0.042). In Framingham risk score group, 47 (47%) underwent at least 1 diagnostic test for CHD, compared with 30 (29%) in IRS g (hazard ratio, 0.51 [95% CI, 0.32–0.81]; P =0.004). A higher proportion of IRS g participants were on statin therapy during the first 4 years postrandomization and had a greater reduction in low-density lipoprotein cholesterol for up to 3 years postrandomization. No significant differences were observed between 2 groups in other traditional cardiovascular risk factors during follow-up. CONCLUSIONS: Disclosure of an integrated risk score that included a polygenic risk score to individuals at intermediate risk for CHD was associated with lower MACE incidence after 10 years, likely due to higher statin initiation, leading to lower low-density lipoprotein cholesterol levels.

Introduction: The MI-GENES randomized clinical trial (NCT01936675) assessed the effect of disclosing a polygenic risk score (PRS) for coronary heart disease (CHD), in addition to a clinical risk based on Framingham risk score (FRS), on LDL-C levels. The trial enrolled participants from Olmsted County, Minnesota, without cardiovascular disease, at intermediate CHD risk (10-y risk: 5-20%), and not on statins. There was a significant LDL-C reduction in the integrated risk score group (IRS g ; received PRS information in addition to the FRS) compared to the FRS group (FRS g ; received their risk based on FRS), due to more frequent statin initiation. Research Question: Does disclosure of an IRS for CHD lead to a lower rate of major adverse cardiovascular events (MACE)? Methods: Participants were followed from randomization beginning in October 2013 until September 2023 to ascertain cardiovascular events, testing for CHD, and risk factor changes, by blinded review of electronic health records. The primary outcome was time from randomization to the first MACE— defined as cardiovascular death, nonfatal MI, coronary revascularization, and nonfatal stroke. Analyses were done using Cox and linear mixed-effects models. Results: We followed all 203 participants, who completed the MI-GENES trial, 100 in FRS g and 103 in IRS g (mean age at the end of follow-up 68.2±5.2 years, 48% male). During a median follow-up of 9.5 years, 9 MACE occurred in FRS g and 2 in IRS g (HR, 0.20; 95% CI, 0.04 to 0.94; P =0.042, Figure 1A). In FRS g , 47 (47%) underwent at least one test for CHD, compared to 30 (29%) in IRS g (HR, 0.51; 95% CI, 0.32 to 0.81; P =0.004, Figure 1B). IRS g participants had a longer duration of statin therapy during the first four years post-randomization (Figure 1C) and a greater reduction in LDL-C for up to 3 years post-randomization (Figure 1D). No significant differences between the two groups were observed for hemoglobin A1C, blood pressure, weight, and smoking cessation rate during follow-up. Conclusion: The disclosure of 10-year CHD risk that included a PRS to those at intermediate risk was associated with lower incidence of MACE after a decade, likely due to more frequent and prolonged statin use, leading to lower LDL-C levels.

Background: Coronary heart disease (CHD) results from environmental and genetic factors. Lifestyle-psychosocial factors that capture environmental risk and polygenic risk scores (PRS) that capture genetic risk have been associated with CHD in prior studies. Aim: To assess whether higher CHD risk traditionally attributed to non-White race/ethnicty is mediated by PSS CHD or PRS CHD . Methods: In UK Biobank, we ascertained incident CHD (MI/coronary revascularization) and calculated an ancestry-specific PRS for CHD (PGS000018). Based on self-reported race/ethnicity, participants were classified as White and non-White. An age, sex, and ethnicity-adjusted polysocial score for CHD (PSS CHD ) was derived from 100 self-reported lifestyle-psychosocial factors across nine domains: Adulthood Relationship, Education, Entertainment, Housing, Income, Occupation, Physical Activity, Psychological Health, and Sleep. Those with CHD or statin use at recruitment or missing age, sex, race/ethnicity or genotype were excluded. Machine learning (elastic net model) was used to develop PSS CHD . Cox and mediation analyses were performed. Results: In 398,403 participants (56±8 y, 43% male, 96.3% White, 1.8% Asian, 1.6% Black, and 0.3% Chinese), 10,033 had an incident CHD event during a 10-year follow-up. The HRs (95% CIs) for a 1 SD increase in PSS CHD and PRS CHD for CHD risk were 1.5 (1.4–1.5, P <10 -16 ), and 1.6 (1.5 - 1.6, P <10 -16 ), respectively (Figure 1A-B). Asians and Blacks had the highest PSS CHD (mean±SD: 0.5±1, and 0.5±1, respectively), followed by Chinese (0.1±0.9), and Whites (0.0±1) (Figure 1C). After adjustment for age, sex, diabetes, hypertension, LDL-C, and smoking, non-Whites had higher CHD risk: HR (95% CI): 1.2 (1.0–1.4, P <10 -16 ), and the higher risk was mediated more substantially by PSS CHD than PRS CHD (63% (38%-100%) vs. 16% (8%-41%), both P <10 -16 ). Conclusions: The higher CHD risk observed in non-Whites in UK Biobank was mainly due to unfavorable lifestyle-psychosocial factors, rather than PRS, consistent with the paradigm that race/ethnicity is not a biological but rather a social construct. Our findings support substituting race/ethnicity with lifestyle-psychosocial factors and social determinants of health in CHD risk equations.

