Clinical use of current polygenic risk scores may exacerbate health disparities
Open accessPublished version of a preprint
Abstract
Polygenic risk scores (PRS) are poised to improve biomedical outcomes via precision medicine. However, the major ethical and scientific challenge surrounding clinical implementation of PRS is that those available today are several times more accurate in individuals of European ancestry than other ancestries. This disparity is an inescapable consequence of Eurocentric biases in genome-wide association studies, thus highlighting that-unlike clinical biomarkers and prescription drugs, which may individually work better in some populations but do not ubiquitously perform far better in European populations-clinical uses of PRS today would systematically afford greater improvement for European-descent populations. Early diversifying efforts show promise in leveling this vast imbalance, even when non-European sample sizes are considerably smaller than the largest studies to date. To realize the full and equitable potential of PRS, greater diversity must be prioritized in genetic studies, and summary statistics must be publically disseminated to ensure that health disparities are not increased for those individuals already most underserved.
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Claims the paper makes
78 of 110 cited sources checked · 10 supported · 1 flagged · accuracy not yet measured
- Premisecitation
Existing findings demonstrate a large reduction in prediction utility in non-European populations.
“Those existing findings indeed demonstrate a large reduction in prediction utility in non-European populations11,”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [11] Khera, A. V. et al. Genetic risk, adherence to a healthy lifestyle, and coronary disease. N. Engl. J. Med. 375, 2349–2358 (2016). source
The Results (page unavailable) report similar findings among black and white participants in the ARIC cohort, rather than a large reduction in non-European populations. The Discussion (page unavailable) says the risk score was associated with coronary events among black participants, while cautioning that generalizability needs further testing; it does not report a comparative measure of prediction utility. (LLM, conf=0.79)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured
- Premisecitation
Population genetics theory predicts that genetic risk prediction accuracy will decay with increasing genetic divergence between the original GWAS sample and the target of prediction, as a function of population history.
“population genetics theory predicts that genetic risk prediction accuracy will decay with increasing genetic divergence between the original GWAS sample and target of prediction, a function of population history13,14.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [13] Martin, A. R. et al. Human demographic history impacts genetic risk prediction across diverse populations. Am. J. Hum. Genet. 100, 635–649 (2017). source
- cites [14] Scutari, M., Mackay, I. & Balding, D. Using genetic distance to infer the accuracy of genomic prediction. PLoS Genet. 12, e1006288 (2016). source
- Interpretationcitation
Even when non-European cohorts are only a fraction the size of the largest European study, they are likely to have disproportionate value for predicting polygenic traits in other individuals of similar ancestry.
“These studies have shown that even when non-European cohorts are only a fraction the size of the largest European study, they are likely to have disproportionate value for predicting polygenic traits in other individuals of similar ancestry.”
Quote in the paperSubstantial claim2 of 3 sources checked- cites [23] Akiyama, M. et al. Genome-wide association study identifies 112 new loci for body mass index in the Japanese population. Nat. Genet. 49, 1458–1467 (2017). source
The Variance explained by variants in the GWAS section (p. 12) reports that variants selected using the Japanese GWAS explained BMI variance in Japanese cohorts better than variants selected using a European GWAS—1.81 times better on average. This supports the value of ancestry-matched data, but the paper tests BMI in Japanese cohorts, not prediction of polygenic traits generally. The passages also do not establish the claimed size comparison with the largest European study. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [24] Li, Z. et al. Genome-wide association analysis identifies 30 new susceptibility loci for schizophrenia. Nat. Genet. 49, 1576–1583 (2017). source
The polygenic risk score results (pp. 17–18) show that adding the smaller Chinese cohort improved prediction of schizophrenia case-control status in a Chinese target sample; at one threshold, variance explained rose from 2.34% with European-only training to 7.86% with combined training. The sample-size comparison (p. 9) supports the cohort-size premise. The paper studies schizophrenia in Chinese ancestry, however, not polygenic traits generally or non-European cohorts generally. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [40] Lam, M. et al. Comparative genetic architectures of schizophrenia in East Asian and European populations. Preprint at https://www.biorxiv.org/content/10.1101/445874v2 (2018).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Evidence of polygenic adaptation and/or its relative magnitude for height is under question.
“These effects are particularly challenging to disentangle, as has clearly been demonstrated for height, where evidence of polygenic adaptation and/or its relative magnitude is under question43,44.”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [43] Sohail, M. et al. Signals of polygenic adaptation on height have been overestimated due to uncorrected population structure in genome-wide association studies. Preprint at https://www.biorxiv.org/content/10.1101/355057v3 (2018). source
- cites [44] Berg, J. J. et al. Reduced signal for polygenic adaptation of height in UK Biobank. Preprint at https://www.biorxiv.org/content/10.1101/354951v4 (2018).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisereasoning
The most significant associations tend to be more common in the populations in which they are discovered than elsewhere.
“This dependence means that the most significant associations tend to be more common in the populations in which they are discovered than elsewhere13,30.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [13] Martin, A. R. et al. Human demographic history impacts genetic risk prediction across diverse populations. Am. J. Hum. Genet. 100, 635–649 (2017). source
- cites [30] 1000 Genomes Project Consortium. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015). source
In “Insights about demography” (page unavailable), the paper reports variants that are much more common in particular populations and suggests that these variants may reveal associations difficult to identify in larger global samples. It does not establish that the most significant associations generally have higher variant frequencies in their discovery populations than elsewhere. (LLM, conf=0.76)
Experimental — accuracy not yet measured
- Premisecitation
GWAS favor the discovery of genetic variants that are common in the study population.
“1) GWAS favor the discovery of genetic variants that are common in the study population;”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [29] Sham, P. C., Cherny, S. S., Purcell, S. & Hewitt, J. K. Power of linkage versus association analysis of quantitative traits, by use of variance-components models, for sibship data. Am. J. Hum. Genet. 66, 1616–1630 (2000). source
The paper’s opening summary (p. 1616) says association-analysis power depends on the proportion of phenotypic variance attributable to a QTL, and its variance formula includes the QTL alleles’ population frequencies. That is consistent with frequency affecting detection power, but the paper studies sibship-based QTL analysis and does not establish the broader claim that GWAS preferentially discover common variants. (LLM, conf=0.74)
Experimental — accuracy not yet measured
- Interpretationcitation
The scientific basis of the imbalance in PRS accuracy has been demonstrated theoretically, in simulations, and empirically across many traits and diseases.
“The scientific basis of this imbalance has been demonstrated theoretically, in simulations, and empirically across many traits and diseases11–22.”
Quote in the paperSubstantial claim9 of 10 sources checked- cites [11] Khera, A. V. et al. Genetic risk, adherence to a healthy lifestyle, and coronary disease. N. Engl. J. Med. 375, 2349–2358 (2016). source
The Methods (Polygenic Risk Score; page unavailable) describe a score for coronary artery disease, and the Results (page unavailable) report similar findings among Black and white participants in one cohort. Searches for ancestry-related differences in PRS accuracy found no passage demonstrating the claimed scientific basis theoretically, in simulations, or empirically across many traits and diseases. (LLM, conf=0.75)
Experimental — accuracy not yet measured - cites [12] Khera, A. V. & Kathiresan, S. Genetics of coronary artery disease: discovery, biology and clinical translation. Nat. Rev. Genet. 18, 331–344 (2017). source
The Genomic medicine section discusses polygenic risk scores for coronary artery disease, but does not address an imbalance in their accuracy. Searches for differences across populations and for theoretical, simulation, or cross-trait evidence found no passage establishing the attributed claim. Page numbers were not available in our copy. (LLM, conf=0.75)
Experimental — accuracy not yet measured - cites [13] Martin, A. R. et al. Human demographic history impacts genetic risk prediction across diverse populations. Am. J. Hum. Genet. 100, 635–649 (2017). source
- cites [14] Scutari, M., Mackay, I. & Balding, D. Using genetic distance to infer the accuracy of genomic prediction. PLoS Genet. 12, e1006288 (2016). source
The Introduction explains why prediction accuracy can differ between training and genetically distinct target populations, and the Simulation Studies examine this using human genotypes and simulated phenotypes. The Real-World Data Analyses test several traits in wheat and mice, but the paper does not empirically demonstrate the imbalance across many human traits and diseases. No page numbers are provided in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [15] Vilhjálmsson, B. J. et al. Modeling linkage disequilibrium increases accuracy of polygenic risk scores. Am. J. Hum. Genet. 97, 576–592 (2015). source
The Discussion (p. 9) reports lower absolute PRS prediction accuracy in non-European than European validation samples, and the results (p. 8) include African- and Asian-descent schizophrenia samples. But the paper’s theory and simulations concern accuracy gains from modeling linkage disequilibrium, not a theoretical and simulated demonstration of the population-level imbalance across many traits and diseases. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites [16] Ware, E. B. et al. Heterogeneity in polygenic scores for common human traits. Preprint at https://www.biorxiv.org/content/10.1101/106062v1 (2017). source
The Cross-race/ethnicity comparison and Discussion (pages not provided) report empirical differences in polygenic-score performance between non-Hispanic White and Black participants across the traits studied. The paper does not establish this imbalance theoretically or through simulations, and its empirical analysis is limited to four traits rather than many traits and diseases. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites [17] Curtis, D. Polygenic risk score for schizophrenia is more strongly associated with ancestry than with schizophrenia. Psychiatr. Genet. 28, 85–89 (2018). source
The Results (page not provided) show that the schizophrenia PRS differed markedly between ancestry groups, and the Discussion warns against applying a score derived from European subjects to subjects with African ancestry. This is empirical evidence of an ancestry-related limitation, but the paper does not demonstrate the imbalance theoretically or through simulations, directly compare prediction accuracy, or establish it across many traits and diseases. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [18] Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). source
The Polygenic risk score profiling section reports that schizophrenia risk-score prediction depends on the target sample, and it evaluates prediction in three samples. It does not demonstrate a theoretical or simulation-based explanation for an imbalance in PRS accuracy, or show that imbalance across many traits and diseases. (LLM, conf=0.79)
Experimental — accuracy not yet measured - cites [19] Belsky, D. W. et al. Development and evaluation of a genetic risk score for obesity. Biodemography Soc. Biol. 59, 85–100 (2013). source
The Results and Discussion report that the obesity genetic risk score predicted BMI and obesity less well among African American than white ARIC participants, supporting an empirical example of unequal accuracy. The paper does not demonstrate the imbalance through simulations or establish it across many traits and diseases; its analysis concerns obesity in these two groups. The indexed passages provide no page numbers. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites [20] Domingue, B. W., Belsky, D., Conley, D., Harris, K. M. & Boardman, J. D. Polygenic influence on educational attainment: new evidence from The National Longitudinal Study of Adolescent to Adult Health. AERA Open 1, 1–13 (2015). source
The Materials > Sample section (page unavailable) explains why differences in linkage disequilibrium can reduce the precision of polygenic scores across ancestry groups. The Results section reports a smaller association with educational attainment in African Americans than in European Americans. The paper thus supports a mechanism and one empirical example, but it does not demonstrate the imbalance through simulations or across many traits and diseases. (LLM, conf=0.86)
Experimental — accuracy not yet measured
- Premisecitation
Other East Asian studies have estimated higher heritability for some quantitative traits than BBJ using the same methods, such as for height (h2 = 0.48±0.04 in Chinese women).
