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Genome-wide association study of peripheral artery disease in the Million Veteran Program

Abstract

Peripheral artery disease (PAD) is a leading cause of cardiovascular morbidity and mortality; however, the extent to which genetic factors increase risk for PAD is largely unknown. Using electronic health record data, we performed a genome-wide association study in the Million Veteran Program testing ~32 million DNA sequence variants with PAD (31,307 cases and 211,753 controls) across veterans of European, African and Hispanic ancestry. The results were replicated in an independent sample of 5,117 PAD cases and 389,291 controls from the UK Biobank. We identified 19 PAD loci, 18 of which have not been previously reported. Eleven of the 19 loci were associated with disease in three vascular beds (coronary, cerebral, peripheral), including LDLR, LPL and LPA, suggesting that therapeutic modulation of low-density lipoprotein cholesterol, the lipoprotein lipase pathway or circulating lipoprotein(a) may be efficacious for multiple atherosclerotic disease phenotypes. Conversely, four of the variants appeared to be specific for PAD, including F5 p.R506Q, highlighting the pathogenic role of thrombosis in the peripheral vascular bed and providing genetic support for Factor Xa inhibition as a therapeutic strategy for PAD. Our results highlight mechanistic similarities and differences among coronary, cerebral and peripheral atherosclerosis and provide therapeutic insights.

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Data availability

The full summary level association data from the MVP transancestry PAD meta-analysis from this report are available through dbGAP, accession code phs001672.v2.p1. Additional data that support the findings of this study are available on request from the corresponding author (S.M.D.); these data are not publicly available due to US Government and Department of Veteran’s Affairs restrictions relating to participant privacy and consent. Data contributed by CARDIoGRAMplusC4D investigators are available online (http://www.CARDIOGRAMPLUSC4D.org/). Data on LAD have been contributed by the MEGASTROKE investigators and are available online (http://www.megastroke.org/). The genetic and phenotypic UK Biobank data are available upon application to the UK Biobank. Source data has been provided for Figs. 2 and 3 and Extended Data Figs. 4, 5 and 7. Additional data that were used to generate the figures in this study are available on request from the corresponding author (S.M.D.) or through dbGAP as listed above.

Code availability

Code to perform analyses in this manuscript are available from the authors upon request (D.K. and S.M.D.), or from the URLs associated with each software in the Methods section.

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Acknowledgements

This research is based on data from the MVP, Office of Research and Development, Veterans Health Administration and was supported by award no. MVP000. This publication does not represent the views of the Department of Veterans Affairs, the US Food and Drug Administration, or the US Government. This research was also supported by funding from: the Department of Veterans Affairs awards nos. I01-BX03340 (K.C. and P.W.F.W.), I01-BX003362 (P.S.T. and K.M.C) and IK2-CX001780 (S.M.D.) and the VA Informatics and Computing Infrastructure (VINCI) VA HSR RES 130457 (P.A., O.V.P. and S.L.D.); the National Institutes of Health grants nos. R01-HL131977 (J.A.B.), R03-AG050930 (S.A.), R01-HL138306 (J.Chen), R01-HL127564 (S.K.) and K08-HL140203 (P.N.); and the American Heart Association grant no. 18SFRN33960373 (J.A.B. and M.S.F.), 17IFUNP33840012 (K.A.) and 15MCPRP25580005 (S.A.). Data on CAD have been contributed by the CARDIoGRAMplusC4D investigators. Data on large artery stroke have been contributed by the MEGASTROKE investigators. The MEGASTROKE project received funding from sources specified at http://www.megastroke.org/acknowledgements.html.

Author information

D.K., J.L., T.L.A., K.A., M.C., M.S.F., J.A.B., J.M.G., J. Concato, D.J.R., K.C., K.-M.C., P.W.F.W., C.J.O., S.K., P.S.T. and S.M.D were responsible for the concept and design. The acquisition, analysis or interpretation of data were performed by D.K., J.L., K.A., M.C., T.L.A., J.H., K.M.L., Q.S., J.E.H., P.N., S.A., A.S., Y.V.S., M.V., M.S.F., L.W., J. Chen, D.S., J.S.L., D.R.M., P.R., P.R.A., O.V.P., S.L.D., W.E.B., J.A.B., J. Concato, J.M.G., D.J.R., K.C., K.-M.C., P.W.F.W., C.J.O., S.K., P.S.T. and S.M.D. The authors D.K., P.S.T. and S.M.D. drafted the manuscript. The critical revision of the manuscript for important intellectual content was carried out by D.K., T.L.A., Y.V.S., K.C., P.N., D.J.R., K.C., K.-M.C., C.J.O., J.A.B., M.S.F., O.V.P., P.W.W., S.K., P.S.T. and S.M.D. The authors D.K., P.N., Y.V.S., M.S.F., J. Chen, J.A.B., J. Concato, J.M.G., D.J.R., K.C., K.-M.C., C.J.O., P.W.F.W., S.K., P.S.T. and S.M.D. provided administrative, technical, or material support.

