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Kobayashi T, Sugiura K, Ojima T, Serizawa M, Hirai K, Morishita E. Thrombosis-related characteristics of pregnant women with antithrombin deficiency, protein C deficiency and protein S deficiency in Japan. Thromb J 2024; 22:18. [PMID: 38331787 PMCID: PMC10854103 DOI: 10.1186/s12959-024-00581-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND We previously conducted a primary survey of pregnant women with hereditary thrombophilia based on national surveillance in Japan, but did not examine their thrombosis-related characteristics. Antithrombin (AT) deficiency, protein C (PC) deficiency and protein S (PS) deficiency are the major types of hereditary thrombophilia in Japan. METHODS We examined their detailed information related to thrombosis, and evaluated peripartum outcomes in comparison with control data obtained from the Japan Society of Obstetrics and Gynecology. RESULTS Definite or probable AT deficiency, PC deficiency and PS deficiency were observed in 80, 50, and 317 pregnancies, respectively, from 2014 to 2018 in Japan, with prevalence rates among total deliveries of 0.011%, 0.007%, 0.044%. The number of pregnancies with AT, PC and PS deficiency might have been as many as 27, 17 and 108 every year if complete answers had been provided. In the peripartum period of current pregnancies, 27.5% of women with AT deficiency, 28.0% with PC deficiency and 13.2% with PS deficiency developed thrombosis (p < 0.001 vs. control). Pregnant women with AT and PC deficiency were more susceptible to thrombosis than those with PS deficiency (P < 0.01). Of the thromboses, 92.3% occurred during pregnancy, 62.8% at less than 15 gestational weeks. The earliest onset of thrombosis was 5 gestational weeks. Prophylactic anticoagulation significantly prevented the onset of both antepartum and postpartum thrombosis (p < 0.0001). The rate of recurrent pregnancy loss in women with low PC or PS activities was significantly higher than in controls (p < 0.0001); however, it is unknown whether recurrent pregnancy loss is related to hereditary PS deficiency. There seem to have been few serious maternal or fetal/neonatal complications due to placental insufficiency related to a hypercoagulable state other than growth restriction. CONCLUSIONS This survey revealed the thrombosis-related characteristics of pregnant women with hereditary thrombophilia in Japan. We suggest prophylactic anticoagulation to prevent maternal or fetal/neonatal complications.
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Affiliation(s)
- Takao Kobayashi
- Department of Obstetrics and Gynecology, Hamamatsu Medical Center, 328 Tomitsuka-Cho, Chuo-Ku, Hamamatsu, Shizuoka, 432-8580, Japan.
| | - Kazuko Sugiura
- Faculty of Nursing, Department of Women's Health, Nursing and Midwifery, Fukuoka Prefectural University, 4395 Ita, Tagawa, Fukuoka, 825-8585, Japan
| | - Toshiyuki Ojima
- Department of Community Health and Preventive Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Mariko Serizawa
- Department of Obstetrics and Gynecology, Hamamatsu Medical Center, 328 Tomitsuka-Cho, Chuo-Ku, Hamamatsu, Shizuoka, 432-8580, Japan
| | - Kyuya Hirai
- Department of Obstetrics, Gynecology and Family Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Eriko Morishita
- Department of Laboratory Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa, 920-0942, Japan.
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2
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Han J, Li‐Gao R, de Mutsert R, Rosendaal FR, van Hylckama Vlieg A. Association between venous thromboembolism-associated genetic variants, coagulation factor levels, and thrombin generation potential. EJHAEM 2024; 5:47-54. [PMID: 38406509 PMCID: PMC10887265 DOI: 10.1002/jha2.863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/27/2024]
Abstract
Recently three large meta-analyses of genome-wide association studies for venous thromboembolism (VTE) identified over 130 genetic variants. However, mechanisms by which newly identified and therefore underexplored VTE-associated genetic variants influence VTE remain unclear. To elucidate the mechanism, we investigated the association between 61 newly identified VTE-associated genetic variants and the levels of coagulation factor (F) VIII, FIX, FXI, and fibrinogen as well as thrombin generation parameters (lag time, peak, endogenous thrombin potential, time-to-peak, and velocity), which are well-known biological traits associated with VTE. This study was conducted on 5341 participants of the Netherlands Epidemiology of Obesity study. The associations between VTE-associated genetic variants and coagulation factor levels and thrombin generation parameters were examined using linear regression analyses, adjusted for age, sex, body mass index, oral contraceptive use, hormone replacement therapy, and menopausal status. Of 61 genetic variants, 33 were associated with one or more of the coagulation factor levels and thrombin generation parameters. Following multiple testing corrections, five genetic variants remained significant, of which MAP1A rs55707100 exhibited the most robust association with thrombin generation parameters and FXI levels (β = -5.33%, 95% confidence interval: -8.44, -2.22). Our findings shed light on the underlying mechanisms by which these genetic variants influence the risk of VTE.
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Affiliation(s)
- Jihee Han
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenthe Netherlands
| | - Ruifang Li‐Gao
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenthe Netherlands
| | - Renée de Mutsert
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenthe Netherlands
| | - Frits R. Rosendaal
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenthe Netherlands
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3
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Jee YH, Thibord F, Dominguez A, Sept C, Boulier K, Venkateswaran V, Ding Y, Cherlin T, Verma SS, Faro VL, Bartz TM, Boland A, Brody JA, Deleuze JF, Emmerich J, Germain M, Johnson AD, Kooperberg C, Morange PE, Pankratz N, Psaty BM, Reiner AP, Smadja DM, Sitlani CM, Suchon P, Tang W, Trégouët DA, Zöllner S, Pasaniuc B, Damrauer SM, Sanna S, Snieder H, Kabrhel C, Smith NL, Kraft P. Multi-ancestry polygenic risk scores for venous thromboembolism. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.09.24300914. [PMID: 38260294 PMCID: PMC10802635 DOI: 10.1101/2024.01.09.24300914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Venous thromboembolism (VTE) is a significant contributor to morbidity and mortality, with large disparities in incidence rates between Black and White Americans. Polygenic risk scores (PRSs) limited to variants discovered in genome-wide association studies in European-ancestry samples can identify European-ancestry individuals at high risk of VTE. However, there is limited evidence on whether high-dimensional PRS constructed using more sophisticated methods and more diverse training data can enhance the predictive ability and their utility across diverse populations. We developed PRSs for VTE using summary statistics from the International Network against Venous Thrombosis (INVENT) consortium GWAS meta-analyses of European- (71,771 cases and 1,059,740 controls) and African-ancestry samples (7,482 cases and 129,975 controls). We used LDpred2 and PRSCSx to construct ancestry-specific and multi-ancestry PRSs and evaluated their performance in an independent European- (6,261 cases and 88,238 controls) and African-ancestry sample (1,385 cases and 12,569 controls). Multi-ancestry PRSs with weights tuned in European- and African-ancestry samples, respectively, outperformed ancestry-specific PRSs in European- (PRSCSXEUR: AUC=0.61 (0.60, 0.61), PRSCSX_combinedEUR: AUC=0.61 (0.60, 0.62)) and African-ancestry test samples (PRSCSXAFR: AUC=0.58 (0.57, 0.6), PRSCSX_combined AFR: AUC=0.59 (0.57, 0.60)). The highest fifth percentile of the best-performing PRS was associated with 1.9-fold and 1.68-fold increased risk for VTE among European- and African-ancestry subjects, respectively, relative to those in the middle stratum. These findings suggest that the multi-ancestry PRS may be used to identify individuals at highest risk for VTE and provide guidance for the most effective treatment strategy across diverse populations.
