Thrombotic Risk Determined by STAB 2 Variants in a Population-Based Cohort Study

HomeCirculation: Genomic and Precision MedicineVol. 14, No. 5Thrombotic Risk Determined by STAB 2 Variants in a Population-Based Cohort Study Free AccessLetterPDF/EPUBAboutView PDFView EPUBSections ToolsAdd to favoritesDownload citationsTrack citationsPermissions ShareShare onFacebookTwitterLinked InMendeleyRedditDiggEmail Jump toFree AccessLetterPDF/EPUBThrombotic Risk Determined by STAB 2 Variants in a Population-Based Cohort Study Eric Manderstedt, MSc, Christer Halldén, PhD, Christina Lind-Halldén, PhD, Johan Elf, MD, PhD, Peter J. Svensson, MD, PhD, Gunnar Engström, MD, PhD, Olle Melander, MD, PhD, Aris Baras, MD, Luca A Lotta, MD and Bengt Zöller, MD, PhD Eric ManderstedtEric Manderstedt Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad (E.M., C.H., C.L.-H.). Search for more papers by this author , Christer HalldénChrister Halldén https://orcid.org/0000-0002-9355-3901 Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad (E.M., C.H., C.L.-H.). Search for more papers by this author , Christina Lind-HalldénChristina Lind-Halldén Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad (E.M., C.H., C.L.-H.). Search for more papers by this author , Johan ElfJohan Elf Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden (J.E., P.J.S., G.E., O.M.). Search for more papers by this author , Peter J. SvenssonPeter J. Svensson https://orcid.org/0000-0003-2901-6877 Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden (J.E., P.J.S., G.E., O.M.). Search for more papers by this author , Gunnar EngströmGunnar Engström https://orcid.org/0000-0002-8618-9152 Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden (J.E., P.J.S., G.E., O.M.). Search for more papers by this author , Olle MelanderOlle Melander Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden (J.E., P.J.S., G.E., O.M.). Search for more papers by this author , Aris BarasAris Baras Regeneron Genetics Center, Tarrytown, NY (A.B., L.A.L.). Search for more papers by this author , Luca A LottaLuca A Lotta Regeneron Genetics Center, Tarrytown, NY (A.B., L.A.L.). Search for more papers by this author and Bengt ZöllerBengt Zöller Correspondence to: Bengt Zöller, MD, PhD, Center for Primary Health Care Research, Skane University Hospital, CRC, Bldg 28, floor 11, Entrance 72, S-205 02 Malmö, Sweden. Email E-mail Address: [email protected] https://orcid.org/0000-0002-8250-5613 Center for Primary Health Care Research, Lund University & Region Skåne, Malmö, Sweden (B.Z.). Search for more papers by this author and for the Regeneron Genetics Center* Originally published31 Aug 2021https://doi.org/10.1161/CIRCGEN.121.003449Circulation: Genomic and Precision Medicine. 2021;14:e003449Recently Desch et al1 reported that rare variants in stabilin-2 (STAB 2) are associated with increased risk for venous thromboembolism (VTE).1 They performed a whole-exome study of 393 selected individuals with unprovoked VTE and 6114 controls. In total, 7.8% of VTE cases and 2.4% of controls had a qualifying rare variant in STAB 2. Qualifying variants (minor allele frequency<0.05%) were defined either by being loss-of-function or missense nonbenign variants according to PolyPhen-2 (Polymorphism Phenotyping v2).1 Desch et al1 also performed cell culture studies showing that certain qualifying STAB 2 variants resulted in reduced STAB 2 expression.1 Their results were obtained by analysis of selected VTE patients that were likely to be enriched for genetic factors. No study has yet confirmed the findings of Desch et al1 nor evaluated the contribution of STAB 2 variants to VTE in the general population. In the present study, we determined the importance of STAB 2 variants for thrombotic risk by analysis of the MDC study (Malmö Diet and Cancer), consisting of unselected middle-aged and older individuals.2MDC is a population-based cohort study from the city of Malmö in the south of Sweden, previously described.2 Clinical data and DNA were available for 29 387 subjects sampled at baseline (1991–1996) and followed for incident VTE until December 31, 2018. The Regional Ethics Review Board at Lund University, Sweden, approved the study (LU 51/90) and all participants provided informed written consent. VTE events were identified through linkage with the Swedish National Patient Registry. The diagnosis of VTE in the National Patient Registry has been shown to have an accuracy of 95%,3 whereas the overall validity of the National Patient Registry is 87%.4 Whole-exome study was performed by Regeneron Genetics Center (Tarrytown, NY) such that >85% of targeted bases were covered at a read depth of >20X. ANNOVAR was used to aggregate variant annotation, allele frequencies, and in silico predictions of deleteriousness. Logistic regression was conducted to calculate odds ratios for different combinations of prevalent or incident VTE. Cox regression was used to examine the association between genotype and incident VTE. Age and sex were included as covariates in the sex- and age-adjusted model, whereas body mass index, smoking status, blood pressure (systolic), and high alcohol consumption (>30 g/day women, >40 g/day men) were added in the multivariate model. R (version 4.0.0) was used for all statistical analyses.Due to ethical and legal restrictions related to the Swedish Biobanks in Medical Care Act (2002:297) and the Personal Data Act (1998:204), data are available upon request from the data access group of MDC Study by contacting Anders Dahlin (anders.