“Indeed, other East Asian studies have estimated higher heritability for some quantitative traits than BBJ using the same methods, such as for height (h2 = 0.48±0.04 in Chinese women60).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [60] Liu, S. et al. Genomic analyses from non-invasive prenatal testing reveal genetic associations, patterns of viral infections, and Chinese population history. Cell 175, 347–359.e14 (2018). source
In “Phenotype-Genotype Associations of Multiple Complex Traits” (page unavailable), the paper reports an LD-score-regression SNP heritability of 0.48 for height; the Introduction identifies the study population as pregnant Chinese women. Our copy does not give the claimed ±0.04 uncertainty or establish the comparison with BBJ, so those parts remain unsupported. (LLM, conf=0.84)
Experimental — accuracy not yet measured
- Interpretationcitation
Multi-ethnic work has been slow in most disease areas, limiting even the opportunity to assess PRS in non-European cohorts.
“So far, multi-ethnic work has been slow in most disease areas54, limiting even the opportunity to assess PRS in non-European cohorts.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [54] Duncan, L. E. et al. Largest GWAS of PTSD (N=20 070) yields genetic overlap with schizophrenia and sex differences in heritability. Mol. Psychiatry 23, 666–673 (2018). source
The Discussion says that external data resources needed for PRS are far less common for non-European populations and nonexistent for many, supporting the claimed limitation on assessing PRS. It does not establish that multi-ethnic work has been slow in most disease areas; that scope goes beyond what this PTSD paper states. (LLM, conf=0.82)
Experimental — accuracy not yet measured
- Premisecitation
Integrated models of PRS together with other lifestyle and clinical factors have enabled clinicians to more accurately quantify the risk of heart attack.
“Additionally, integrated models of PRS together with other lifestyle and clinical factors have enabled clinicians to more accurately quantify the risk of heart attack for patients;”
Quote in the paperNot a substantial claim4 of 5 sources checked- cites [5] Khera, A. V. et al. Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations. Nat. Genet. 50, 1219–1224 (2018). source
The paper reports that its polygenic score identified people at elevated coronary artery disease risk (Abstract; page not provided). It describes combining genetic risk with clinical and environmental factors as a future issue, not an integrated model already used by clinicians to improve heart-attack risk estimates. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [6] Kullo, I. J. et al. Incorporating a genetic risk score into coronary heart disease risk estimates: effect on low-density lipoprotein cholesterol levels (the MI-GENES Clinical Trial). Circulation 133, 1181–1188 (2016). source
Methods > Study Design describes combining a genetic risk score with a conventional score to estimate 10-year coronary heart disease risk. But Discussion says the genetic score was not prospectively validated and presents refinement of risk estimates as a future possibility. The paper therefore does not establish that the combined model quantified heart-attack risk more accurately, or that lifestyle measures were included in the model. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [7] Natarajan, P. et al. Polygenic risk score identifies subgroup with higher burden of atherosclerosis and greater relative benefit from statin therapy in the primary prevention setting. Circulation 135, 2091–2101 (2017). source
The Methods (Statistical Analysis; page unavailable) describe models that assess PRS alongside clinical factors, including smoking, and the Results (page unavailable) find that high PRS predicts coronary events after adjustment for traditional risk factors. The paper does not show that integrating PRS with lifestyle and clinical factors improves the accuracy of heart-attack risk estimates, or that clinicians have used such a model for patients. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [8] Paquette, M. et al. Polygenic risk score predicts prevalence of cardiovascular disease in patients with familial hypercholesterolemia. J. Clin. Lipidol. 11, 725–732.e5 (2017). source
- cites [9] Tikkanen, E., Havulinna, A. S., Palotie, A., Salomaa, V. & Ripatti, S. Genetic risk prediction and a 2-stage risk screening strategy for coronary heart disease. Arterioscler. Thromb. Vasc. Biol. 33, 2261–2266 (2013). source
The Methods and Results show that adding a genetic risk score to models with traditional factors, including smoking and clinical measures, improved coronary heart disease risk prediction and reclassification. The Discussion describes potential clinical value, but the paper models screening rather than showing that clinicians used these models to quantify patients’ heart-attack risk in practice. (LLM, conf=0.82)
Experimental — accuracy not yet measured
- Premisecitation
Linkage disequilibrium differentiates marginal effect size estimates for polygenic traits across populations, even when causal variants are the same.
“2) linkage disequilibrium (LD) differentiates marginal effect size estimates for polygenic traits across populations, even when causal variants are the same;”
Quote in the paperSubstantial claim4 of 5 sources checked- cites [35] Liu, J. Z. et al. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat. Genet. 47, 979–986 (2015). source
The Online Methods (Trans-ethnic association analysis; page unavailable) say that differences in LD with a causal variant can produce differences in observed allelic effects across populations. The Discussion (page unavailable) likewise identifies differential tagging of untyped causal variants as a possible explanation for effect-size heterogeneity. The paper does not establish that LD does so generally for polygenic traits; it presents the mechanism as a possibility in its IBD analysis. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [37] Easton, D. F. et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447, 1087–1093 (2007). source
The Pattern of risks section (page unavailable) reports a smaller per-allele odds ratio for the FGFR2 marker rs2981582 in Asian than European populations and says this is consistent with the marker not being the functional variant. The FGFR2 and Discussion sections (pages unavailable) describe different LD patterns across populations. These passages support a locus-specific example, but do not establish the claim for polygenic traits generally or demonstrate that the causal variants are the same across populations. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [38] DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium. et al. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat. Genet. 46, 234–244 (2014). source
- cites [39] Waters, K. M. et al. Consistent association of type 2 diabetes risk variants found in europeans in diverse racial and ethnic groups. PLoS Genet. 6, e1001078–e1001079 (2010). source
The Discussion (page unavailable) says weaker associations across racial and ethnic groups may reflect differences in linkage disequilibrium, among other factors, and suggests lower linkage disequilibrium could explain two marker-SNP results. It does not establish that linkage disequilibrium causes differences in marginal effect estimates generally across polygenic traits; it also says the causal alleles at the studied type 2 diabetes loci have yet to be found. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [40] Lam, M. et al. Comparative genetic architectures of schizophrenia in East Asian and European populations. Preprint at https://www.biorxiv.org/content/10.1101/445874v2 (2018).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
The power to discover an association in a genetic study depends on the effect size and frequency of the variant.