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Affiliation(s)
- Yon Ho Jee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, MA, USA
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, MD, USA
- The Framingham Heart Study, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702 USA
| | - Alicia Dominguez
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Corriene Sept
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kristin Boulier
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Vidhya Venkateswaran
- Department of Oral Biology, University of California Los Angeles School of Dentistry, Los Angeles, CA, USA
| | - Yi Ding
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Tess Cherlin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shefali Setia Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Valeria Lo Faro
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Departments of Biostatistics and Medicine, University of Washington, 4333 Brooklyn Ave, Seattle, WA 98195
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
- Laboratory of Excellence in Medical Genomics, GENMED, Evry, France
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 4333 Brooklyn Ave, Seattle, WA 98195
| | - Jean-Francois Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
- Laboratory of Excellence in Medical Genomics, GENMED, Evry, France
- Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Joseph Emmerich
- Department of Vascular Medicine, Paris Saint-Joseph Hospital Group, University of Paris, Paris, France
- UMR1153, INSERM CRESS, Paris, France
| | - Marine Germain
- University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, Bordeaux, France
| | - Andrew D. Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, MD, USA
- The Framingham Heart Study, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702 USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinbson Cancer Center, Seattle WA 98109
| | - Pierre-Emmanuel Morange
- Aix-Marseille University, INSERM, INRAE, Centre de Recherche en CardioVasculaire et Nutrition, Laboratory of Haematology, CRB Assistance Publique – Hôpitaux de Marseille, HemoVasc, Marseille, France
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 4333 Brooklyn Ave, Seattle, WA 98195
- Department of Epidemiology, University of Washington, 4333 Brooklyn Ave, Seattle, WA 98195
- Department of Health Systems and Population Health, University of Washington, 4333 Brooklyn Ave, Seattle, WA 98195
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinbson Cancer Center, Seattle WA 98109
- Department of Epidemiology, University of Washington, 4333 Brooklyn Ave, Seattle, WA 98195
| | - David M. Smadja
- Innovative Therapies in Hemostasis, Université de Paris, INSERM, F-75006 Paris, France
- Hematology Department and Biosurgical Research Lab (Carpentier Foundation), Assistance Publique Hôpitaux de Paris, Centre-Université de Paris (APHP-CUP), F-75015 Paris, France
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 4333 Brooklyn Ave, Seattle, WA 98195
| | - Pierre Suchon
- Aix-Marseille University, INSERM, INRAE, Centre de Recherche en CardioVasculaire et Nutrition, Laboratory of Haematology, CRB Assistance Publique – Hôpitaux de Marseille, HemoVasc, Marseille, France
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, 55454, USA
| | - David-Alexandre Trégouët
- University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, Bordeaux, France
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Bogdan Pasaniuc
- Department of Oral Biology, University of California Los Angeles School of Dentistry, Los Angeles, CA, USA
| | - Scott M. Damrauer
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Surgery, Department of Genetics, and Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA
- Department of Surgery, Corporal Michael Crescenz VA Medical Center, Philadelphia PA
| | - Serena Sanna
- University of Groningen, UMCG, Department of Genetics, Groningen, the Netherlands
- Institute for Genetics and Biomedical Research, National Research Council, Monserrato, Italy
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Christopher Kabrhel
- Center for Vascular Emergencies, Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicholas L. Smith
- Department of Health Systems and Population Health, University of Washington, 4333 Brooklyn Ave, Seattle, WA 98195
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle WA 98108, USA
| | - Peter Kraft
- Transdivisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, MD, USA
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Han J, van Hylckama Vlieg A, Rosendaal FR. Genomic science of risk prediction for venous thromboembolic disease: convenient clarification or compounding complexity. J Thromb Haemost 2023; 21:3292-3303. [PMID: 37838557 DOI: 10.1016/j.jtha.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 09/07/2023] [Indexed: 10/16/2023]
Abstract
Venous thromboembolism (VTE) refers to abnormal blood clots in veins occurring in 1 to 2 per 1000 individuals every year. While anticoagulant treatment can prevent VTE, it increases the risk of bleeding. This emphasizes the importance of identifying individuals with a high risk of VTE and providing prophylactic interventions to these individuals to reduce both VTE and bleeding risks. Current risk assessment of VTE is based on the combination of mainly clinical risk factors. With the identification of an increasing number of genetic variants associated with the risk of VTE, the addition of genetic findings to clinical prediction models can improve risk prediction for VTE. Especially for individuals in high-risk situations, the added value of genetic findings to clinical prediction models may have benefits such as better prophylaxis of VTE and the reduced side effects of bleeding from unnecessary treatment. Nevertheless, the question of whether these models will eventually have clinical utility remains to be proven. Here, we review the current state of knowledge on genetic risk factors for VTE, explore genetic prediction models for VTE, and discuss their clinical implications and challenges.
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Affiliation(s)
- Jihee Han
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands.
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5
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Neto BV, Tavares V, da Silva JB, Liz-Pimenta J, Marques IS, Carvalho L, Salgado L, Pereira D, Medeiros R. Thrombogenesis-associated genetic determinants as predictors of thromboembolism and prognosis in cervical cancer. Sci Rep 2023; 13:9519. [PMID: 37308506 DOI: 10.1038/s41598-023-36161-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/30/2023] [Indexed: 06/14/2023] Open
Abstract
Venous thromboembolism (VTE) is a leading cause of death among cancer patients. Khorana score (KS) is the most studied tool to predict cancer-related VTE, however, it exerts poor sensitivity. Several single-nucleotide polymorphisms (SNPs) have been associated with VTE risk in the general population, but whether they are predictors of cancer-related VTE is a matter of discussion. Compared to other solid tumours, little is known about VTE in the setting of cervical cancer (CC) and whether thrombogenesis-related polymorphisms could be valuable biomarkers in patients with this neoplasia. This study aims to analyse the effect of VTE occurrence on the prognosis of CC patients, explore the predictive capability of KS and the impact of thrombogenesis-related polymorphisms on CC-related VTE incidence and patients' prognosis regardless of VTE. A profile of eight SNPs was evaluated. A retrospective hospital-based cohort study was conducted with 400 CC patients under chemoradiotherapy. SNP genotyping was carried on by using TaqMan® Allelic Discrimination methodology. Time to VTE occurrence and overall survival were the two measures of clinical outcome evaluated. The results indicated that VTE occurrence (8.5%) had a significant impact on the patient's survival (log-rank test, P < 0.001). KS showed poor performance (KS ≥ 3, χ2, P = 0.191). PROCR rs10747514 and RGS7 rs2502448 were significantly associated with the risk of CC-related VTE development (P = 0.021 and P = 0.006, respectively) and represented valuable prognostic biomarkers regardless of VTE (P = 0.004 and P = 0.010, respectively). Thus, thrombogenesis-related genetic polymorphisms may constitute valuable biomarkers among CC patients allowing a more personalized clinical intervention.
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Affiliation(s)
- Beatriz Vieira Neto
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/ Pathology and Laboratory Medicine Dep., Clinical Pathology SV/ RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072, Porto, Portugal
- FMUP, Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal
- Research Department, Portuguese League Against Cancer (NRNorte), 4200-172, Porto, Portugal
| | - Valéria Tavares
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/ Pathology and Laboratory Medicine Dep., Clinical Pathology SV/ RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072, Porto, Portugal
- FMUP, Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal
- ICBAS, Abel Salazar Institute for the Biomedical Sciences, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
- Research Department, Portuguese League Against Cancer (NRNorte), 4200-172, Porto, Portugal
| | - José Brito da Silva
- Oncology Department, Portuguese Institute of Oncology of Porto (IPOP), 4200-072, Porto, Portugal
| | - Joana Liz-Pimenta
- FMUP, Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal
- Department of Medical Oncology, Centro Hospitalar de Trás-os-Montes e Alto Douro (CHTMAD), 5000-508, Vila Real, Portugal
| | - Inês Soares Marques
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/ Pathology and Laboratory Medicine Dep., Clinical Pathology SV/ RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072, Porto, Portugal
- FCUP, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
| | - Luísa Carvalho
- External Radiotherapy Department, Portuguese Institute of Oncology of Porto (IPOP), 4200-072, Porto, Portugal
| | - Lurdes Salgado
- External Radiotherapy Department, Portuguese Institute of Oncology of Porto (IPOP), 4200-072, Porto, Portugal
| | - Deolinda Pereira
- Oncology Department, Portuguese Institute of Oncology of Porto (IPOP), 4200-072, Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/ Pathology and Laboratory Medicine Dep., Clinical Pathology SV/ RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072, Porto, Portugal.
- FMUP, Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal.
- ICBAS, Abel Salazar Institute for the Biomedical Sciences, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
- FCUP, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal.
- Research Department, Portuguese League Against Cancer (NRNorte), 4200-172, Porto, Portugal.
- CEBIMED, Faculty of Health Sciences, Fernando Pessoa University, 4200-150, Porto, Portugal.
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6
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Muñoz A, Ay C, Grilz E, López S, Font C, Pachón V, Castellón V, Martínez-Marín V, Salgado M, Martínez E, Calzas J, Ortega L, Rupérez A, Salas E, Pabinger I, Soria JM. A Clinical-Genetic Risk Score for Predicting Cancer-Associated Venous Thromboembolism: A Development and Validation Study Involving Two Independent Prospective Cohorts. J Clin Oncol 2023; 41:2911-2925. [PMID: 36730884 PMCID: PMC10414737 DOI: 10.1200/jco.22.00255] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 10/25/2022] [Accepted: 12/01/2022] [Indexed: 02/04/2023] Open
Abstract
PURPOSE Venous thromboembolism (VTE) is a leading cause of death among patients with cancer. The Khorana score was developed for assessing the risk of VTE in outpatients with cancer receiving chemotherapy, but its accuracy in identifying patients at high risk has been questioned. The aim of this study was to develop and validate a clinical-genetic score that improves the assessment of VTE risk in oncology outpatients within 6 months of diagnosis. METHODS The new score was developed using the data of 364 outpatients belonging to the Spanish ONCOTHROMB 12-01 population. In this cohort, clinical data associated with the risk of VTE were collected at the time of diagnosis, including the Khorana score. These patients were also genotyped for the 51 genetic variants known to be associated with VTE. Multivariate logistic regression was performed to determine the weight of each genetic and clinical variable in relation to VTE risk, allowing a clinical-genetic risk score (the ONCOTHROMB score) to be developed. The Khorana and the ONCOTHROMB scores were then compared via the area under the receiver operating characteristic curve (AUC), calibration, and the number of patients needed to treat. The new score was then validated in a study of 263 patients in the Vienna Cancer and Thrombosis Study population. RESULTS Nine genetic variants, tumor site, TNM stage, and a body mass index of > 25 kg/m2 were found to be associated with VTE and were used to build the ONCOTHROMB score, which better predicted the overall risk of VTE than did the Khorana score (AUC, 0.781 v 0.580; P < .001). Similar AUC results were recorded in the validation study the Vienna Cancer and Thrombosis Study cohort involving patients with the same type of tumor (AUC for the ONCOTHROMB score v the Khorana score: 0.686 v 0.577; P < .001) and with all type of tumors (AUC for the ONCOTHROMB score v the Khorana score: 0.720 v 0.561; P < .0001). CONCLUSION The ONCOTHROMB score for VTE risk in outpatients with cancer, which takes into account both clinical and genetic variables, better identifies patients who might benefit from primary thromboprophylaxis than does the Khorana score.