Correspondence to Scott M. Damrauer.

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Competing interests

J.A.B. reports consulting with AstraZeneca, Bristol Myers Squibb, Amgen, Merck, Sanofi, Antidote Pharmaceutical and Boehringer Ingelheim. He serves on the DSMC for Bayer and Novartis. S.L.D. has received research grant support from the following for-profit companies through the University of Utah or the Western Institute for Biomedical Research (VA Salt Lake City’s affiliated non-profit): AbbVie Inc., Anolinx LLC, Astellas Pharma Inc., AstraZeneca Pharmaceuticals LP, Boehringer Ingelheim International GmbH, Celgene Corporation, Eli Lilly and Company, Genentech Inc., Genomic Health, Inc., Gilead Sciences Inc., GlaxoSmithKline PLC, Innocrin Pharmaceuticals Inc., Janssen Pharmaceuticals, Inc., Kantar Health, Myriad Genetic Laboratories, Inc., Novartis International AG and PAREXEL International Corporation. S.M.D. receives research support to his institution from CytoVAS and RenalytixAI. S.K. is a founder of Maze Therapeutics, Verve Therapeutics and San Therapeutics. He holds equity in Catabasis and San Therapeutics. He is a member of the scientific advisory boards for Regeneron Genetics Center and Corvidia Therapeutics; served as a consultant for Acceleron, Eli Lilly, Novartis, Merck, NovoNordisk, Novo Ventures, Ionis, Alnylam, Aegerion, Huag Partners, Noble Insights, Leerink Partners, Bayer Healthcare, Illumina, Color Genomics, MedGenome, Quest and Medscape; and reports patents related to a method of identifying and treating a person having a predisposition to or afflicted with cardiometabolic disease (20180010185) and a genetics risk predictor (20190017119). O.V.P. has received research grants from the following for-profit organizations through the University of Utah or Western Institute for Biomedical Research: Anolinx LLC, AstraZeneca Pharmaceuticals LP, Genentech Inc., Genomic Health, Inc., Gilead Sciences Inc., Janssen Pharmaceuticals, Inc., Novartis International AG and PAREXEL International Corporation.

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Peer review information: Michael Basson was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 Distribution of minimum ankle–brachial index values in the MVP.

Histogram of minimum mABI values extracted from the electronic health record for 17,861 participants of the MVP. These values, restricted to those with an minimum ABI of <1.4, were used for the subsequent mABI GWAS.

Extended Data Fig. 2 Quantile-quantile plot for the discovery trans-ethnic PAD GWAS in MVP.

The expected logistic regression association P values versus the observed distribution of P values for PAD association (N = 31,307 PAD cases and 211,753 controls) are displayed. Quantile–quantile plots were inspected for ancestry-specific analyses and genomic control values were <1.20 for each racial group (data not shown). No systemic inflation was observed (λGC = 1.05). All P values were two-sided.

Extended Data Fig. 3 Manhattan plot for the PAD GWAS.

Plot of –log10(P) for association of imputed variants by chromosomal position for all autosomal polymorphisms analyzed in the PAD GWAS (N = 36,424 PAD cases and 601,044 controls). The genes nearest to the top associated variants are displayed. Genes highlighted in red represent novel PAD loci (18). Genes for variants that are outside the transcript boundary of a protein-coding gene are shown with nearest candidate gene in parentheses (for example, (LDLR)). Logistic regression two-sided P values are displayed.

Extended Data Fig. 4 TCF7L2 mediates its effect on PAD via T2D.

a, Forest plot depicting the replication of the known TCF7L2/rs7903146-T2D association signal12 in MVP for both white and black participants. b, The same variant is also associated with PAD risk in whites and blacks in MVP. However, when controlling for T2D status in the regression model, c, the association signal is dramatically reduced, suggesting that TCF7L2 PAD risk is mediated through its effect on T2D. Logistic regression two-sided values of P are displayed. Gray boxes reflect the inverse-variance weight for each ancestry. Source Data

Extended Data Fig. 5 Forest plot for association of the CHRNA3 locus and peripheral artery disease risk stratified by smoking status.