“First, the power to discover an association in a genetic study depends on the effect size and frequency of the variant29.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [29] Sham, P. C., Cherny, S. S., Purcell, S. & Hewitt, J. K. Power of linkage versus association analysis of quantitative traits, by use of variance-components models, for sibship data. Am. J. Hum. Genet. 66, 1616–1630 (2000). source
- Premisecitation
Substantially different rates of alcohol use disorder across populations are partially explained by differences in availability and genetic differences impacting alcohol metabolism.
“substantially different rates of alcohol use disorder across populations are partially explained by differences in availability and genetic differences impacting alcohol metabolism50.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [50] Li, D., Zhao, H. & Gelernter, J. Strong protective effect of the aldehyde dehydrogenase gene (ALDH2) 504lys (*2) allele against alcoholism and alcohol-induced medical diseases in Asians. Hum. Genet. 131, 725–737 (2012). source
The Results (page not provided) report that the protective ALDH2 allele varies in frequency across populations and is strongly associated with lower odds of alcohol abuse or dependence. The Introduction explains how the allele impairs alcohol metabolism and can deter drinking. The paper does not establish that differences in alcohol availability explain population-level differences in alcohol use disorder rates. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Premisecitation
Poor generalizability of genetic studies across populations arises from the overwhelming abundance of European descent studies and dearth of well-powered studies in globally diverse populations.
“Poor generalizability of genetic studies across populations arises from the overwhelming abundance of European descent studies and dearth of well-powered studies in globally diverse populations25–28.”
Quote in the paperSubstantial claim3 of 4 sources checked- cites [25] Need, A. C. & Goldstein, D. B. Next generation disparities in human genomics: concerns and remedies. Trends Genet. 25, 489–494 (2009). source
- cites [26] Popejoy, A. B. & Fullerton, S. M. Genomics is failing on diversity. Nature 538, 161–164 (2016). source
- cites [27] Morales, J. et al. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biol. 19, 21 (2018). source
The Results (Improving data analysis and assessing diversity; page unavailable) show a strong European-ancestry bias and very low representation of several other populations. The Background links ancestry differences to the generalizability of genetic findings. The paper does not establish that this imbalance causes poor generalizability or document a dearth of specifically well-powered studies across globally diverse populations. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [28] Rosenberg, N. A. et al. Genome-wide association studies in diverse populations. Nat. Rev. Genet. 11, 356–366 (2010). source
The Abstract (page unavailable) says GWA studies were overwhelmingly centered on European-descent populations and that transferability of their findings to other populations had not been extensively investigated. “The case for more populations” explains why findings may differ across populations and calls for large-scale studies. The paper does not establish that generalizability is poor or that the study imbalance itself causes poor generalizability; it presents transferability as an open question. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Premisecitation
Many earlier criticisms of limited prediction power are now recognized to have been chiefly an issue of insufficient sample size, which is no longer the case for many outcomes.
“Many earlier criticisms of limited prediction power are now recognized to have been chiefly an issue of insufficient sample size, which is no longer the case for many outcomes1.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [1] Knowles, J. W. & Ashley, E. A. Cardiovascular disease: the rise of the genetic risk score. PLoS Med. 15, e1002546–e1002547 (2018). source
- Premisecitation
Polygenic risk scores alone already predict breast cancer, prostate cancer, and type 1 diabetes risk in European descent patients more accurately than current clinical models.
“For example, polygenic risk scores alone already predict breast cancer, prostate cancer, and type 1 diabetes risk in European descent patients more accurately than current clinical models2–4.”
Quote in the paperNot a substantial claim3 of 3 sources checked- cites [2] Maas, P. et al. Breast cancer risk from modifiable and nonmodifiable risk factors among white women in the United States. JAMA Oncol. 2, 1295–1302 (2016). source
The Results (Assessment of Interactions and Risk Model Building; page not provided) report a higher AUC for PRS-92 alone (0.623) than for a model using questionnaire-based risk factors alone (0.588) in breast cancer risk prediction. They do not compare the PRS with established clinical models, and the PRS-92 included simulated data for 68 SNPs. This source addresses breast cancer in white women, not the sentence’s prostate cancer or type 1 diabetes examples. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [3] Schumacher, F. R. et al. Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci. Nat. Genet. 50, 928–936 (2018). source
The paper’s Abstract reports that a polygenic risk score stratified prostate cancer risk, and Methods > Proportion of familial risk explained describes estimating scores for men of European ancestry. It does not compare the score’s predictive accuracy with current clinical models. Breast cancer and type 1 diabetes are not assessed as claims attributed specifically to this prostate cancer paper. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [4] Sharp, S. A. et al. Development and standardization of an improved type 1 diabetes genetic risk score for use in newborn screening and incident diagnosis. Diabetes Care 42, 200–207 (2019). source
The Results and Conclusions (pages not provided) show that the type 1 diabetes genetic risk score predicts risk in cohorts of European descent and improves simulated newborn screening over HLA genotyping alone and earlier genetic scores. They do not show that the score alone outperforms current clinical models. This citation is assessed for the type 1 diabetes portion of the sentence, not the breast or prostate cancer portions supported by other citations. (LLM, conf=0.86)
Experimental — accuracy not yet measured
- Premisecitation
Complex traits are highly polygenic, meaning most prediction power comes from small effects that do not meet genome-wide significance and/or cannot be fine-mapped, even in many of the best-powered GWAS to date.
“This is because complex traits are highly polygenic, meaning most of our prediction power comes from small effects that do not meet genome-wide significance and/or cannot be fine-mapped, even in many of the best-powered GWAS to date42.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [42] Huang, H. et al. Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature 547, 173–178 (2017). source
The Methods section on confounders reports a polygenic signal in the IBD data, and Extended Data Figure 1 says fine-mapping power increases with association significance. The paper does not establish that most predictive power across complex traits comes from small effects below genome-wide significance or from effects that cannot be fine-mapped, even in well-powered GWAS. (LLM, conf=0.83)
Experimental — accuracy not yet measured
- Premisecitation
LD differences drive differences in effect size estimates from GWAS across populations in proportion to LD between tagging and causal SNP pairs, even when causal effects are the same.
“These LD differences in turn drive differences in effect size estimates (i.e. predictors) from GWAS across populations in proportion to LD between tagging and causal SNP pairs, even when causal effects are the same35,37–40 (Supplementary Note).”
Quote in the paperSubstantial claim4 of 5 sources checked- cites [35] Liu, J. Z. et al. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat. Genet. 47, 979–986 (2015). source
Online Methods (Trans-ethnic association analysis; page not provided) says differences in LD between populations can produce differences in allelic effect estimates, and the Discussion says differential tagging of untyped causal variants could explain observed effect-size heterogeneity. The paper does not establish that the differences are proportional to LD between tagging and causal SNPs, or show this occurring when causal effects are the same; it presents differential tagging as a possibility rather than the demonstrated cause. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [37] Easton, D. F. et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447, 1087–1093 (2007). source
The Pattern of risks section reports a smaller odds ratio for rs2981582 in Asian than European populations and says this is consistent with rs2981582 not being the functional variant. The FGFR2 section reports weaker LD in the Asian studies. The paper does not establish that effect-size differences are proportional to LD between tagging and causal SNPs, or that the causal effects are the same across populations; it says the causal variant remains unresolved. Page numbers are unavailable in our copy. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [38] DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium. et al. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat. Genet. 46, 234–244 (2014). source
The Results section ('Improved fine-mapping resolution at T2D susceptibility loci'; page unavailable) says that differences in LD with a shared causal variant can produce differences in allelic odds ratios across ancestry groups. The Online Methods ('Fine-mapping analyses'; page unavailable) makes the same point, but neither passage states that the effect-size differences are proportional to LD between tagging and causal SNPs. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [39] Waters, K. M. et al. Consistent association of type 2 diabetes risk variants found in europeans in diverse racial and ethnic groups. PLoS Genet. 6, e1001078–e1001079 (2010). source
The Discussion (page not provided) says weaker associations across racial and ethnic groups may be due to differences in linkage disequilibrium, and suggests lower LD between a marker and a biologically relevant allele for two loci. It does not establish that LD drives effect-size differences in proportion to LD between tagging and causal SNPs, or test that relationship while holding causal effects constant. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [40] Lam, M. et al. Comparative genetic architectures of schizophrenia in East Asian and European populations. Preprint at https://www.biorxiv.org/content/10.1101/445874v2 (2018).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationcitation
Residual stratification can lead to over-predicted differences across geographical space.
“This residual stratification can lead to over-predicted differences across geographical space45.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [45] Kerminen, S. et al. Geographic variation and bias in polygenic scores of complex diseases and traits in Finland. Preprint at https://www.biorxiv.org/content/10.1101/485441v1 (2018). source
- Interpretationcitation
Comparisons of geographically stratified phenotypes like height across populations with highly divergent genetic backgrounds and mean environmental differences are especially prone to confounding from correlated environmental and genetic divergence.