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Affiliation(s)
- Andrés Muñoz
- Medical Oncology, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Cancer and Thrombosis Working Section, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
| | - Cihan Ay
- Clinical Division of Haematology and Haemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Ella Grilz
- Clinical Division of Haematology and Haemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Sonia López
- Genomics of Complex Diseases Unit, Biomedical Research Institute Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Carme Font
- Cancer and Thrombosis Working Section, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
- Medical Oncology, Hospital Clínic, Barcelona, Spain
| | - Vanesa Pachón
- Cancer and Thrombosis Working Section, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
- Medical Oncology, Hospital Universitario Ramón y Cajal Madrid, Madrid, Spain
| | - Victoria Castellón
- Cancer and Thrombosis Working Section, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
- Medical Oncology, Complejo Hospitalario de Torrecárdenas, Almería, Spain
| | - Virginia Martínez-Marín
- Cancer and Thrombosis Working Section, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
- Medical Oncology, Hospital Universitario La Paz, Madrid, Spain
| | - Mercedes Salgado
- Cancer and Thrombosis Working Section, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
- Medical Oncology, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Eva Martínez
- Cancer and Thrombosis Working Section, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
- Medical Oncology, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Julia Calzas
- Cancer and Thrombosis Working Section, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
- Medical Oncology, Hospital Universitario de Fuenlabrada, Madrid, Spain
| | - Laura Ortega
- Medical Oncology, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Cancer and Thrombosis Working Section, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
| | - Ana Rupérez
- Cancer and Thrombosis Working Section, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
- Medical Oncology, Fundación Jiménez Díaz, Madrid, Spain
| | - Eduardo Salas
- Scientific Department, Gendiag.exe, Barcelona, Spain
| | - Ingrid Pabinger
- Clinical Division of Haematology and Haemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Jose Manuel Soria
- Genomics of Complex Diseases Unit, Biomedical Research Institute Sant Pau (IIB-Sant Pau), Barcelona, Spain
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7
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Zhang Z, Li H, Weng H, Zhou G, Chen H, Yang G, Zhang P, Zhang X, Ji Y, Ying K, Liu B, Xu Q, Tang Y, Zhu G, Liu Z, Xia S, Yang X, Dong L, Zhu L, Zeng M, Yuan Y, Yang Y, Zhang N, Xu X, Pang W, Zhang M, Zhang Y, Zhen K, Wang D, Lei J, Wu S, Shu S, Zhang Y, Zhang S, Gao Q, Huang Q, Deng C, Fu X, Chen G, Duan W, Wan J, Xie W, Zhang P, Wang S, Yang P, Zuo X, Zhai Z, Wang C. Genome-wide association analyses identified novel susceptibility loci for pulmonary embolism among Han Chinese population. BMC Med 2023; 21:153. [PMID: 37076872 PMCID: PMC10116678 DOI: 10.1186/s12916-023-02844-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/22/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND A large proportion of pulmonary embolism (PE) heritability remains unexplained, particularly among the East Asian (EAS) population. Our study aims to expand the genetic architecture of PE and reveal more genetic determinants in Han Chinese. METHODS We conducted the first genome-wide association study (GWAS) of PE in Han Chinese, then performed the GWAS meta-analysis based on the discovery and replication stages. To validate the effect of the risk allele, qPCR and Western blotting experiments were used to investigate possible changes in gene expression. Mendelian randomization (MR) analysis was employed to implicate pathogenic mechanisms, and a polygenic risk score (PRS) for PE risk prediction was generated. RESULTS After meta-analysis of the discovery dataset (622 cases, 8853 controls) and replication dataset (646 cases, 8810 controls), GWAS identified 3 independent loci associated with PE, including the reported loci FGG rs2066865 (p-value = 3.81 × 10-14), ABO rs582094 (p-value = 1.16 × 10-10) and newly reported locus FABP2 rs1799883 (p-value = 7.59 × 10-17). Previously reported 10 variants were successfully replicated in our cohort. Functional experiments confirmed that FABP2-A163G(rs1799883) promoted the transcription and protein expression of FABP2. Meanwhile, MR analysis revealed that high LDL-C and TC levels were associated with an increased risk of PE. Individuals with the top 10% of PRS had over a fivefold increased risk for PE compared to the general population. CONCLUSIONS We identified FABP2, related to the transport of long-chain fatty acids, contributing to the risk of PE and provided more evidence for the essential role of metabolic pathways in PE development.
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Affiliation(s)
- Zhu Zhang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China
| | - Haobo Li
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China
| | - Haoyi Weng
- Shenzhen WeGene Clinical Laboratory; WeGene, Shenzhen Zaozhidao Technology Co. Ltd; Hunan Provincial Key Lab On Bioinformatics, School of Computer Science and Engineering, Central South University, Shenzhen, 518042, China
| | - Geyu Zhou
- Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hong Chen
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Guoru Yang
- Department of Pulmonary and Critical Care Medicine, Weifang No.2 People's Hospital, Weifang, 261021, China
| | - Ping Zhang
- Department of Pulmonary and Critical Care Medicine, Dongguan People's Hospital, Dongguan, 523059, China
| | - Xiangyan Zhang
- Department of Pulmonary and Critical Care Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Yingqun Ji
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital Affiliated by Tongji University, Shanghai, 200120, China
| | - Kejing Ying
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310020, China
| | - Bo Liu
- Department of Pulmonary and Critical Care Medicine, Department of Clinical Microbiology, Zibo City Key Laboratory of Respiratory Infection and Clinical Microbiology, Linzi District People's Hospital, Zibo, 255400, China
| | - Qixia Xu
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, China
| | - Yongjun Tang
- Department of Pulmonary and Critical Care Medicine, Xiangya Hospital Central South University, Changsha, 410008, China
| | - Guangfa Zhu
- Department of Pulmonary and Critical Care, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Zhihong Liu
- Fuwai Hospital, Chinese Academy of Medical Science; National Center for Cardiovascular Diseases, Beijing, 100037, China
| | - Shuyue Xia
- Department of Pulmonary and Critical Care Medicine, Central Hospital Affiliated to Shenyang Medical College, Shenyang, 110001, China
| | - Xiaohong Yang
- Department of Pulmonary and Critical Care Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang, 830001, China
| | - Lixia Dong
- Department of Pulmonary and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, 300050, China
| | - Ling Zhu
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital, Jinan, 250021, China
| | - Mian Zeng
- Department of Medical Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yadong Yuan
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, 050004, China
| | - Yuanhua Yang
- Department of Pulmonary and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100026, China
| | - Nuofu Zhang
- State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510230, China
| | - Xiaomao Xu
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, Beijing, 100080, China
| | - Wenyi Pang
- Department of Pulmonary and Critical Care Medicine, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Meng Zhang
- Department of Pulmonary and Critical Care, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Yu Zhang
- China-Japan Friendship Hospital, Capital Medical University; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China
| | - Kaiyuan Zhen
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China
| | - Dingyi Wang
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, China, 100029
| | - Jieping Lei
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, China, 100029
| | - Sinan Wu
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, China, 100029
| | - Shi Shu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China
| | - Yunxia Zhang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China
| | - Shuai Zhang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China
| | - Qian Gao
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China
| | - Qiang Huang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China
| | - Chao Deng
- Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xi Fu
- Shenzhen WeGene Clinical Laboratory; WeGene, Shenzhen Zaozhidao Technology Co. Ltd; Hunan Provincial Key Lab On Bioinformatics, School of Computer Science and Engineering, Central South University, Shenzhen, 518042, China
| | - Gang Chen
- Shenzhen WeGene Clinical Laboratory; WeGene, Shenzhen Zaozhidao Technology Co. Ltd; Hunan Provincial Key Lab On Bioinformatics, School of Computer Science and Engineering, Central South University, Shenzhen, 518042, China
| | - Wenxin Duan
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Jun Wan
- Department of Pulmonary and Critical Care, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Wanmu Xie
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China
| | - Peng Zhang
- Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Shengfeng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Peiran Yang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Xianbo Zuo
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China; Department of Pharmacy, China-Japan Friendship Hospital, No. 2, East Yinghua Road, Chaoyang District, Beijing, 100029, China.
| | - Zhenguo Zhai
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, 100029, China.
| | - Chen Wang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China.
- National Center for Respiratory Medicine, Beijing, China.
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.
- National Clinical Research Center for Respiratory Diseases, Beijing, China.
- Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
- Department of Respiratory Medicine, Capital Medical University, Beijing, China.
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8
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Seyerle AA, Laurie CA, Coombes BJ, Jain D, Conomos MP, Brody J, Chen MH, Gogarten SM, Beutel KM, Gupta N, Heckbert SR, Jackson RD, Johnson AD, Ko D, Manson JE, McKnight B, Metcalf GA, Morrison AC, Reiner AP, Sofer T, Tang W, Wiggins KL, Boerwinkle E, de Andrade M, Gabriel SB, Gibbs RA, Laurie CC, Psaty BM, Vasan RS, Rice K, Kooperberg C, Pankow JS, Smith NL, Pankratz N. Whole Genome Analysis of Venous Thromboembolism: the Trans-Omics for Precision Medicine Program. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:e003532. [PMID: 36960714 PMCID: PMC10151032 DOI: 10.1161/circgen.121.003532] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/04/2023] [Indexed: 03/25/2023]
Abstract
BACKGROUND Risk for venous thromboembolism has a strong genetic component. Whole genome sequencing from the TOPMed program (Trans-Omics for Precision Medicine) allowed us to look for new associations, particularly rare variants missed by standard genome-wide association studies. METHODS The 3793 cases and 7834 controls (11.6% of cases were individuals of African, Hispanic/Latino, or Asian ancestry) were analyzed using a single variant approach and an aggregate gene-based approach using our primary filter (included only loss-of-function and missense variants predicted to be deleterious) and our secondary filter (included all missense variants). RESULTS Single variant analyses identified associations at 5 known loci. Aggregate gene-based analyses identified only PROC (odds ratio, 6.2 for carriers of rare variants; P=7.4×10-14) when using our primary filter. Employing our secondary variant filter led to a smaller effect size at PROC (odds ratio, 3.8; P=1.6×10-14), while excluding variants found only in rare isoforms led to a larger one (odds ratio, 7.5). Different filtering strategies improved the signal for 2 other known genes: PROS1 became significant (minimum P=1.8×10-6 with the secondary filter), while SERPINC1 did not (minimum P=4.4×10-5 with minor allele frequency <0.0005). Results were largely the same when restricting the analyses to include only unprovoked cases; however, one novel gene, MS4A1, became significant (P=4.4×10-7 using all missense variants with minor allele frequency <0.0005). CONCLUSIONS Here, we have demonstrated the importance of using multiple variant filtering strategies, as we detected additional genes when filtering variants based on their predicted deleteriousness, frequency, and presence on the most expressed isoforms. Our primary analyses did not identify new candidate loci; thus larger follow-up studies are needed to replicate the novel MS4A1 locus and to identify additional rare variation associated with venous thromboembolism.