[email protected]lu.se).Of the 29 387 individuals available for analysis a total of 26210 individuals (15818 [60.4%] females) were not affected by VTE (age at baseline [mean±SD] 57.8±7.6). A total of 3177 (10.8%) individuals (1869 [58.8%] females) with mean (±SD) age at baseline of 59.7 years (±7.4) were affected with prevalent or incident VTE.A total of 351 different nonsynonymous or loss-of-function variants were identified in STAB 2 in the study population. Using collapsing analysis and variant criteria according to Desch et al,1 162 of these were classified as qualifying (135 missense and 27 loss-of-function variants). The total prevalence of qualifying variants was 2.7%. The number of alleles of qualifying variants and the odds ratios for different combinations of prevalent/incident VTE is shown in Table. Incident VTE was significant (odds ratio, 1.3 [95% CI, 1.06–1.65], P=0.01) as was any VTE (prevalent or incident) with an odds ratio 1.31 (95% CI, 1.06–1.59, P=0.01). The hazard ratio for incident VTE in the fully adjusted model was 1.33 (95% CI, 1.07–1.64, P=0.01) for carrying only one STAB 2 variant (not shown). The corresponding hazard ratio for those carrying two qualifying alleles was 1.74 (95% CI, 0.43–6.95, P=0.44). Using only variants present in single individuals (singletons), the fully adjusted hazard ratio was 1.88 (95% CI, 1.13–3.13, P=0.01). When instead the 70 STAB 2 variants with allele frequencies >0.05% were evaluated for differences between VTE cases and controls, only 2 showed skewed allele frequencies but in different directions (rs144900279 and rs17034433).Table. ORs for VTE for Either All Qualifying* or Loss-of-Function STAB 2 VariantsAll qualifying* variantsLoss-of-function variantsNumber of allelesOR (95% CI)P valueNumber of allelesOR (95% CI)P valueNo VTE ever (n=26 210)681Reference…57Reference…Any VTE, prevalent or incident (n=3177)1081.31 (1.06–1.59)0.0160.87 (0.33–1.86)0.74Only incident VTE (n=2584)901.33 (1.06–1.65)0.0150.89 (0.31–2.02)0.81Only prevalent VTE (n=397)90.84 (0.40–1.52)0.610NANAIncident and prevalent VTE (n=196)91.71 (0.82–3.08)0.1112.41 (0.14–11)0.38Number of alleles for individuals with no VTE and combinations of incident or prevalent VTE. NA indicates not applicable; OR, odds ratio; and VTE, venous thromboembolism.* A variant with minor allele frequency <0.05% and either is a loss-of-function variant or is a nonbenign missense variant according to Polymorphism Phenotyping v2This study is the first to determine the VTE risk of STAB 2 variants in an unselected population. By using identical definition and collapsing analysis as Desch et al,1 we verified their results. However, the effect size in the present study was lower. This was not explained by the prevalence of qualifying variants in the different control groups because the frequencies were similar, 2.6% in the present study compared to 2.4% in the study of Desch et al.1 Instead, STAB 2 variants were more enriched among the selected patients in the Desch et al’s1 study (7.8%) compared with the present population-based study consisting of middle-aged and older individuals (3.4%). For comparison, in the MDC cohort heterozygosity for rs6025 was associated with a hazard ratio of 1.8.5 It is a common feature of complex disorders that heritability is lower at higher ages.In conclusion, this study showed that STAB 2 variants are associated with VTE also at older ages in a large population-based study. This verifies the Desch et al’s1 study and indicates that rare variants in STAB 2 are associated with increased VTE risk. However, the discrimination between neutral and VTE-causing STAB 2 variants is challenging.AcknowledgmentsB. Zöller was supported by the Swedish Research Council, Sparbanken Skåne, and The Medical Training and Research Agreement from Region Skåne. E. Manderstedt, Drs Halldén, and Zöller conceived and designed the study, analyzed and interpreted data, drafted the article, and gave final approval of the submitted article. All authors interpreted data, critically revised the article for important intellectual content, and gave final approval of the submitted article. Whole-exome sequencing was performed by the Regeneron Genetics Center (see the Regeneron Genetics Center Banner Author List and Contribution Statements below). E. Manderstedt, Drs Halldén, and Zöller are the guarantors of this work and, as such, had full access to all the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis.Sources of FundingThe sponsors had no role in study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the