“Comparisons of geographically stratified phenotypes like height across populations with highly divergent genetic backgrounds and mean environmental differences, such as differences in resource abundance during development across continents, are especially prone to confounding from correlated environmental and genetic divergence43,44.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [43] Sohail, M. et al. Signals of polygenic adaptation on height have been overestimated due to uncorrected population structure in genome-wide association studies. Preprint at https://www.biorxiv.org/content/10.1101/355057v3 (2018). source
The Results (lines 101–111) and Discussion (lines 365–386; page unavailable) show that population structure can distort comparisons of genetic height scores and create misleading signals across populations. The paper examines predominantly European genetic comparisons; it does not establish the claim’s more specific account of correlated environmental and genetic divergence across continents, including differences in developmental resources. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [44] Berg, J. J. et al. Reduced signal for polygenic adaptation of height in UK Biobank. Preprint at https://www.biorxiv.org/content/10.1101/354951v4 (2018).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Reference intervals for biomarkers can sometimes deviate considerably by reported ethnicity.
“Consequently, reference intervals for biomarkers can sometimes deviate considerably by reported ethnicity66–68.”
Quote in the paperNot a substantial claim1 of 3 sources checked- cites [66] Carroll, M. D., Kit, B. K., Lacher, D. A., Shero, S. T. & Mussolino, M. E. Trends in lipids and lipoproteins in US adults, 1988–2010. JAMA 308, 1545–1554 (2012). source
- cites [67] Rappoport, N. et al. Comparing ethnicity-specific reference intervals for clinical laboratory tests from EHR data. J. Appl. Lab. Med. 3, 366–377 (2018). source
- cites [68] Lim, E., Miyamura, J. & Chen, J. J. Racial/ethnic-specific reference intervals for common laboratory tests: a comparison among Asians, Blacks, Hispanics, and White. Hawaii J. Med. Public Health 74, 302–310 (2015).
- Premisecitation
The lack of supporting resources for diverse ancestries creates financial challenges for association studies with limited resources.
“The lack of supporting resources for diverse ancestries creates financial challenges for association studies with limited resources, e.g. raising questions about whether to genotype samples on GWAS arrays that may favor European allele frequencies versus sequence samples, and how dense of an array to choose or how deeply to sequence71,72.”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [71] Gilly, A. et al. Very low depth whole genome sequencing in complex trait association studies. Bioinformatics https://doi.org/10.1093/bioinformatics/bty1032 (2018). source
The Introduction (page not available in our copy) says high-depth sequencing is costly and presents low-depth sequencing as a cost-efficient alternative to imputed GWAS arrays. It does not attribute those costs to a lack of resources for diverse ancestries, discuss European-favoring array design, or specifically address studies with limited resources. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [72] Pasaniuc, B. et al. Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat. Genet. 44, 631–635 (2012). source
The Discussion (page not provided) compares the costs and effective sample sizes of sequencing at different depths versus SNP-array genotyping under a fixed budget, supporting the financial study-design trade-off. It also says large reference-haplotype panels are important, but does not say that a lack of resources for diverse ancestries creates these financial challenges or that arrays favor European allele frequencies. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Interpretationcitation
PRS are uniformly less useful in understudied populations due to differences in genomic variation and population history.
“In contrast, PRS are uniformly less useful in understudied populations due to differences in genomic variation and population history13,14.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [13] Martin, A. R. et al. Human demographic history impacts genetic risk prediction across diverse populations. Am. J. Hum. Genet. 100, 635–649 (2017). source
- cites [14] Scutari, M., Mackay, I. & Balding, D. Using genetic distance to infer the accuracy of genomic prediction. PLoS Genet. 12, e1006288 (2016). source
The Introduction (page not available) says genomic prediction has lower average accuracy when a target population is more genetically distant from the training population, and notes that causal variants can differ between ancestry groups. It does not establish that PRS are uniformly less useful in all understudied populations: its finding concerns genetic distance, not whether a population is understudied, and is expressed as an average rather than a universal rule. (LLM, conf=0.88)
Experimental — accuracy not yet measured
- Findingcitation
According to the GWAS catalog, approximately 79% of all GWAS participants are of European descent despite making up only 16% of the global population.
“According to the GWAS catalog, ~79% of all GWAS participants are of European descent despite making up only 16% of the global population (Figure 1).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Figure 1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingown data
Prediction accuracy is consistently higher with GWAS summary statistics from ancestry-matched summary statistics.
“We symmetrically demonstrate that prediction accuracy is consistently higher with GWAS summary statistics from ancestry-matched summary statistics (Figure 4, Supplementary Figures 2–6).”
Quote in the paperSubstantial claim0 of 2 sources checked- cites Figure 4
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites Supplementary Figures 2–6
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingown data
The fraction of non-European individuals in GWAS has stagnated or declined since late 2014.
“More concerningly, the fraction of non-European individuals in GWAS has stagnated or declined since late 2014 (Figure 1), suggesting that we are not on a trajectory to correct this imbalance.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Figure 1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingreasoning
GWAS catalog variants are more common on average in European populations compared to East Asian and African populations.
“For example, GWAS catalog variants are more common on average in European populations compared to East Asian and African populations (Figure 2B), an observation not representative of genomic variants at large.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Figure 2B
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingnone given
African descent populations are often predicted marginally better, if at all, compared to random by polygenic risk scores (Figure 4F).
“Conversely, African descent populations, which already endure many of the largest health disparities globally, are often predicted marginally better, if at all, compared to random (Figure 4F).”
Quote in the paperNot a substantial claim - Interpretationreasoning
It may not be feasible to fine-map most variants to a single locus to solve issues of low generalizability, even with very large GWAS.
“While it would be ideal to use causal effects rather than correlated effect size estimates to calculate PRS, it may not be feasible to fine-map most variants to a single locus to solve issues of low generalizability, even with very large GWAS.”
Quote in the paperSubstantial claim - Interpretationreasoning
Early diversifying GWAS efforts have been especially productive for informing on questions surrounding risk prediction.
“Early diversifying GWAS efforts have been especially productive for informing on questions surrounding risk prediction.”
Quote in the paperSubstantial claim - Premiseown data
Linkage disequilibrium, the correlation structure of the genome, varies across populations due to demographic history.
“Second, LD, the correlation structure of the genome, varies across populations due to demographic history (Figure 2A,C–E).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Figure 2A,C–E
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationreasoning
Other effects on polygenic adaptation or risk scores, such as long-standing environmental differences across global populations that have resulted in differing responses of natural selection, can impact populations differently based on their unique histories.
“In contrast, other effects on polygenic adaptation or risk scores such as long-standing environmental differences across global populations that have resulted in differing responses of natural selection can impact populations differently based on their unique histories.”
Quote in the paperNot a substantial claim - Interpretationreasoning
These population studies demonstrate the power and utility of increasingly diverse GWAS for prediction, especially in populations of non-European descent.
“These population studies demonstrate the power and utility of increasingly diverse GWAS for prediction, especially in populations of non-European descent.”
Quote in the paperSubstantial claim - Interpretationreasoning
Understudied populations offer low-hanging fruit for genetic discovery because variants that are common in these groups but rare or absent in European populations could not be discovered even with very large European sample sizes.
“Understudied populations offer low-hanging fruit for genetic discovery because variants that are common in these groups but rare or absent in European populations could not be discovered even with very large European sample sizes.”
Quote in the paperSubstantial claim - Interpretationreasoning
Other cohort considerations may further worsen prediction accuracy differences across populations in less predictable ways.
“Lastly, other cohort considerations may further worsen prediction accuracy differences across populations in less predictable ways.”
Quote in the paperNot a substantial claim - Premisecitation
Schizophrenia has a nearly identical genetic basis across East Asians and Europeans (rg=0.98).
“Among psychiatric disorders for example, whereas schizophrenia has a nearly identical genetic basis across East Asians and Europeans (rg=0.98)40,”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [40] Lam, M. et al. Comparative genetic architectures of schizophrenia in East Asian and European populations. Preprint at https://www.biorxiv.org/content/10.1101/445874v2 (2018).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationcitation
Previous work has assessed prediction accuracy across diverse populations in several traits and diseases for which GWAS summary statistics are available and identified large disparities across populations.
“Nonetheless, some previous work has assessed prediction accuracy across diverse populations in several traits and diseases for which GWAS summary statistics are available and identified large disparities across populations (Supplementary Note).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Supplementary Note
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationcitation
The disparities in PRS accuracy across populations are not simply methodological issues, as various approaches and accuracy metrics illustrate consistently poorer performance in populations distinct from discovery samples across a range of polygenic traits.
“These disparities are not simply methodological issues, as various approaches (e.g. pruning and thresholding versus LDPred) and accuracy metrics (R2 for quantitative traits and various pseudo-R2 metrics for binary traits) illustrate this consistently poorer performance in populations distinct from discovery samples across a range of polygenic traits (Supplementary Table 1).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Supplementary Table 1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationreasoning
PRS are unique in that even with multi-ethnic population references, these scores are fundamentally less informative in populations more diverged from GWAS study cohorts.