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Affiliation(s)
- Amanda A. Seyerle
- Division of Pharmaceutical Outcomes & Policy, Eshelman School of Pharmacy, Univ of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Health Informatics Program, Univ of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Deepti Jain
- Dept of Biostatistics, Univ of Washington, Seattle, WA
| | | | - Jennifer Brody
- Cardiovascular Health Rsrch Unit, Univ of Washington, Seattle, WA
| | - Ming-Huei Chen
- NHLB’s The Framingham Heart Study, Population Sciences Branch, Division of Intramural Rsrch, National Heart, Lung, and Blood Inst, Framingham, MA
| | | | - Kathleen M. Beutel
- Dept of Laboratory Medicine & Pathology, School of Medicine, Univ of Minnesota, Minneapolis, MN
| | | | - Susan R. Heckbert
- Cardiovascular Health Rsrch Unit, Univ of Washington, Seattle, WA
- Dept of Epidemiology, Univ of Washington, Seattle, WA
| | - Rebecca D. Jackson
- Division of Endocrinology, Diabetes & Metabolism, Ohio State Univ, Columbus, OH
| | - Andrew D. Johnson
- NHLB’s The Framingham Heart Study, Population Sciences Branch, Division of Intramural Rsrch, National Heart, Lung, and Blood Inst, Framingham, MA
| | - Darae Ko
- Cardiovascular Medicine Section, Boston Univ School of Medicine
| | - JoAnn E. Manson
- Dept of Epidemiology, TH Chan School of Public Health, Harvard Univ, Boston, MA
| | | | | | - Alanna C. Morrison
- Human Genetics Ctr, Dept of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, Univ of Texas Health Science Ctr at Houston, Houston, TX
| | | | - Tamar Sofer
- Division of Sleep & Circadian Disorders, Brigham and Women’s Hospital
- Dept of Medicine, Harvard Medical School, Boston, MA
| | - Weihong Tang
- Division of Epidemiology & Community Health, Univ of Minnesota, Minneapolis, MN
| | - Kerri L. Wiggins
- Cardiovascular Health Rsrch Unit, Univ of Washington, Seattle, WA
| | | | - Eric Boerwinkle
- Human Genetics Ctr, Dept of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, Univ of Texas Health Science Ctr at Houston, Houston, TX
| | | | | | | | | | - Bruce M. Psaty
- Cardiovascular Health Rsrch Unit, Univ of Washington, Seattle, WA
- Dept of Epidemiology, Univ of Washington, Seattle, WA
- Depts of Medicine & Health Services, Univ of Washington, Seattle, WA
- Kaiser Permanente Washington Health Rsrch Inst, Seattle, WA
| | | | - Ken Rice
- Dept of Biostatistics, Univ of Washington, Seattle, WA
| | | | - James S. Pankow
- Division of Epidemiology & Community Health, Univ of Minnesota, Minneapolis, MN
| | - Nicholas L. Smith
- Cardiovascular Health Rsrch Unit, Univ of Washington, Seattle, WA
- Dept of Epidemiology, Univ of Washington, Seattle, WA
- Seattle Epidemiologic Rsrch & Information Ctr, VA Office of Rsrch & Development, Seattle, WA
| | - Nathan Pankratz
- Dept of Laboratory Medicine & Pathology, School of Medicine, Univ of Minnesota, Minneapolis, MN
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9
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Chong M, Paré G. Identifying individuals at extreme risk of venous thromboembolism using polygenic risk scores. Nat Genet 2023; 55:358-360. [PMID: 36894711 DOI: 10.1038/s41588-023-01330-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Affiliation(s)
- Michael Chong
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada.
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada.
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
| | - Guillaume Paré
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada.
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada.
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada.
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10
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Zhang H, Alarcon C, Cavallari LH, Nutescu E, Carvill GL, Perera MA, Hernandez W. Genomewide Association Study Identifies Copy Number Variants Associated With Warfarin Dose Response and Risk of Venous Thromboembolism in African Americans. Clin Pharmacol Ther 2023; 113:624-633. [PMID: 36507737 DOI: 10.1002/cpt.2820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The anticoagulant warfarin is commonly used to control and prevent thrombotic disorders, such as venous thromboembolism (VTE), which disproportionately afflicts African Americans. Despite the importance of copy number variants (CNVs), few studies have focused on characterizing and understanding their role in drug response and disease risk among African Americans. In this study, we conduct the first genome-wide analysis of CNVs to more comprehensively account for the contribution of genetic variation in warfarin dose requirement and VTE risk among African Americans. We used hidden Markov models to detect CNVs from high-throughput single-nucleotide polymorphism arrays for 340 African American participants in the International Warfarin Pharmacogenetics Consortium. We identified 11,570 CNVs resulting in 2,038 copy number variable regions (CNVRs) and found 3 CNVRs associated with warfarin dose requirement and 3 CNVRs associated with VTE risk in African Americans. CNVRs 1q31.2del and 6q14.1del were associated with increased warfarin dose requirement (β = 11.18 and 4.94, respectively; Pemp = < 0.002); CNVR 19p13.31del was associated with decreased warfarin dose requirement (β = -1.41, Pemp = 0.0004); CNVRs (2p22.1del and 5q35.1-q35.2del) were found to be associated with increased risk of VTE (odds ratios (ORs) = 1.88 and 14.9, respectively; Pemp ≤0.02); and CNVR 10q26.12del was associated with a decreased risk of VTE (OR = 0.6; Pemp = 0.05). Modeling of the 10q26.12del in HepG2 cells revealed that this deletion results in decreased fibrinogen gene expression, decreased fibrinogen and WDR11 protein levels, and decreased secretion of fibrinogen into the extracellular matrix. We found robust evidence that CNVRs could contribute to warfarin dose requirement and risk of VTE in African Americans and for 10q26.3del describe a possible pathogenic mechanism.
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Affiliation(s)
- Honghong Zhang
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Cristina Alarcon
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Edith Nutescu
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois, USA
| | - Gemma L Carvill
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Minoli A Perera
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Wenndy Hernandez
- Section of Cardiology, University of Chicago, Chicago, Illinois, USA
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11
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Thibord F, Klarin D, Brody JA, Chen MH, Levin MG, Chasman DI, Goode EL, Hveem K, Teder-Laving M, Martinez-Perez A, Aïssi D, Daian-Bacq D, Ito K, Natarajan P, Lutsey PL, Nadkarni GN, de Vries PS, Cuellar-Partida G, Wolford BN, Pattee JW, Kooperberg C, Braekkan SK, Li-Gao R, Saut N, Sept C, Germain M, Judy RL, Wiggins KL, Ko D, O’Donnell CJ, Taylor KD, Giulianini F, De Andrade M, Nøst TH, Boland A, Empana JP, Koyama S, Gilliland T, Do R, Huffman JE, Wang X, Zhou W, Soria JM, Souto JC, Pankratz N, Haessler J, Hindberg K, Rosendaal FR, Turman C, Olaso R, Kember RL, Bartz TM, Lynch JA, Heckbert SR, Armasu SM, Brumpton B, Smadja DM, Jouven X, Komuro I, Clapham KR, Loos RJ, Willer CJ, Sabater-Lleal M, Pankow JS, Reiner AP, Morelli VM, Ridker PM, van Hylckama Vlieg A, Deleuze JF, Kraft P, Rader DJ, Lee KM, Psaty BM, Skogholt AH, Emmerich J, Suchon P, Rich SS, Vy HMT, Tang W, Jackson RD, Hansen JB, Morange PE, Kabrhel C, Trégouët DA, Damrauer SM, Johnson AD, Smith NL. Cross-Ancestry Investigation of Venous Thromboembolism Genomic Predictors. Circulation 2022; 146:1225-1242. [PMID: 36154123 PMCID: PMC10152894 DOI: 10.1161/circulationaha.122.059675] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/09/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND Venous thromboembolism (VTE) is a life-threatening vascular event with environmental and genetic determinants. Recent VTE genome-wide association studies (GWAS) meta-analyses involved nearly 30 000 VTE cases and identified up to 40 genetic loci associated with VTE risk, including loci not previously suspected to play a role in hemostasis. The aim of our research was to expand discovery of new genetic loci associated with VTE by using cross-ancestry genomic resources. METHODS We present new cross-ancestry meta-analyzed GWAS results involving up to 81 669 VTE cases from 30 studies, with replication of novel loci in independent populations and loci characterization through in silico genomic interrogations. RESULTS In our genetic discovery effort that included 55 330 participants with VTE (47 822 European, 6320 African, and 1188 Hispanic ancestry), we identified 48 novel associations, of which 34 were replicated after correction for multiple testing. In our combined discovery-replication analysis (81 669 VTE participants) and ancestry-stratified meta-analyses (European, African, and Hispanic), we identified another 44 novel associations, which are new candidate VTE-associated loci requiring replication. In total, across all GWAS meta-analyses, we identified 135 independent genomic loci significantly associated with VTE risk. A genetic risk score of the significantly associated loci in Europeans identified a 6-fold increase in risk for those in the top 1% of scores compared with those with average scores. We also identified 31 novel transcript associations in transcriptome-wide association studies and 8 novel candidate genes with protein quantitative-trait locus Mendelian randomization analyses. In silico interrogations of hemostasis and hematology traits and a large phenome-wide association analysis of the 135 GWAS loci provided insights to biological pathways contributing to VTE, with some loci contributing to VTE through well-characterized coagulation pathways and others providing new data on the role of hematology traits, particularly platelet function. Many of the replicated loci are outside of known or currently hypothesized pathways to thrombosis. CONCLUSIONS Our cross-ancestry GWAS meta-analyses identified new loci associated with VTE. These findings highlight new pathways to thrombosis and provide novel molecules that may be useful in the development of improved antithrombosis treatments.