BACKGROUND: Coronary atherosclerotic burden and adverse coronary heart disease events are related phenotypes with likely shared genetic cause. METHODS: We analyzed 6021 patients with available coronary angiography, genotyping, and exome sequencing data. We tested for associations of polygenic risk scores for coronary heart disease (PRS CHD ) with multiple measures of coronary artery disease (CAD) severity. We assessed the joint associations of PRS CHD and pathogenic/likely pathogenic variants in 3 familial hypercholesterolemia genes, with CAD severity. We performed mediation analyses to explore whether CAD severity mediated the association of PRS CHD with prevalent coronary heart disease and incident myocardial infarction. RESULTS: A 1-SD increase in PRS CHD was associated with multiple measures of CAD severity, including the log Gensini score (β, 0.31 [95% CI, 0.28–0.33]). Carrying a pathogenic/likely pathogenic familial hypercholesterolemia variant was associated with a higher log Gensini score after adjustment for PRS CHD (β, 0.21 [95% CI, 0.03–0.38]). A 1-SD increase in PRS CHD was associated with incident myocardial infarction over a mean follow-up of 9.2 years (hazard ratio, 1.20 [95% CI, 1.13–1.27]; P =5×10 − 10 ), and the Gensini score mediated 90% of this association. CONCLUSIONS: PRS CHD was associated with multiple measures of CAD severity. The association of PRS CHD with incident myocardial infarction was almost fully mediated by CAD severity, indicating a considerable genetic overlap between the 2 phenotypes.

Introduction. We assessed the effects of a polygenic risk score (PRS), monogenic variants (Mono + ), and family history (FamHx) on the risk of coronary heart disease (CHD) and whether incorporating a PRS into the Pooled Cohort Equations (PCE) improves risk prediction. Method. In 199,997 UK Biobank participants, we calculated a PRS CHD (metaGRS, based on ~1.6 million single nucleotide variants), identified individuals with monogenic etiology (presence of a pathogenic variant in LDLR , APOB , or PCSK9 ), and ascertained family history of CHD (CHD in a first-degree relative). Odds of CHD (myocardial infarction/ coronary revascularization/ cardiovascular death) associated with PRS CHD , Mono + , and FamHx at age 55 were computed using logistic regression analyses adjusted for age, sex, and first 4 principal components of ancestry. We combined PRS CHD and PCE into an integrated score (IS) and assessed net reclassification using an actionable risk threshold of 7.5%. Results. The odds ratio (OR) for CHD in the top 5 th percentile of PRS CHD (PRS P95 ), Mono + , and FamHx were 3.37 (2.98 - 3.81), 2.68 (1.67 - 4.07), and 1.61 (1.47 - 1.76), respectively (all p<0.001). These effects were independent and similar in different subgroups. ( Figure 1-A ) Compared to PRS Q2-4 Mono - (3 middle quintiles of PRS CHD and no monogenic variants), the OR for CHD ranged from 1.73 (0.28 - 5.48, p = 0.446) in PRS Q1 Mono + to 5.10 (2.14 - 10.24, p <0.001) in PRS Q5 Mono + . A similar pattern was seen for other combinations, indicating additive effects ( Figure 1-B ). Incorporating PRS CHD into PCE resulted in a net reclassification improvement of 4.56%. Compared to those with high PCE and low IS, the hazard ratio for CHD in those with low PCE and high IS was 1.48 (1.34 - 1.64, p <0.001). Conclusion. The CHD risk associated with PRS CHD , monogenic variants, and family history is independent and additive. Combining PRS CHD and PCE improved risk prediction, that could improve further by adding monogenic variants and family history.