“Rather, as we and others demonstrate, PRS are unique in that even with multi-ethnic population references, these scores are fundamentally less informative in populations more diverged from GWAS study cohorts.”
Quote in the paperSubstantial claim - Interpretationreasoning
African descent populations are least likely to benefit from improvements in precision healthcare delivery from genetic risk scores with existing data due to human population history and study biases.
“They are therefore least likely to benefit from improvements in precision healthcare delivery from genetic risk scores with existing data due to human population history and study biases.”
Quote in the paperSubstantial claim- Rests on an assumption: Human population history and study biases cause African descent populations to be predicted marginally better, if at all, compared to random by PRS.
- Interpretationreasoning
Comparisons of PRS utility across populations often use odds ratios among arbitrary breakpoints in the risk distribution that make comparisons across studies challenging.
“though often with comparisons of odds ratios among arbitrary breakpoints in the risk distribution that make comparisons across studies challenging.”
Quote in the paperNot a substantial claim - Interpretationreasoning
PRS may have a larger potential to raise health disparities than other clinical factors.
“Our impetus for raising these statistical issues limiting the generalizability of PRS across population stems from our concerns that, while they are legitimately clinically promising for improving health out comes for many biomedical phenotypes, they may have a larger potential to raise health disparities than other clinical factors for several reasons.”
Quote in the paperNot a substantial claim
- Classified as probably not a substantial claim. 18
- May combine two claims. 30
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationReturn of genetic risk of complex disease to at-risk patients does not induce significant self-reported negative behavior or psychological function, and some potentially positive behavioral changes have been detected.
“Promisingly, return of genetic risk of complex disease to at-risk patients does not induce significant self-reported negative behavior or psychological function, and some potentially positive behavioral changes have been detected10.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [10] Frieser, M. J., Wilson, S. & Vrieze, S. Behavioral impact of return of genetic test results for complex disease: systematic review and meta-analysis. Health Psychol. 37, 1134–1144 (2018). source
Probably not a substantial claim: may not pass S3 (load-bearing).
InterpretationcitationCardiovascular research has led the charge towards clinical translation of PRS.
“Cardiovascular research, for example, has led the charge towards clinical translation of PRS1.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [1] Knowles, J. W. & Ashley, E. A. Cardiovascular disease: the rise of the genetic risk score. PLoS Med. 15, e1002546–e1002547 (2018). source
The Summary points describe a cardiovascular pilot study that showed the feasibility of delivering a genetic risk score in a clinical setting, and the authors propose incorporating such scores into practice. They also say few studies have addressed practical implementation. The paper does not establish that cardiovascular research has led other fields in clinical translation. (LLM, conf=0.83)
Experimental — accuracy not yet measured
May combine two claims.
InterpretationcitationPRS are many-fold more accurate in European ancestry individuals than in others, and this disparity is the major ethical and scientific challenge surrounding clinical implementation.
“However, the major ethical and scientific challenge surrounding clinical implementation is that they are many-fold more accurate in European ancestry individuals than others.”
- Also stated in: § Abstract · boosted
“the consistent observation that they are currently of far greater predictive value in individuals of recent European descent than in others to be the major ethical and scientific challenge surrounding clinical translation and, at present, the most critical limitation to genetics in precision medicine.”
- Also stated in: § Abstract · boosted
“All studies to date using well-powered genome-wide association studies (GWAS) to assess the predictive value of PRS across a range of traits and populations have made a consistent observation: PRS predict individual risk far more accurately in Europeans. than non-Europeans15,16,18–24.”
Quote in the paperSubstantial claim9 of 10 sources checked- cites [11] Khera, A. V. et al. Genetic risk, adherence to a healthy lifestyle, and coronary disease. N. Engl. J. Med. 375, 2349–2358 (2016). source
The Results (page not provided) note a paucity of well-validated genetic loci in black populations, and the Discussion (page not provided) calls for testing the score in more diverse populations. But the paper reports similar findings among black and white ARIC participants; it does not show that scores are many-fold more accurate in people of European ancestry or identify that disparity as the major ethical and scientific challenge to clinical implementation. (LLM, conf=0.82)
Experimental — accuracy not yet measured - cites [12] Khera, A. V. & Kathiresan, S. Genetics of coronary artery disease: discovery, biology and clinical translation. Nat. Rev. Genet. 18, 331–344 (2017). source
The Genomic medicine section describes polygenic risk scores and their potential clinical use, but does not compare their accuracy across ancestry groups. The Common variant association studies section mentions a genotyping chip designed for individuals of European ancestry; it does not establish a many-fold accuracy difference or identify that disparity as the major ethical and scientific challenge. Searches for ancestry-related accuracy and clinical-implementation challenges found no passage addressing the claim. (LLM, conf=0.76)
Experimental — accuracy not yet measured - cites [13] Martin, A. R. et al. Human demographic history impacts genetic risk prediction across diverse populations. Am. J. Hum. Genet. 100, 635–649 (2017). source
- cites [14] Scutari, M., Mackay, I. & Balding, D. Using genetic distance to infer the accuracy of genomic prediction. PLoS Genet. 12, e1006288 (2016). source
The Introduction (page unavailable) says genomic prediction accuracy tends to fall as target populations become more genetically distant from training populations. But the human simulation uses an Asian training population (Materials and Methods, page unavailable); it does not establish that PRS are many-fold more accurate in European-ancestry individuals or identify this disparity as the major ethical and scientific challenge to clinical implementation. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [15] Vilhjálmsson, B. J. et al. Modeling linkage disequilibrium increases accuracy of polygenic risk scores. Am. J. Hum. Genet. 97, 576–592 (2015). source
The Results (p. 8) report lower absolute prediction accuracy in African- and Asian-ancestry schizophrenia validation samples, and the Discussion (p. 9) calls for improving prediction in diverse populations. The paper does not establish a many-fold difference across PRSs generally or characterize that disparity as the major ethical and scientific challenge to clinical implementation. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [16] Ware, E. B. et al. Heterogeneity in polygenic scores for common human traits. Preprint at https://www.biorxiv.org/content/10.1101/106062v1 (2017). source
The Discussion reports that European-ancestry-weighted scores explained approximately twice as much trait variation in the HRS non-Hispanic White sample as in the non-Hispanic Black sample. That supports a performance disparity, but not a general claim about all other ancestries or that the scores are “many-fold more accurate.” The paper does not identify this disparity as the major ethical and scientific challenge to clinical implementation. (LLM, conf=0.89)
Experimental — accuracy not yet measured - cites [17] Curtis, D. Polygenic risk score for schizophrenia is more strongly associated with ancestry than with schizophrenia. Psychiatr. Genet. 28, 85–89 (2018). source
The Discussion (page unavailable) warns that ancestry differences complicate clinical risk prediction and that a PRS derived largely from European samples may not apply to people of African ancestry. It also raises the possibility that non-European populations may be disadvantaged. But its roughly tenfold figure compares differences in PRS values, not predictive accuracy; the paper does not show that PRS are many-fold more accurate in Europeans or rank this as the major implementation challenge. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites [18] Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). source
The Polygenic risk score profiling section (page unavailable) reports limited sensitivity and specificity and cautions against using the scores as a predictive test. The 108 independent associated loci section (page unavailable) identifies European- and East Asian-ancestry samples, but the passages found do not compare score accuracy across ancestries or call such a disparity the major ethical and scientific challenge. Searches for ancestry-related prediction differences and clinical implementation found no supporting passage. (LLM, conf=0.76)
Experimental — accuracy not yet measured - cites [19] Belsky, D. W. et al. Development and evaluation of a genetic risk score for obesity. Biodemography Soc. Biol. 59, 85–100 (2013). source
The Results and Discussion (page unavailable) show that this obesity genetic risk score was substantially less predictive in African American than in white ARIC participants. But the study tested one obesity score in those two groups, not PRS generally across all ancestries. Its Discussion does not identify that disparity as the major ethical and scientific challenge to clinical implementation; it instead says the score's modest added predictive value was insufficient to recommend it for clinical risk assessment. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites [20] Domingue, B. W., Belsky, D., Conley, D., Harris, K. M. & Boardman, J. D. Polygenic influence on educational attainment: new evidence from The National Longitudinal Study of Adolescent to Adult Health. AERA Open 1, 1–13 (2015). source
The Materials > Sample section says that polygenic scores derived from European-ancestry samples may be less precise in African-American samples, and the Results report a smaller association with educational attainment among African Americans. The paper does not establish a many-fold accuracy difference across all other ancestries or characterize that disparity as the major ethical and scientific challenge to clinical implementation. No page numbers are available in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measured
- Also stated in: § Abstract · boosted
May combine two claims.
InterpretationcitationSome machine learning approaches may modestly improve PRS accuracy beyond current approaches for some phenotypes, but most likely for atypical traits with simpler architectures, known interactions, and poor prediction generalizability across populations, such as skin pigmentation.