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Affiliation(s)
- Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
- The Framingham Heart Study, Boston University and NHLBI, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
| | - Derek Klarin
- Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA
- VA Palo Alto Healthcare System, Palo Alto, CA, 94550, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
- The Framingham Heart Study, Boston University and NHLBI, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
| | - Michael G. Levin
- Division of Cardiovascular Medicine, Department of Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA, 19104, USA
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, 900 Commonwealth Ave, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Ellen L. Goode
- Department of Quantitative Health Sciences, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kristian Hveem
- HUNT Research Center, Department of Public Health and Nursing, Norwegian University of Science and Technology, Forskningsvegen 2, Levanger, 7600, Norway
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Håkon Jarls gate 11, Trondheim, 7030, Norway
| | - Maris Teder-Laving
- Institute of Genomics, University of Tartu, Riia 23b, Tartu, Tartu, 51010, Estonia
| | - Angel Martinez-Perez
- Genomics of Complex Disease Unit, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), St Quinti 77-79, Barcelona, 8041, Spain
| | - Dylan Aïssi
- Bordeaux Population Health Research Center, University of Bordeaux, 146 rue Léo Saignat, Bordeaux, 33076, France
- UMR1219, INSERM, 146 rue Léo Saignat, Bordeaux, 33076, France
| | - Delphine Daian-Bacq
- Centre National de Recherche en Génomique Humaine, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02446, USA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, 75 Ames St, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Shattuck St, Boston, MA, 02115, USA
| | - Pamela L. Lutsey
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, Minneapolis, MN, 55454, USA
| | - Girish N. Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gu stave L. Levy Pl, New York, NY, 10029, USA
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, 1200 Pressler St, Houston, TX, 77030, USA
| | | | - Brooke N. Wolford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jack W. Pattee
- Division of Biostatistics, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN, 55455, USA
- Center for Innovative Design & Analysis and Department of Biostatistics & Informatics, Colorado School of Public Health, 13001 East 17th Place, Aurora, CO, 80045, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Sigrid K. Braekkan
- Thrombosis Research Center (TREC), UiT - The Arctic University of Norway, Universitetsvegen 57, Tromsø, 9037, Norway
- Division of internal medicine, University Hospital of North Norway, Tromsø, 9038, Norway
| | - Ruifang Li-Gao
- Clinical Epidemiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
| | - Noemie Saut
- Hematology Laboratory, La Timone University Hospital of Marseille, 264 Rue Saint-Pierre, Marseille, 13385, France
| | - Corriene Sept
- Department of Epidemiology, Harvard TH Chan Harvard School of Public Health, 655 Huntington Ave., Building II, Boston, MA, 02115, USA
| | - Marine Germain
- Bordeaux Population Health Research Center, University of Bordeaux, 146 rue Léo Saignat, Bordeaux, 33076, France
- UMR1219, INSERM, 146 rue Léo Saignat, Bordeaux, 33076, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
| | - Renae L. Judy
- Surgery, University of Pennsylvania, 3401 Walnut Street, Philadelphia, PA, 19104, USA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Darae Ko
- The Framingham Heart Study, Boston University and NHLBI, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
- Section of Cardiovascular Medicine, Boston University School of Medicine, 85 East Newton Street, Boston, MA, 02118, USA
| | - Christopher J. O’Donnell
- Cardiology Section, Department of Medicine, VA Boston Healthcare System, Boston, MA, 02132, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, 1124 W Carson St., Torrance, CA, 90502, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women’s Hospital, 900 Commonwealth Ave, Boston, MA, 02215, USA
| | - Mariza De Andrade
- Department of Quantitative Health Sciences, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Therese H. Nøst
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Håkon Jarls gate 11, Trondheim, 7030, Norway
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
| | - Jean-Philippe Empana
- Integrative Epidemiology of cardiovascular diseases, Université Paris Cité, Paris Cardiovascular Research Center (PARCC), 56 rue Leblanc, Paris, 75015, France
- Department of Cardiology, APHP, Hopital Européen Georges Pompidou, 20 rue Leblanc, Paris, 75015, France
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02446, USA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, 75 Ames St, Cambridge, MA, 02142, USA
| | - Thomas Gilliland
- Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02446, USA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, 75 Ames St, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Shattuck St, Boston, MA, 02115, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gu stave L. Levy Pl, New York, NY, 10029, USA
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Jennifer E. Huffman
- MAVERIC, VA Boston Heathcare System, 2 Avenue de Lafayette, Boston, MA, 02111, USA
| | - Xin Wang
- 23andMe, Inc., 223 N Mathilda Ave, Sunnyvale, CA, 94086, USA
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Jose Manuel Soria
- Genomics of Complex Disease Unit, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), St Quinti 77-79, Barcelona, 8041, Spain
| | - Juan Carlos Souto
- Genomics of Complex Disease Unit, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), St Quinti 77-79, Barcelona, 8041, Spain
- Unit of Thrombosis and Hemostasis, Hospital de la Santa Creu i Sant Pau, St Quinti 89, Barcelona, 8041, Spain
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN, 55455, USA
| | - Jeffery Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Kristian Hindberg
- Thrombosis Research Center (TREC), UiT - The Arctic University of Norway, Universitetsvegen 57, Tromsø, 9037, Norway
| | - Frits R. Rosendaal
- Clinical Epidemiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
| | - Constance Turman
- Department of Epidemiology, Harvard TH Chan Harvard School of Public Health, 655 Huntington Ave., Building II, Boston, MA, 02115, USA
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
| | - Rachel L. Kember
- Psychiatry, University of Pennsylvania, 3401 Walnut Street, Philadelphia, PA, 19104, USA
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Departments of Biostatistics and Medicine, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Julie A. Lynch
- VA Informatics & Computing Infrastructure, VA Salt Lake City Healthcare System, 500 Foothills Drive, Salt Lake City, UT, 84148, USA
- Epidemiology, University of Utah, 500 Foothills Drive, Salt Lake City, UT, 84148, USA
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Sebastian M. Armasu
- Department of Quantitative Health Sciences, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ben Brumpton
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Håkon Jarls gate 11, Trondheim, 7030, Norway
| | - David M. Smadja
- Hematology Department and Biosurgical Research Lab (Carpentier Foundation), European Georges Pompidou Hospital, Assistance Publique Hôpitaux de Paris, 20 rue Leblanc, Paris, 75015, France
- Innovative Therapies in Haemostasis, INSERM, Université de Paris, 4 avenue de l’Observatoire, Paris, 75270, France
| | - Xavier Jouven
- Integrative Epidemiology of cardiovascular diseases, Université Paris Descartes, Sorbonne Paris Cité, 56 rue Leblanc, Paris, 75015, France
- Paris Cardiovascular Research Center, Inserm U970, Université Paris Descartes, Sorbonne Paris Cité, 20 rue Leblanc, Paris, 75015, France
| | - Issei Komuro
- Department of Cardiovascular Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Tokyo, 113-8655, Japan
| | - Katharine R. Clapham
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, 75 Ames St, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Shattuck St, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, 900 Commonwealth Ave, Boston, MA, 02215, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Cristen J. Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maria Sabater-Lleal
- Genomics of Complex Disease Unit, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), St Quinti 77-79, Barcelona, 8041, Spain
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Stockholm, 17176, Sweden
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, Minneapolis, MN, 55454, USA
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Department of Epidemiology, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Vania M. Morelli
- Thrombosis Research Center (TREC), UiT - The Arctic University of Norway, Universitetsvegen 57, Tromsø, 9037, Norway
- Division of internal medicine, University Hospital of North Norway, Tromsø, 9038, Norway
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital, 900 Commonwealth Ave, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Astrid van Hylckama Vlieg
- Clinical Epidemiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
- Centre D’Etude du Polymorphisme Humain, Fondation Jean Dausset, 27 rue Juliette Dodu, Paris, 75010, France
| | - Peter Kraft
- Department of Epidemiology, Harvard TH Chan Harvard School of Public Health, 655 Huntington Ave., Building II, Boston, MA, 02115, USA
| | - Daniel J. Rader
- Departments of Medicine and Genetics and Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | | | | | | | | | | | - Kyung Min Lee
- VA Informatics & Computing Infrastructure, VA Salt Lake City Healthcare System, 500 Foothills Drive, Salt Lake City, UT, 84148, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
- Department of Epidemiology, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
- Department of Health Systems and Population Heath, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Anne Heidi Skogholt