When stratifying European MVP participants by smoking status (ever smokers versus never smokers), nearly all the association signal resides within the ever smoker group. Previous reports of variation at the CHRNA3 locus demonstrate that carriers of the PAD risk allele have a reduced likelihood of cigarette smoking cessation9. This suggests that the PAD-CHRNA3 association is driven by a greater burden of tobacco exposure in those who carry the nicotine dependence/PAD risk allele. Logistic regression two-sided values of P are displayed. Gray boxes reflect the inverse-variance weight for each subgroup. Source Data

Extended Data Fig. 6 Peripheral artery disease risk loci and known causal risk factors.

Peripheral artery disease risk loci identified in this GWAS analysis are depicted along with the plausible relationship to the underling causal risk factor. Loci names are based on the nearest genes; however, the causal gene(s) remains unclear for some associated loci and, as such, the resultant annotation may prove incorrect in some cases.

Extended Data Fig. 7 Peripheral artery disease risk variants and association with LAS and CAD.

For the 19 PAD risk variants identified in our study, logistic regression Z-scores of association (aligned to the PAD risk allele) were obtained from MVP (PAD, N = 31,307 PAD cases and 211,753 controls) and publicly available summary statistics for large artery stroke (MVP+MEGASTROKE consortium25, N = 7,393 LAS cases and 628,737 controls) and coronary artery disease (MVP+CARDIoGRAMplusC4D consortium24, N = 111,216 CAD cases and 248,081 controls). A positive Z-score (red) indicates a positive association between the PAD risk allele and the disease, while a negative Z-score (blue) indicates an inverse association. Boxes are outlined in cyan if the variant is uniquely associated with PAD (two-sided logistic regression PPAD < 5 × 10−8, PCAD and PLAS > 0.05). Source Data

Extended Data Fig. 8 Peripheral artery disease risk variants and mechanistic overlap with LAS and CAD.

Venn diagram of each of the 19 PAD risk loci in a based on their association with PAD (N = 31,307 PAD cases and 211,753 controls; two-sided PPAD < 5 × 10−8), CAD (N = 111,216 CAD cases and 248,081 controls; two-sided P < 0.05) and LAS (N = 7,393 LAS cases and 628,737 controls; two-sided P < 0.05) using logistic regression. Each locus is depicted along with the plausible relationship to the underling causal risk factor separately by color. Loci names are based on the nearest genes; however, the causal gene(s) remains unclear for some associated loci and as such, the resultant annotation may prove incorrect in some cases.

Extended Data Fig. 9 Overall study design.

The primary analysis consisted of a genome-wide association study to identify novel PAD risk variants. Secondary analyses involved a genome-wide association study of minimum ABI, a closer examination the 19 PAD risk variants through PheWAS, a candidate causal gene analysis using eQTL/pQTL/TWAS data, a PAD analysis accounting for CAD/LAS status and a focused Factor V Leiden analysis.

Extended Data Fig. 10 Natural language processing for index extraction.

Examples of semi-structured text that contains targeted indices for extraction using natural language processing (NLP). TBI, toe–brachial index; PT, posterior tibial artery; AT, anterior tibial artery.

Supplementary information

Supplementary Information

Supplementary Tables 1, 3, 13, 15; MVP and MEGASTROKE investigators

Reporting Summary

Supplementary Tables

Supplementary Tables 2, 4, 5–12, 14, 16–26

Source data

Source Data Fig. 2

Raw Z Scores used for HeatMap Creation

Source Data Fig. 3

Raw Association Statistics for Forest Plot Creation

Source Data Extended Data Fig. 4

Raw Association Statistics for Forest Plot Creation

Source Data Extended Data Fig. 5

Raw Association Statistics for Forest Plot Creation

Source Data Extended Data Fig. 7

Raw Z Scores used for HeatMap Creation

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Fig. 1: Discovery study design for the PAD genome-wide association analysis.
Fig. 2: Representative heatmap of phenome-wide association results and biologic pathways underlying genetic loci associated with PAD.
Fig. 3: Factor V Leiden mutation and vascular disease.
Extended Data Fig. 1: Distribution of minimum ankle–brachial index values in the MVP.
Extended Data Fig. 2: Quantile-quantile plot for the discovery trans-ethnic PAD GWAS in MVP.
Extended Data Fig. 3: Manhattan plot for the PAD GWAS.
Extended Data Fig. 4: TCF7L2 mediates its effect on PAD via T2D.
Extended Data Fig. 5: Forest plot for association of the CHRNA3 locus and peripheral artery disease risk stratified by smoking status.
Extended Data Fig. 6: Peripheral artery disease risk loci and known causal risk factors.
Extended Data Fig. 7: Peripheral artery disease risk variants and association with LAS and CAD.
Extended Data Fig. 8: Peripheral artery disease risk variants and mechanistic overlap with LAS and CAD.
Extended Data Fig. 9: Overall study design.
Extended Data Fig. 10: Natural language processing for index extraction.