“Some machine learning approaches may thus modestly improve PRS accuracy beyond current approaches for some phenotypes52, but most likely for atypical traits with simpler architectures, known interactions, and poor prediction generalizability across populations, such as skin pigmentation53.”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [52] Paré, G., Mao, S. & Deng, W. Q. A machine-learning heuristic to improve gene score prediction of polygenic traits. Sci. Rep. 7, 12665 (2017). source
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured - cites [53] Martin, A. R. et al. An unexpectedly complex architecture for skin pigmentation in Africans. Cell 171, 1340–1353.e14 (2017). source
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationNon-linear genetic factors explain little variation in complex traits beyond a purely additive model.
“While non-linear genetic factors explain little variation in complex traits beyond a purely additive model51,”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [51] Zhu, Z. et al. Dominance genetic variation contributes little to the missing heritability for human complex traits. Am. J. Hum. Genet. 96, 377–385 (2015). source
The Discussion (page not supplied) reports that dominance variance averaged about one-fifth of additive variance across 79 quantitative traits. That supports the claim for dominance, but the study did not estimate all non-linear genetic factors, including epistasis, so the broader wording goes beyond its findings. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
InterpretationcitationAssessments of PRS across diverse populations are becoming increasingly feasible with the growth and public availability of global biobanks as well as diversifying priorities from funding agencies.
“These assessments are becoming increasingly feasible with the growth and public availability of global bio banks as well as diversifying priorities from funding agencies55,56.”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [55] H3Africa Consortium. et al. Enabling the genomic revolution in Africa. Science 344, 1346–1348 (2014). source
In “Enabling the genomic revolution in Africa” (page not provided), the paper describes funding for H3Africa and plans to make its genomic data publicly accessible through an access committee. It does not discuss polygenic risk score (PRS) assessments or establish that growing global biobanks and diversifying funding priorities are making those assessments increasingly feasible. (LLM, conf=0.80)
Experimental — accuracy not yet measured - cites [56] Hindorff, L. A. et al. Prioritizing diversity in human genomics research. Nat. Rev. Genet. 19, 175–185 (2018). source
The sections on foundational genomic data resources and dedicated funding support describe expanding diverse reference datasets, benefits of publicly accessible reference populations, and funding programmes that prioritize diversity (page numbers unavailable). They do not specifically establish that global biobanks are growing and publicly available, or that these developments are making assessments of polygenic risk scores across populations increasingly feasible. (LLM, conf=0.83)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationA polygenic burden of LDL-increasing SNPs can confer monogenic-equivalent risk of cardiovascular disease, with polygenic scores improving clinical models for risk assessment and statin prescription that can reduce coronary heart disease and improve healthcare delivery efficiency.
“This enthusiasm is driven by observations that a polygenic burden of LDL-increasing SNPs can confer monogenic-equivalent risk of cardiovascular disease, with polygenic scores improving clinical models for risk assessment and statin prescription that can reduce coronary heart disease and improve healthcare delivery efficiency5–7.”
Quote in the paperNot a substantial claim3 of 3 sources checked- cites [5] Khera, A. V. et al. Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations. Nat. Genet. 50, 1219–1224 (2018). source
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured - cites [6] Kullo, I. J. et al. Incorporating a genetic risk score into coronary heart disease risk estimates: effect on low-density lipoprotein cholesterol levels (the MI-GENES Clinical Trial). Circulation 133, 1181–1188 (2016). source
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured - cites [7] Natarajan, P. et al. Polygenic risk score identifies subgroup with higher burden of atherosclerosis and greater relative benefit from statin therapy in the primary prevention setting. Circulation 135, 2091–2101 (2017). source
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
May combine two claims.
InterpretationcitationDifferences in environmental exposure, gene-gene interactions, gene-environment interactions, historical population size dynamics, statistical noise, some potential causal effect differences, and/or other factors will further limit generalizability for genetic risk scores in an unpredictable, trait-specific fashion.
“Differences in environmental exposure, gene-gene interactions, gene-environment interactions, historical population size dynamics, statistical noise, some potential causal effect differences, and/or other factors will further limit generalizability for genetic risk scores in an unpredictable, trait-specific fashion46–49.”
Quote in the paperSubstantial claim4 of 4 sources checked- cites [46] Novembre, J. & Barton, N. H. Tread lightly interpreting polygenic tests of selection. Genetics 208, 1351–1355 (2018). source
In the paper’s discussion of transferring effect sizes across space and time (page unavailable), the authors say that differences in genetic and environmental background, including gene–gene and gene–environment interactions, may affect polygenic scores across populations. They also discuss environmental differences and changes in effects between populations. Our copy does not establish historical population-size dynamics or statistical noise as limits on genetic-risk-score generalizability, nor does it characterize those limits as unpredictable and trait-specific. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites [47] Henn, B. M., Botigué, L. R., Bustamante, C. D., Clark, A. G. & Gravel, S. Estimating the mutation load in human genomes. Nat. Rev. Genet. 16, 333–343 (2015). source
The Conclusions (page unavailable) discuss epistasis, adaptation to different environments, and differences in complex-disease architecture across populations. Demographic Simulations of Mutation Load (page unavailable) discusses bottlenecks and founder effects. The paper does not establish that these factors limit genetic risk-score generalizability in an unpredictable, trait-specific way, and the cited passages do not address statistical noise or gene–environment interactions as risk-score limitations. (LLM, conf=0.82)
Experimental — accuracy not yet measured - cites [48] Brown, B. C., Asian Genetic Epidemiology Network Type 2 Diabetes Consortium, Ye, C. J., Price, A. L. & Zaitlen, N. Transethnic genetic-correlation estimates from summary statistics. Am. J. Hum. Genet. 99, 76–88 (2016). source
The Discussion (page not provided) identifies gene-gene and gene-environment interactions and statistical noise as possible reasons genetic effects differ between populations; the Introduction says such differences may make disease-risk prediction from current GWAS results problematic. The paper does not establish historical population-size dynamics or environmental exposure as specific limits on risk-score generalizability, nor does it conclude that these limits will be unpredictable and trait-specific. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites [49] Galinsky, K. J. et al. Estimating cross-population genetic correlations of causal effect sizes. Genet. Epidemiol. 43, 180–188 (2019). source
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationImputation reference panels share the same study biases as in GWAS, creating challenges for imputing sites that are rare in European populations but common elsewhere when the catalog of non-European haplotypes is substantially smaller.
“Furthermore, imputation reference panels share the same study biases as in GWAS41, creating challenges for imputing sites that are rare in European populations but common elsewhere when the catalog of non-European haplotypes is substantially smaller.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [41] McCarthy, S. et al. A reference panel of 64,976 haplotypes for genotype imputation. Nat. Genet. 48, 1279–1283 (2016). source
The Abstract (page not provided) says the HRC panel draws mainly on studies of predominantly European ancestry and proposes increasing its ethnic diversity. It also links larger, more diverse panels to better imputation accuracy. Online Methods > Site filtering (page not provided) notes variants frequent in non-European populations that were called only in 1000 Genomes. The paper does not explicitly establish that reference panels share GWAS study biases or assess the claimed imputation difficulty for variants rare in Europeans but common elsewhere. (LLM, conf=0.82)
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationAfrica retains the most genetic diversity, and Africans are understudied but disproportionately informative for genetic analyses and evolutionary history.
“These considerations notwithstanding, there are critical needs and challenges for expanding the scale of genetic studies of heritable traits in diverse populations; this is especially apparent in Africa where humans originated and retain the most genetic diversity, as Africans are understudied but disproportionately informative for genetic analyses and evolutionary history27,73.”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [27] Morales, J. et al. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biol. 19, 21 (2018). source
The Results (Improving data analysis and assessing diversity; page not provided) show that African-ancestry participants account for 2.4% of individuals in the GWAS Catalog but contribute 7% of associations. The Discussion (Assessing diversity in genomics; page not provided) links this yield to higher genetic diversity and reduced linkage disequilibrium. Our copy does not state that Africa has the most genetic diversity, that humans originated there, or that African populations are disproportionately informative for evolutionary history. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [73] Martin, A. R., Teferra, S., Möller, M., Hoal, E. G. & Daly, M. J. The critical needs and challenges for genetic architecture studies in Africa. Curr. Opin. Genet. Dev. 53, 113–120 (2018). source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThe H3Africa Initiative has increased genomics research capacity in Africa through more than $216 million in funding from the NIH (USA) and Wellcome Trust (UK) for genetics research led by African investigators.