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Håkon Jarls gate 11, Trondheim, 7030, Norway
| | - Joseph Emmerich
- Department of vascular medicine, Paris Saint-Joseph Hospital Group, University of Paris, 185 rue Raymond Losserand, Paris, 75674, France
- UMR1153, INSERM CRESS, 185 rue Raymond Losserand, Paris, 75674, France
| | - Pierre Suchon
- Hematology Laboratory, La Timone University Hospital of Marseille, 264 Rue Saint-Pierre, Marseille, 13385, France
- C2VN, INSERM, INRAE, Aix-Marseille University, 27, bd Jean Moulin, Marseille, 13385, France
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, 3242 West Complex, Charlottesville, VA, 22908-0717, USA
| | - Ha My T. Vy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gu stave L. Levy Pl, New York, NY, 10029, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, Minneapolis, MN, 55454, USA
| | - Rebecca D. Jackson
- College of Medicine, Ohio State University, 376 W. 10th Ave, Columbus, OH, 43210, USA
| | - John-Bjarne Hansen
- Thrombosis Research Center (TREC), UiT - The Arctic University of Norway, Universitetsvegen 57, Tromsø, 9037, Norway
- Division of internal medicine, University Hospital of North Norway, Tromsø, 9038, Norway
| | - Pierre-Emmanuel Morange
- Hematology Laboratory, La Timone University Hospital of Marseille, 264 Rue Saint-Pierre, Marseille, 13385, France
- C2VN, INSERM, INRAE, Aix-Marseille University, 27, bd Jean Moulin, Marseille, 13385, France
| | - Christopher Kabrhel
- Emergency Medicine, Massachusetts General Hospital, Zero Emerson Place, Suite 3B, Boston, MA, 02114, USA
- Emergency Medicine, Harvard Medical School, Zero Emerson Place, Suite 3B, Boston, MA, 02114, USA
| | - David-Alexandre Trégouët
- Bordeaux Population Health Research Center, University of Bordeaux, 146 rue Léo Saignat, Bordeaux, 33076, France
- UMR1219, INSERM, 146 rue Léo Saignat, Bordeaux, 33076, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
| | - Scott M. Damrauer
- Corporal Michael J. Crescenz Philadelphia VA Medical Center, 3900 Woodland Ave, Philadelphia, PA, 19104, USA
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrew D. Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
- The Framingham Heart Study, Boston University and NHLBI, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, 98108, USA
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12
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Peripartum management of hereditary thrombophilia: results of primary surveillance in Japan. Int J Hematol 2022; 116:364-371. [PMID: 35551617 DOI: 10.1007/s12185-022-03354-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
Abstract
This study investigated patients with thrombophilia and current peripartum management practices based on national surveillance in Japan. Between 2014 and 2018, antithrombin (AT), protein C (PC) and protein S (PS) deficiency were observed in 84, 67, and 443 pregnancies, respectively, with incidence rates among total deliveries at 0.012%, 0.009%, and 0.061%. The percentage of institutions that measured both antigens and AT, PC, and PS activity for the diagnosis of thrombophilia was 50.2%, and 46.9% of institutions did not perform gene analysis. Prophylactic anticoagulation therapy was used in the ante- and postpartum management of patients with AT deficiency at 67.1% and 66.3% of institutions, most commonly with 10,000 units of unfractionated heparin. Ante- and postpartum management of PC and PS deficiency was performed at 75.3% and 67.1% of institutions. Approximately half of the institutions performed peripartum prophylactic AT supplementation for AT deficiency. Low trough AT activity before supplementation was most commonly 50 ≤ < 70%, and the highest AT supplementation was 1500 ≤ < 3000 units. The number of pregnancies with AT, PC and PS deficiency might be as many as 29, 23 and 151 every year in Japan if complete answers were provided.
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Oral postmenopausal hormone therapy and genetic risk on venous thromboembolism: gene-hormone interaction results from a large prospective cohort study. Menopause 2022; 29:293-303. [PMID: 35013060 PMCID: PMC8881382 DOI: 10.1097/gme.0000000000001924] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Oral postmenopausal hormone therapy (HT) has been shown to be associated with venous thromboembolism (VTE), but whether this association is modified by VTE-associated genetic susceptibility is unknown. We examined interactions between oral HT use and a genetic risk score (GRS) of VTE. METHOD Eligible women were postmenopausal women who had data on oral HT use, VTE incidence between 1990 and 2012, and genetic data in the Nurses' Health Study. We built a GRS aggregating 16 VTE-related genetic variants. We used Cox regression to estimate associations of HT use with incident VTE and assessed interactions between HT use and VTE GRS. We also estimated incidence of VTE between age 50 and 79 years for groups of women defined by HT use and VTE GRS. RESULTS We identified 432 incident VTE cases. Current HT users were at higher risk of VTE than never users (HR: 1.9, 95% CI: 1.5-2.6), with slightly higher risk for estrogen plus progestin HT than estrogen only (HR: 2.4 vs 1.9). The GRS was associated with VTE risk (HR comparing 4th quartile to 1st: 2.0, 95% CI: 1.2-3.4). We did not observe significant multiplicative interactions between HT use and GRS. The estimated VTE risk difference (per 10,000 person-years) comparing 50-year-old current HT users to never users was 22.5 for women in the highest GRS quartile and 9.8 for women in the lowest GRS quartile. CONCLUSION The VTE GRS might inform clinical guidance regarding the balance of risks and benefits of HT use, especially among younger women.
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Alotaibi RN, Howe BJ, Moreno Uribe LM, Ramirez CV, Restrepo C, Deleyiannis FW, Padilla C, Orioli IM, Buxó CJ, Hecht JT, Wehby GL, Neiswanger K, Murray JC, Shaffer JR, Weinberg SM, Marazita ML. Multivariate GWAS of Structural Dental Anomalies and Dental Caries in a Multi-Ethnic Cohort. FRONTIERS IN DENTAL MEDICINE 2022; 2:771116. [PMID: 36267138 PMCID: PMC9581442 DOI: 10.3389/fdmed.2021.771116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
Odontogenesis is a complex process, where disruption can result in dental anomalies and/or increase the risk of developing dental caries. Based on previous studies, certain dental anomalies tend to co-occur in patients, suggesting that these traits may share common genetic and etiological components. The main goal of this study was to implement a multivariate genome-wide association study approach to identify genetic variants shared between correlated structural dental anomalies and dental caries. Our cohort (N = 3,579) was derived from the Pittsburgh Orofacial Clefts Study, where multiple dental traits were assessed in both the unaffected relatives of orofacial cleft (OFC) cases (n = 2,187) and unaffected controls (n = 1,392). We identified four multivariate patterns of correlated traits in this data: tooth agenesis, impaction, and rotation (AIR); enamel hypoplasia, displacement, and rotation (HDR); displacement, rotation, and mamelon (DRM); and dental caries, tooth agenesis and enamel hypoplasia (CAH). We analyzed each of these four models using genome-wide multivariate tests of association. No genome-wide statistically significant results were found, but we identified multiple suggestive association signals (P < 10-5) near genes with known biological roles during tooth development, including ADAMTS9 and PRICKLE2 associated with AIR; GLIS3, WDR72, and ROR2 associated with HDR and DRM; ROBO2 associated with DRM; BMP7 associated with HDR; and ROBO1, SMAD2, and MSX2 associated with CAH. This is the first study to investigate genetic associations for multivariate patterns of correlated dental anomalies and dental caries. Further studies are needed to replicate these results in independent cohorts.
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Affiliation(s)
- Rasha N. Alotaibi
- Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brian J. Howe
- Department of Family Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA
- The Iowa Center for Oral Health Research, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Lina M. Moreno Uribe
- The Iowa Center for Oral Health Research, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Department of Orthodontics, School of Dentistry, University of Iowa, Iowa City, IA, USA
| | | | | | | | - Carmencita Padilla
- Department of Pediatrics, College of Medicine, University of the Philippines, Manila
| | - Ieda M. Orioli
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carmen J. Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Jacqueline T. Hecht
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, Texas, TX, USA
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Katherine Neiswanger
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeffery C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - John R. Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
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15
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Kvasnička J, Kovářová-Kudrnová Z, Zenáhlíková Z, Brzežková R, Šťastná S, Bobčíková P, Kvasnička T. Today's view of hereditary thrombophilia. VNITRNI LEKARSTVI 2022; 68:488-492. [PMID: 36575065 DOI: 10.36290/vnl.2022.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Venous thromboembolism (VTE) is still a serious medical problem with the non-decreasing incidence of new cases despite prophylaxis in risky situations. It is a multifactorial disease, in which the hereditary component is also significantly involved. The aim of the current research is to search for new polymorphisms that are involved in thrombogenesis in addition to classical thrombophilia (deficiency of natural coagulation inhibitors and FVL and FII prothrombin mutations). The article provides an overview of the results of already performed genome-wide association studies of VTE and their use for the calculation of the so-called polygenic risk score, which could be used for individualized prevention of VTE after standardization of the method.