article for publication.AppendixAll authors/contributors are listed in alphabetic order. RGC Management and Leadership Team: Goncalo Abecasis, Aris Baras, Michael Cantor, Giovanni Coppola, Aris Economides, Luca A. Lotta, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Katia Karalis, and Katherine Siminovitch. Contribution: All authors contributed to securing funding, study design, and oversight. All authors reviewed the final version of the article. Sequencing and Lab Operations: Christina Beechert, Caitlin Forsythe, M.S., Erin D. Fuller, Zhenhua Gu, M.S., Michael Lattari, Alexander Lopez, M.S., John D. Overton, Thomas D. Schleicher, M.S., Maria Sotiropoulos Padilla, M.S., Louis Widom, Sarah E. Wolf, M.S., Manasi Pradhan, M.S., Kia Manoochehri, Ricardo H. Ulloa. Contribution: C.B., C.F., A.L., and J.D.O. performed and are responsible for sample genotyping. C.B, C.F., E.D.F., M.L., M.S.P., L.W., S.E.W., A.L., and J.D.O. performed and are responsible for exome sequencing. T.D.S., Z.G., A.L., and J.D.O. conceived and are responsible for laboratory automation. M.S.P., K.M., R.U., and J.D.O are responsible for sample tracking and the library information management system. Genome Informatics: Xiaodong Bai, Suganthi Balasubramanian, Andrew Blumenfeld, Boris Boutkov, Gisu Eom, Lukas Habegger, Alicia Hawes, B.S., Shareef Khalid, Olga Krasheninina, M.S., Rouel Lanche, Adam J. Mansfield, B.A., Evan K. Maxwell, Mrunali Nafde, Sean O’Keeffe, M.S., Max Orelus, Razvan Panea, Tommy Polanco, B.A., Ayesha Rasool, M.S., Jeffrey G. Reid, William Salerno, Jeffrey C. Staples. Contribution: X.B., A.H., O.K., A.M., S.O., R.P., T.P., A.R., W.S., and J.G.R. performed and are responsible for the compute logistics, analysis, and infrastructure needed to produce exome and genotype data. G.E., M.O., M.N., and J.G.R. provided compute infrastructure development and operational support. S.B., S.K., and J.G.R. provide variant and gene annotations and their functional interpretation of variants. E.M., J.S., R.L., B.B., A.B., L.H., J.G.R. conceived and are responsible for creating, developing, and deploying analysis platforms and computational methods for analyzing genomic data. Translational Genetics: Niek Verweij, Jonas Nielsen, Tanima De. Contribution: All authors contributed to the analytical analysis of the project. Research Program Management: Marcus B. Jones, Jason Mighty, Michelle G. LeBlanc, and Lyndon J. Mitnaul. Contribution: All authors contributed to the management and coordination of all research activities, planning, and execution. All authors contributed to the review process for the final version of the article.Disclosures None.Footnotes*A list of the Regeneron Genetics Center members is provided in the Appendix.For Sources of Funding and Disclosures, see page 660.Correspondence to: Bengt Zöller, MD, PhD, Center for Primary Health Care Research, Skane University Hospital, CRC, Bldg 28, floor 11, Entrance 72, S-205 02 Malmö, Sweden. Email bengt.[email protected]lu.seReferences1. Desch KC, Ozel AB, Halvorsen M, et al.. Whole-exome sequencing identifies rare variants in STAB 2 associated with venous thromboembolic disease.Blood. 2020; 136:533541. doi: 10.1182/blood.2019004161CrossrefMedlineGoogle Scholar2. Melander O, Newton-Cheh C, Almgren P, Hedblad B, Berglund G, Engström G, Persson M, Smith JG, Magnusson M, Christensson A, et al.. Novel and conventional biomarkers for prediction of incident cardiovascular events in the community.JAMA. 2009; 302:4957. doi: 10.1001/jama.2009.943CrossrefMedlineGoogle Scholar3. Rosengren A, Fredén M, Hansson PO, Wilhelmsen L, Wedel H, Eriksson H. Psychosocial factors and venous thromboembolism: a long-term follow-up study of Swedish men.J Thromb Haemost. 2008; 6:558–564. doi: 10.1111/j.1538-7836.2007.02857.xCrossrefMedlineGoogle Scholar4. Ludvigsson JF, Andersson E, Ekbom A, Feychting M, Kim JL, Reuterwall C, Heurgren M, Olausson PO. External review and validation of the Swedish national inpatient register.BMC Public Health. 2011; 11:450. doi: 10.1186/1471-2458-11-450CrossrefMedlineGoogle Scholar5. Zöller B, Melander O, Svensson PJ, Engström G. Factor V Leiden paradox in a middle-aged Swedish population: a prospective study.Vasc Med. 2018; 23:52–59. doi: 10.1177/1358863X17745591CrossrefMedlineGoogle Scholar Previous Back to top Next FiguresReferencesRelatedDetailsCited ByZöller B, Pirouzifard M, Svensson P, Holmquist B, Stenman E, Elston R, Song Y, Sundquist J and Sundquist K (2021) Familial Segregation of Venous Thromboembolism in Sweden: A Nationwide Family Study of Heritability and Complex Segregation Analysis, Journal of the American Heart Association, 10:24, Online publication date: 21-Dec-2021. October 2021Vol 14, Issue 5Article InformationMetrics Download: 74 © 2021 American Heart Association, Inc.https://doi.org/10.1161/CIRCGEN.121.003449PMID: 34461736 Originally publishedAugust 31, 2021 Keywordsthrombosispopulationriskvenous thromboembolismgeneticsPDF download SubjectsEmbolismGenetic, Association StudiesGeneticsThrombosisVascular Disease