“The most notable investment here comes from the Human Heredity and Health in Africa (H3Africa) Initiative, increasing genomics research capacity in Africa through more than $216 million in funding from the NIH (USA) and Wellcome Trust (UK) for genetics research led by African investigators55,74.”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [55] H3Africa Consortium. et al. Enabling the genomic revolution in Africa. Science 344, 1346–1348 (2014). source
In “Enabling the genomic revolution in Africa” (page unavailable), the paper says the NIH and Wellcome Trust fund H3Africa, which focuses on capacity building and awards research grants directly to African institutions with African principal investigators. It gives the funding amount as $76 million over five years, not more than $216 million. (LLM, conf=0.90)
Experimental — accuracy not yet measured - cites [74] Coles, E. & Mensah, G. A. Geography of genetics and genomics research funding in Africa. Glob. Heart 12, 173–176 (2017). source
The Introduction says substantial NIH and Wellcome Trust investment in H3Africa gave genetics and genomics research in sub-Saharan Africa momentum. But the Results and Summary and Conclusions identify approximately $216 million as 2015 funding for 185 genetics and genomics projects across Africa, not funding for H3Africa alone; the paper also does not establish that those projects were led by African investigators. (LLM, conf=0.89)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThe U.S. leads other middle- and high-income countries in both real and perceived healthcare disparities.
“This is a major concern globally and especially in the U.S., which already leads other middle-and high-income countries in both real and perceived healthcare disparities69,70.”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [69] Hero, J. O., Zaslavsky, A. M. & Blendon, R. J. The United States leads other nations in differences by income in perceptions of health and health care. Health Aff. (Millwood) 36, 1032–1040 (2017). source
- cites [70] Williams, D. R., Priest, N. & Anderson, N. B. Understanding associations among race, socioeconomic status, and health: Patterns and prospects. Health Psychol. 35, 407–411 (2016). source
The opening section describes poorer quality of care for racial and ethnic minorities in the U.S. and globally. It does not say the U.S. leads middle- and high-income countries in healthcare disparities or compare perceived disparities across countries. (LLM, conf=0.85)
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationGuidelines state that as few as 120 individuals define reference intervals for clinical factors (though often smaller numbers from only one subpopulation are used) and there is no clear definition of who is "normal".
“Currently, guidelines state that as few as 120 individuals define reference intervals for clinical factors (though often smaller numbers from only one subpopulation are used) and there is no clear definition of who is “normal”64.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [64] Manrai, A. K., Patel, C. J. & Ioannidis, J. P. A. In the era of precision medicine and big data, who is normal? JAMA 319, 1981–1982 (2018). source
In “Defining Normality,” the paper says CLSI guidelines call for 120 reference individuals, that laboratories may use fewer, and that health lacks a universal definition. The “Multiplicity” section mentions sampling from the same subpopulation only as a simulation example; it does not establish that smaller samples are often drawn from just one subpopulation. Page numbers are unavailable in our copy. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationH3ABioNet provides cost-effective examples for training local scientists in LMICs.
“Frameworks such as the H3ABioNet, a pan-African bioinformatics network designed to build capacity to enable H3Africa researchers to analyze their data in Africa, provide cost-effective examples for training local scientists in LMICs75.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [75] Mulder, N. J. et al. Development of bioinformatics infrastructure for genomics research. Glob. Heart 12, 91–98 (2017). source
The Approach and implementation section describes H3ABioNet as a pan-African network building local capacity, and Genomics skills training describes its courses and other training for African scientists. Our copy does not establish that the training is cost-effective or assess it as a model across LMICs; the cited evidence is specific to Africa. Page numbers were not available in the indexed passages. (LLM, conf=0.86)
Experimental — accuracy not yet measured
May combine two claims.
InterpretationcitationIndividual clinical tests, biomarkers, and prescription drug efficacy may vary across populations in their utility, but are fundamentally informed by the same underlying biology.
“Individual clinical tests, biomarkers, and prescription drug efficacy may vary across populations in their utility, but are fundamentally informed by the same underlying biology64,65.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [64] Manrai, A. K., Patel, C. J. & Ioannidis, J. P. A. In the era of precision medicine and big data, who is normal? JAMA 319, 1981–1982 (2018). source
The paper’s discussion of population variation in laboratory tests and its Potential Solutions section (page not provided) support the point that a clinical test’s utility can differ across populations. The copy does not establish population differences in prescription-drug efficacy or the claim that all three are informed by the same underlying biology. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [65] Plenge, R. M., Scolnick, E. M. & Altshuler, D. Validating therapeutic targets through human genetics. Nat. Rev. Drug Discov. 12, 581–594 (2013). source
May combine two claims.
Findingown dataPrediction accuracy was far lower in individuals of African descent in the UK Biobank using GWAS summary statistics from either European or Japanese ancestry individuals, consistent with reduced prediction accuracy with increasing genetic divergence.
“Prediction accuracy was far lower in individuals of African descent in the UK Bio bank (Supplementary Figures 4 and 11) using GWAS summary statistics from either European or Japanese ancestry individuals, consistent with reduced prediction accuracy with increasing genetic divergence (Figures 3 and 4).”
Quote in the paperSubstantial claim0 of 2 sources checked- cites Supplementary Figures 4 and 11
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites Figures 3 and 4
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
Findingown dataAverage sample sizes of GWAS in Europeans continue to grow, while they have stagnated and remain several-fold smaller in other populations.
“However, whereas the average sample sizes of GWAS in Europeans continue to grow, they have stagnated and remain several-fold smaller in other populations (Supplementary Figure 1).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Supplementary Figure 1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
Findingown dataTrans-ethnic correlation estimates indicate that effect sizes were mostly highly correlated across ancestries, with a few traits somewhat lower than expected (e.g. height and BMI, with ρge=0.69 and 0.75, respectively).
“These trans-ethnic correlation estimates indicate that effect sizes were mostly highly correlated across ancestries, with a few traits that were somewhat lower than excepted (e.g. height and BMI, with ρge=0.69 and 0.75, respectively).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataRelative to European prediction accuracy, genetic prediction accuracy using European-derived summary statistics was far lower in other populations in the UK Biobank: 1.6-fold lower in Hispanic/Latino Americans, 1.7-fold lower in South Asians, 2.5-fold lower in East Asians, and 4.9-fold lower in Africans on average.
“Consistent with previous studies, we find that relative to European prediction accuracy, genetic prediction accuracy was far lower in other populations: 1.6-fold lower in Hispanic/Latino Americans, 1.7-fold lower in South Asians, 2.5-fold lower in East Asians, and 4.9-fold lower in Africans on average (Figure 3).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Figure 3
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
Findingnone givenDiversifying progress in GWAS has stalled over the last five years, with current imbalance.
“An equal investment in GWAS across all major ancestries and global populations is the most obvious solution to generate a substrate for equally informative risk scores but is not likely to occur any time soon absent a dramatic priority shift given the current imbalance and stalled diversifying progress over the last five years (Figure 1, Supplementary Figure 1).”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based). May combine two claims.
Interpretationnone givenMost PRS methods do not explicitly address recent admixture and none consider recently admixed individuals' unique local mosaic of ancestry; further methods development is needed.
“Related to stratification, most PRS methods do not explicitly address recent admixture and none consider recently admixed individuals’ unique local mosaic of ancestry; further methods development is needed.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationcitationThe issues of Eurocentric GWAS biases and imputation panel biases are insurmountable through statistical methods alone, but motivate substantial investments in more diverse populations to produce similar-sized GWAS of biomedical phenotypes in other populations.
“These issues are insurmountable through statistical methods alone13, but rather motivate substantial investments in more diverse populations to produce similar-sized GWAS of biomedical phenotypes in other populations.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [13] Martin, A. R. et al. Human demographic history impacts genetic risk prediction across diverse populations. Am. J. Hum. Genet. 100, 635–649 (2017). source
May combine two claims.
InterpretationreasoningSome unrecognized nonlinearities and gene-gene interactions can induce genetic risk prediction challenges, as pairwise interactions are likely to vary more across populations than individual SNPs.
“some unrecognized nonlinearities and gene-gene interactions can also induce genetic risk prediction challenges, as pairwise interactions are likely to vary more across populations than individual SNPs.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based).
Interpretationnone givenEarly diversifying efforts show promise in levelling the imbalance in PRS accuracy, even when non-European sample sizes are considerably smaller than the largest studies to date.
“Early diversifying efforts show promise in levelling this vast imbalance, even when non-European sample sizes are considerably smaller than the largest studies to date.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningThe phenomena of GWAS favoring common variants and LD differentiating effect size estimates degrade prediction performance across populations substantially even when there exist no biological, environmental, or diagnostic differences.
“Notably, the first two phenomena degrade prediction performance across populations substantially even when there exist no biological, environmental, or diagnostic differences,”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationcitationEurocentric GWAS biases mean that variants associated with risk are disproportionately common and discovered in European populations, accounting for a larger fraction of the phenotypic variance there.
“Eurocentric GWAS biases mean that variants associated with risk are disproportionately common and discovered in European populations, accounting for a larger fraction of the phenotypic variance there13.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [13] Martin, A. R. et al. Human demographic history impacts genetic risk prediction across diverse populations. Am. J. Hum. Genet. 100, 635–649 (2017). source
- The authors state this as an assumption: Causal genetic variants have an equal effect across all populations.
Probably not a substantial claim: may not pass S4 (based).
Premisenone givenEnvironment and demography differ across populations.