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Cross B, Turner R, Pirmohamed M. Polygenic risk scores: An overview from bench to bedside for personalised medicine. Front Genet 2022; 13:1000667. [PMID: 36437929 PMCID: PMC9692112 DOI: 10.3389/fgene.2022.1000667] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
Since the first polygenic risk score (PRS) in 2007, research in this area has progressed significantly. The increasing number of SNPs that have been identified by large scale GWAS analyses has fuelled the development of a myriad of PRSs for a wide variety of diseases and, more recently, to PRSs that potentially identify differential response to specific drugs. PRSs constitute a composite genomic biomarker and potential applications for PRSs in clinical practice encompass risk prediction and disease screening, early diagnosis, prognostication, and drug stratification to improve efficacy or reduce adverse drug reactions. Nevertheless, to our knowledge, no PRSs have yet been adopted into routine clinical practice. Beyond the technical considerations of PRS development, the major challenges that face PRSs include demonstrating clinical utility and circumnavigating the implementation of novel genomic technologies at scale into stretched healthcare systems. In this review, we discuss progress in developing disease susceptibility PRSs across multiple medical specialties, development of pharmacogenomic PRSs, and future directions for the field.
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Affiliation(s)
- Benjamin Cross
- The Wolfson Centre for Personalised Medicine, Institute of Systems, Molecular and Integrative Biology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Richard Turner
- The Wolfson Centre for Personalised Medicine, Institute of Systems, Molecular and Integrative Biology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- The Wolfson Centre for Personalised Medicine, Institute of Systems, Molecular and Integrative Biology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, United Kingdom
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A Christensen M, Bonde A, Sillesen M. An assessment of the effect of the genotype on postoperative venous thromboembolism risk in 140,831 surgical patients. Ann Med Surg (Lond) 2021; 71:102938. [PMID: 34777790 PMCID: PMC8577341 DOI: 10.1016/j.amsu.2021.102938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 11/08/2022] Open
Abstract
Background Postoperative Venous Thromboembolism Events (VTE) constitute a major source of morbidity and mortality after surgery. The aim of this study was to investigate whether commonly occurring Single Nucleotide Polymorphisms (SNPs) are associated with VTE in the surgical setting. Methods Retrospective study using data from the United Kingdom (UK) biobank, a genome biobank containing healthcare and genotyping data from more than 500.000 individuals. A cohort of 140,831patients with a registered surgical procedure was identified and used for a discovery genome wide association study (GWAS), with the remainder of the cohort (305,349 non-surgical patients) used as a replication cohort. Primary outcome was associations between SNPs and VTE within 30 days after a surgical procedure. Genome wide significance was set at p = 5 × 10−8. Results In the surgical (discovery) cohort, no SNPs reached genome wide significance. The VTE association of the top candidate SNP in the ABO gene rs505922 (p = 3.33 × 10−7), was replicated in the general (replication) cohort (p = 2.42 × 10−59). Conclusions and Relevance: This study did not identify associations between SNPs and postoperative VTE events reaching genome-wide significance, although the VTE relevance of top candidates were demonstrated. •Venous thromboembolisms are common after surgery. •Large biobanks help identify common genetic risk factors. •Common variants in ABO may increase the risk of postoperative venous thromboembolisms. •Genotyping surgical patients may benefit preoperative risk assessment.
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Affiliation(s)
- Mathias A Christensen
- Department of Surgical Gastroenterology and Transplantation C-TX, Copenhagen University Hospital, Rigshosptialet, Denmark.,Center for Surgical Translational and Artificial Intelligence Research CSTAR, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Alexander Bonde
- Department of Surgical Gastroenterology and Transplantation C-TX, Copenhagen University Hospital, Rigshosptialet, Denmark.,Center for Surgical Translational and Artificial Intelligence Research CSTAR, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Martin Sillesen
- Department of Surgical Gastroenterology and Transplantation C-TX, Copenhagen University Hospital, Rigshosptialet, Denmark.,Center for Surgical Translational and Artificial Intelligence Research CSTAR, Copenhagen University Hospital, Rigshospitalet, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Denmark
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18
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Kolin DA, Kulm S, Elemento O. Prediction of primary venous thromboembolism based on clinical and genetic factors within the U.K. Biobank. Sci Rep 2021; 11:21340. [PMID: 34725413 PMCID: PMC8560817 DOI: 10.1038/s41598-021-00796-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/15/2021] [Indexed: 01/18/2023] Open
Abstract
Both clinical and genetic factors drive the risk of venous thromboembolism. However, whether clinically recorded risk factors and genetic variants can be combined into a clinically applicable predictive score remains unknown. Using Cox proportional-hazard models, we analyzed the association of risk factors with the likelihood of venous thromboembolism in U.K. Biobank, a large prospective cohort. We then created a polygenic risk score of 36 single nucleotide polymorphisms and a clinical score determined by age, sex, body mass index, previous cancer diagnosis, smoking status, and fracture in the last 5 years. Participants were at significantly increased risk of venous thromboembolism if they were at high clinical risk (subhazard ratio, 4.37 [95% CI, 3.85-4.97]) or high genetic risk (subhazard ratio, 3.02 [95% CI, 2.63-3.47]) relative to participants at low clinical or genetic risk, respectively. The combined model, consisting of clinical and genetic components, was significantly better than either the clinical or the genetic model alone (P < 0.001). Participants at high risk in the combined score had nearly an eightfold increased risk of venous thromboembolism relative to participants at low risk (subhazard ratio, 7.51 [95% CI, 6.28-8.98]). This risk score can be used to guide decisions regarding venous thromboembolism prophylaxis, although external validation is needed.
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Affiliation(s)
- David A Kolin
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
- Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
| | - Scott Kulm
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
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19
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Glavan D, Gheorman V, Gresita A, Hermann DM, Udristoiu I, Popa-Wagner A. Identification of transcriptome alterations in the prefrontal cortex, hippocampus, amygdala and hippocampus of suicide victims. Sci Rep 2021; 11:18853. [PMID: 34552157 PMCID: PMC8458545 DOI: 10.1038/s41598-021-98210-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/30/2021] [Indexed: 11/09/2022] Open
Abstract
Suicide is one of the leading causes of death globally for all ages, and as such presents a very serious problem for clinicians worldwide. However, the underlying neurobiological pathology remains to a large extent unknown. In order to address this gap, we have carried out a genome-wide investigation of the gene expression in the amygdala, hippocampus, prefrontal cortex and thalamus in post-mortem brain samples obtained from 20 suicide completers and 7 control subjects. By KEGG enrichment analysis indicated we identified novel clusters of downregulated pathways involved in antigen neutralization and autoimmune thyroid disease (amygdala, thalamus), decreased axonal plasticity in the hippocampus. Two upregulated pathways were involved in neuronal death in the hippocampus and olfactory transduction in the thalamus and the prefrontal cortex. Autoimmune thyroid disease pathway was downregulated only in females. Metabolic pathways involved in Notch signaling amino acid metabolism and unsaturated lipid synthesis were thalamus-specific. Suicide-associated changes in the expression of several genes and pseudogenes that point to various functional mechanisms possibly implicated in the pathology of suicide. Two genes (SNORA13 and RNU4-2) involved in RNA processing were common to all brain regions analyzed. Most of the identified gene expression changes were related to region-specific dysregulated manifestation of genetic and epigenetic mechanisms underlying neurodevelopmental disorders (SNORD114-10, SUSd1), motivation, addiction and motor disorders (CHRNA6), long-term depression (RAB3B), stress response, major depression and schizophrenia (GFAP), signal transduction at the neurovascular unit (NEXN) and inhibitory neurotransmission in spatial learning, neural plasticity (CALB2; CLIC6, ENPP1). Some of the differentially expressed genes were brain specific non-coding RNAs involved in the regulation of translation (SNORA13). One, (PARM1) is a potential oncogene and prognostic biomarker for colorectal cancer with no known function in the brain. Disturbed gene expression involved in antigen neutralization, autoimmunity, neural plasticity, stress response, signal transduction at the neurovascular unit, dysregulated nuclear RNA processing and translation and epigenetic imprinting signatures is associated with suicide and point to regulatory non-coding RNAs as potential targets of new drugs development.
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Affiliation(s)
- Daniela Glavan
- Department of Psychiatry, University of Medicine and Pharmacy, Craiova, Romania
| | - Victor Gheorman
- Department of Psychiatry, University of Medicine and Pharmacy, Craiova, Romania
| | - Andrei Gresita
- Griffith University Menzies Health Institute of Queensland, Gold Coast Campus, Brisbane, QLD, 4000, Australia
| | - Dirk M Hermann
- Chair of Vascular Neurology, Dementia and Ageing Research, Department of Neurology, University Hospital Essen, University of Duisburg, Essen, Germany
| | - Ion Udristoiu
- Department of Psychiatry, University of Medicine and Pharmacy, Craiova, Romania.
| | - Aurel Popa-Wagner
- Griffith University Menzies Health Institute of Queensland, Gold Coast Campus, Brisbane, QLD, 4000, Australia. .,Chair of Vascular Neurology, Dementia and Ageing Research, Department of Neurology, University Hospital Essen, University of Duisburg, Essen, Germany.
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20
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Li Y, Nieuwenhuis LM, Voskuil MD, Gacesa R, Hu S, Jansen BH, Venema WTU, Hepkema BG, Blokzijl H, Verkade HJ, Lisman T, Weersma RK, Porte RJ, Festen EAM, de Meijer VE. Donor genetic variants as risk factors for thrombosis after liver transplantation: A genome-wide association study. Am J Transplant 2021; 21:3133-3147. [PMID: 33445220 PMCID: PMC8518362 DOI: 10.1111/ajt.16490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 01/25/2023]
Abstract
Thrombosis after liver transplantation substantially impairs graft- and patient survival. Inevitably, heritable disorders of coagulation originating in the donor liver are transmitted by transplantation. We hypothesized that genetic variants in donor thrombophilia genes are associated with increased risk of posttransplant thrombosis. We genotyped 775 donors for adult recipients and 310 donors for pediatric recipients transplanted between 1993 and 2018. We determined the association between known donor thrombophilia gene variants and recipient posttransplant thrombosis. In addition, we performed a genome-wide association study (GWAS) and meta-analyzed 1085 liver transplantations. In our donor cohort, known thrombosis risk loci were not associated with posttransplant thrombosis, suggesting that it is unnecessary to exclude liver donors based on thrombosis-susceptible polymorphisms. By performing a meta-GWAS from children and adults, we identified 280 variants in 55 loci at suggestive genetic significance threshold. Downstream prioritization strategies identified biologically plausible candidate genes, among which were AK4 (rs11208611-T, p = 4.22 × 10-05 ) which encodes a protein that regulates cellular ATP levels and concurrent activation of AMPK and mTOR, and RGS5 (rs10917696-C, p = 2.62 × 10-05 ) which is involved in vascular development. We provide evidence that common genetic variants in the donor, but not previously known thrombophilia-related variants, are associated with increased risk of thrombosis after liver transplantation.