“3) environment and demography differ across populations.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningComplex traits do not behave in a genetically deterministic manner, with some environmental factors dwarfing individual genetic effects, creating outsized issues of comparability across globally diverse populations.
“Complex traits do not behave in a genetically deterministic manner, with some environmental factors dwarfing individual genetic effects, creating outsized issues of comparability across globally diverse populations.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningClinical uses of PRS today would systematically afford greater improvement to European descent populations than clinical biomarkers and prescription drugs, which may individually work better in some populations but do not ubiquitously perform far better in European populations.
“This highlights that—unlike clinical biomarkers and prescription drugs, which may individually work better in some populations but do not ubiquitously perform far better in European populations—clinical uses of PRS today would systematically afford greater improvement to European descent populations.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
InterpretationreasoningEnvironment and demography may interact to drive differential forces of natural selection that in turn drive differences in causal genetic architecture.
“whereas the environment and demography may interact to drive differential forces of natural selection that in turn drive differences in causal genetic architecture.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningMany cardiovascular PRS studies have been conducted exclusively in European descent populations, with few studies rigorously evaluating population-level applicability to non-Europeans.
“However, many of these studies have been conducted exclusively in European descent populations, with few studies rigorously evaluating population-level applicability to non-Europeans.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningDifferences in effect size estimates due to LD differences may typically be small for most regions of the genome, but PRS sum across these effects, also aggregating these population differences.
“Differences in effect size estimates due to LD differences may typically be small for most regions of the genome (Figure 2C–E), but PRS sum across these effects, also aggregating these population differences.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Figure 2C–E
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
InterpretationreasoningResidual uncorrected population stratification may impact risk prediction accuracy across populations, but the magnitude of its effect is currently unclear.
“Additionally, residual uncorrected population stratification may impact risk prediction accuracy across populations, but the magnitude of its effect is currently unclear.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based).
Interpretationnone givenThe disparity in PRS accuracy between European ancestry individuals and others is an inescapable consequence of Eurocentric genome-wide association study biases.
“This disparity is an inescapable consequence of Eurocentric genome-wide association study biases.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable), S4 (based). May combine two claims.
Interpretationnone givenMethodological improvements that better define risk scores by accounting for population allele frequency, LD, and/or admixture differences are underway and may help considerably but will not by themselves bring equality.
“Methodological improvements that better define risk scores by accounting for population allele frequency, LD, and/or admixture differences appropriately are underway and may help considerably but will not by themselves bring equality.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based). May combine two claims.
Interpretationnone givenVastly increasing the diversity of participants included and analyzed in genetic studies will improve PRS utility for all and most rapidly for underrepresented groups.
“The single most important step towards parity in PRS accuracy is by vastly increasing the diversity of participants included and analyzed in genetic studies, which will improve utility for all and most rapidly for underrepresented groups.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based).
InterpretationreasoningFiner scale continental ancestries and phenotypes in large, multi-ethnic projects enable ancestry-matched analyses not possible with a single set of summary statistics.
“Existing GWAS consortia also need to carefully consider the granularity of summary statistics they release, as finer scale continental ancestries and phenotypes in large, multi-ethnic projects enable ancestry-matched analyses not possible with a single set of summary statistics.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningNo analogous solution of defining ethnicity-specific reference intervals would ameliorate health disparities implications for PRS or fundamentally aid interpretability in non-European populations.
“No analogous solution of defining ethnicity-specific reference intervals would ameliorate health disparities implications for PRS or fundamentally aid interpretability in non-European populations.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).
Interpretationnone givenUnifying phenotype definitions, normalization approaches, and GWAS methods among studies will improve comparability.
“Efforts to unify phenotype definitions, normalization approaches, and GWAS methods among studies will also improve comparability.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based). May combine two claims.
Interpretationnone givenPRS have potential to improve health outcomes for all individuals and many complex diseases.
“Given the acute recent attention on clinical use of PRS, we believe it is paramount to recognize their potential to improve health outcomes for all individuals and many complex diseases.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationcitationSome biomarkers or clinical tests scale directly with health outcomes independent of ancestry, and many others may have distributional differences by ancestry but are equally valid after centering with respect to a readily collected population reference.
“Simply put, some biomarkers or clinical tests scale directly with health outcomes independent of ancestry, and many others may have distributional differences by ancestry but are equally valid after centering with respect to a readily collected population reference.”
Quote in the paperNot a substantial claim
The authors state this as an assumption.
Causal genetic variants have an equal effect across all populations.
“If we assume that causal genetic variants have an equal effect across all populations—an assumption with some empirical support that offers the best case scenario for transferability35–40—”
The authors state this as an assumption.
All causal loci have the same impact and are under equivalent selective pressure in all populations.
“these issues actually make many favorable assumptions that all causal loci have the same impact and are under equivalent selective pressure in all populations.”
The paper relies on this without support.
The prerequisite data for dramatically increasing diversity exist in large-scale publicly funded datasets such as the Million Veterans Project and TOPMed, but data access issues prevent even GWAS summary data within and across populations from being publicly shared.
“The prerequisite data for dramatically increasing diversity also hypothetically exist in several large-scale publicly funded datasets such as the Million Veterans Project and Trans-Omics for Precision Medicine (TOP Med), but with problematic data access issues in which even GWAS summary data within and across populations are not publicly shared.”
The paper relies on this without support.
African descent populations already endure many of the largest health disparities globally.
“Conversely, African descent populations, which already endure many of the largest health disparities globally, are often predicted marginally better, if at all, compared to random (Figure 4F).”
The paper relies on this without support.
Human population history and study biases cause African descent populations to be predicted marginally better, if at all, compared to random by PRS.
“They are therefore least likely to benefit from improvements in precision healthcare delivery from genetic risk scores with existing data due to human population history and study biases.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
PGIs constructed from GWAS in European genetic ancestries generally have much lower predictive power in samples with other genetic ancestries; on average across phenotypes, relative accuracy in African-ancestry to European-ancestry samples has been 22% and 36%.
“PGIs like ours that are constructed from GWAS in samples of European genetic ancestries are generally found to have much lower predictive power in samples with other genetic ancestries; for example, on average across phenotypes, estimates of relative accuracy (ratio of R2) in African-genetic-ancestry to European-genetic-ancestry samples have been 22%23 and 36%24.”
From Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals (2022) · cites this paper as [23]
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredPrevious studies have shown that while polygenic risk scores and eQTLs have limited cross-population portability, biochemically active functional regulatory elements tend to be under evolutionary constraint within the human lineage.
“Previous studies have shown that, while polygenic risk scores [65] and eQTLs [66] have limited cross-population portability, biochemically active functional regulatory elements tend to be under evolutionary constraint within the human lineage [67, 68].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [65]
For most diseases, large-scale GWAS aggregation efforts have been disproportionately powered by information from individuals of European descent.
“For most diseases, large-scale GWAS-aggregation efforts have been disproportionately powered by information from individuals of European descent55.”
From A brief history of human disease genetics (2020) · cites this paper as [55]
The historical concentration of genetic discovery on populations of European descent has adverse consequences for both discovery and translation.
“An elegant distillation of the ways in which the historical focus of genetic discovery among populations of European descent has adverse consequences for both discovery and translation.”
From A brief history of human disease genetics (2020) · cites this paper as [55]
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“Although many traits show a high degree of shared genetic correlation across ancestries 32,36,37 , others have distinct genetic variants with large effects that are more common in specific ancestry groups 34 , which may limit the utility of multi-ancestry PRS for particular phenotypes in some…”
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Self-citation
- Authors
- Martin, A. R., Kanai, M., Kamatani, Y., Okada, Y., Neale, B. M., & Daly, M. J.
- Affiliations
- Broad Institute (US)
- Kyoto University (JP)
- RIKEN Center for Integrative Medical Sciences (JP)
- Corresponding author
- Martin, Alicia R.
- ORCID
- Venue
- Nature Genetics
- Published
- 2019-03-29
- Volume
- 51
- Issue
- 4
- Pages
- 584-591
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC6563838
- OpenAlex
- W2932671560
- Cited by
- 2,831
- References
- 77
- Citations by year
- 2026: 417 · 2025: 419 · 2024: 400 · 2023: 454 · 2022: 412 · 2021: 396 · 2020: 230 · 2019: 96 · 2018: 3 · 2017: 1
- FWCI
- 154.40
- Type
- journal article
- Language
- en
- Update notices
- correction (2021-01-28)
- Open access
- green
- doi.org
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (submittedVersion)
- PubMed Central (submittedVersion)
- Funders
- Japan Agency for Medical Research and Development
- Masason Foundation
- National Institutes of Health (31063, K99MH117229)
- National Institute of Mental Health (K99 MH117229)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30 DK043351)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- polygenic risk score, health disparities, ancestry bias, genome-wide association study, precision medicine, underrepresented groups
- MeSH terms
- Genotype, Humans, Risk Factors, Genetic Predisposition to Disease, Multifactorial Inheritance, White People, Healthcare Disparities, Genome-Wide Association Study, Precision Medicine
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