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Affiliation(s)
- Yanni Li
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands,Department of GeneticsUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Lianne M. Nieuwenhuis
- Department of SurgerySection of Hepatobiliary Surgery and Liver TransplantationUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Michiel D. Voskuil
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Shixian Hu
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Bernadien H. Jansen
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Werna T. U. Venema
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Bouke G. Hepkema
- Department of Laboratory MedicineUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Hans Blokzijl
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Henkjan J. Verkade
- Department of Pediatric Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Ton Lisman
- Department of SurgerySection of Hepatobiliary Surgery and Liver TransplantationUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Robert J. Porte
- Department of SurgerySection of Hepatobiliary Surgery and Liver TransplantationUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Eleonora A. M. Festen
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands,Department of GeneticsUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Vincent E. de Meijer
- Department of SurgerySection of Hepatobiliary Surgery and Liver TransplantationUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
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21
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Kobayashi T, Morishita E, Tsuda H, Neki R, Kojima T, Ohga S, Ochiai M, Adachi T, Miyata T. Clinical guidance for peripartum management of patients with hereditary thrombophilia. J Obstet Gynaecol Res 2021; 47:3008-3033. [PMID: 34169611 DOI: 10.1111/jog.14879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/13/2021] [Accepted: 05/29/2021] [Indexed: 12/24/2022]
Abstract
Hereditary thrombophilia is a condition in which individuals are susceptible to the formation of thrombi due to a hereditary deficiency in anticoagulant factors, antithrombin (AT), protein C (PC), or protein S (PS). Many Japanese thrombophilia patients have PS deficiency, especially PS p.K196E (also called as PS Tokushima), which is exclusive to the Japanese population, and thrombosis sometimes occurs during pregnancy. At present, no management guidelines for pregnancy and delivery in thrombophilia patients have been developed. The Study Group for Hereditary Thrombophilia, one of the research groups of blood coagulation abnormalities in the Research Program on Rare and Intractable Diseases supported with the Research Grants of the Ministry of Health, Labour and Welfare Science, has therefore developed this clinical guidance to provide healthcare workers with necessary information on safe pregnancy, parturition and neonatal management, adopting a format of responses to seven clinical questions (CQ). At the end of each answer, the corresponding Recommendation Level (A, B, C) is indicated.
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Affiliation(s)
- Takao Kobayashi
- Department of Obstetrics and Gynecology, Hamamatsu Medical Center, Hamamatsu, Japan.,The Study Group for Hereditary Thrombophilia, Research on Blood Coagulation Abnormalities, Research Program on Rare and Intractable Diseases, The Ministry of Health, Labour and Welfare Science Research Grants, Tokyo, Japan
| | - Eriko Morishita
- The Study Group for Hereditary Thrombophilia, Research on Blood Coagulation Abnormalities, Research Program on Rare and Intractable Diseases, The Ministry of Health, Labour and Welfare Science Research Grants, Tokyo, Japan.,Department of Laboratory Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroko Tsuda
- The Study Group for Hereditary Thrombophilia, Research on Blood Coagulation Abnormalities, Research Program on Rare and Intractable Diseases, The Ministry of Health, Labour and Welfare Science Research Grants, Tokyo, Japan.,Institute of Distribution Sciences, Nakamura Gakuen University, Fukuoka, Japan
| | - Reiko Neki
- The Study Group for Hereditary Thrombophilia, Research on Blood Coagulation Abnormalities, Research Program on Rare and Intractable Diseases, The Ministry of Health, Labour and Welfare Science Research Grants, Tokyo, Japan.,Division of Counseling for Medical Genetics, Department of Obstetrics and Gynecology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Tetsuhito Kojima
- The Study Group for Hereditary Thrombophilia, Research on Blood Coagulation Abnormalities, Research Program on Rare and Intractable Diseases, The Ministry of Health, Labour and Welfare Science Research Grants, Tokyo, Japan.,Medical Division, Aichi Health Promotion Foundation, Nagoya, Japan
| | - Shouichi Ohga
- The Study Group for Hereditary Thrombophilia, Research on Blood Coagulation Abnormalities, Research Program on Rare and Intractable Diseases, The Ministry of Health, Labour and Welfare Science Research Grants, Tokyo, Japan.,Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masayuki Ochiai
- The Study Group for Hereditary Thrombophilia, Research on Blood Coagulation Abnormalities, Research Program on Rare and Intractable Diseases, The Ministry of Health, Labour and Welfare Science Research Grants, Tokyo, Japan.,Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoko Adachi
- Department of Obstetrics and Gynecology, Aiiku Maternal and Child Health Center, Aiiku Hospital, Tokyo, Japan
| | - Toshiyuki Miyata
- The Study Group for Hereditary Thrombophilia, Research on Blood Coagulation Abnormalities, Research Program on Rare and Intractable Diseases, The Ministry of Health, Labour and Welfare Science Research Grants, Tokyo, Japan.,Department of Cerebrovascular Medicine, National Cerebral and Cardiovascular Center, Suita, Japan
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22
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Cis-Segregation of c.1171C>T Stop Codon (p.R391*) in SERPINC1 Gene and c.1691G>A Transition (p.R506Q) in F5 Gene and Selected GWAS Multilocus Approach in Inherited Thrombophilia. Genes (Basel) 2021; 12:genes12060934. [PMID: 34207366 PMCID: PMC8234447 DOI: 10.3390/genes12060934] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/21/2022] Open
Abstract
Inherited thrombophilia (e.g., venous thromboembolism, VTE) is due to rare loss-of-function mutations in anticoagulant factors genes (i.e., SERPINC1, PROC, PROS1), common gain-of-function mutations in procoagulant factors genes (i.e., F5, F2), and acquired risk conditions. Genome Wide Association Studies (GWAS) recently recognized several genes associated with VTE though gene defects may unpredictably remain asymptomatic, so calculating the individual genetic predisposition is a challenging task. We investigated a large family with severe, recurrent, early-onset VTE in which two sisters experienced VTE during pregnancies characterized by a perinatal in-utero thrombosis in the newborn and a life-saving pregnancy-interruption because of massive VTE, respectively. A nonsense mutation (CGA > TGA) generating a premature stop-codon (c.1171C>T; p.R391*) in the exon 6 of SERPINC1 gene (1q25.1) causing Antithrombin (AT) deficiency and the common missense mutation (c.1691G>A; p.R506Q) in the exon 10 of F5 gene (1q24.2) (i.e., FV Leiden; rs6025) were coinherited in all the symptomatic members investigated suspecting a cis-segregation further confirmed by STR-linkage-analyses [i.e., SERPINC1 IVS5 (ATT)5–18, F5 IVS2 (AT)6–33 and F5 IVS11 (GT)12–16] and SERPINC1 intragenic variants (i.e., rs5878 and rs677). A multilocus investigation of blood-coagulation balance genes detected the coexistence of FV Leiden (rs6025) in trans with FV HR2-haplotype (p.H1299R; rs1800595) in the aborted fetus, and F11 rs2289252, F12 rs1801020, F13A1 rs5985, and KNG1 rs710446 in the newborn and other members. Common selected gene variants may strongly synergize with less common mutations tuning potential life-threatening conditions when combined with rare severest mutations. Merging classic and newly GWAS-identified gene markers in at risk families is mandatory for VTE risk estimation in the clinical practice, avoiding partial risk score evaluation in unrecognized at risk patients.
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23
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Abstract
Venous disease is a term that broadly covers both venous thromboembolic disease and chronic venous disease. The basic pathophysiology of venous thromboembolism and chronic venous disease differ as venous thromboembolism results from an imbalance of hemostasis and thrombosis while chronic venous disease occurs in the setting of tissue damage because of prolonged venous hypertension. Both diseases are common and account for significant mortality and morbidity, respectively, and collectively make up a large health care burden. Despite both diseases having well-characterized environmental components, it has been known for decades that family history is an important risk factor, implicating a genetic element to a patient's risk. Our understanding of the pathogenesis of these diseases has greatly benefited from an expansion of population genetic studies from pioneering familial studies to large genome-wide association studies; we now have multiple risk loci for each venous disease. In this review, we will highlight the current state of knowledge on the epidemiology and genetics of venous thromboembolism and chronic venous disease and directions for future research.
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Affiliation(s)
- Richard A. Baylis
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, CA
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, Seattle WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle WA 98108, USA
| | - Derek Klarin
- Division of Vascular Surgery, University of Florida College of Medicine, Gainesville, FL
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eri Fukaya
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, CA
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24
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Ooi BNS, Raechell, Ying AF, Koh YZ, Jin Y, Yee SWL, Lee JHS, Chong SS, Tan JWC, Liu J, Lee CG, Drum CL. Robust Performance of Potentially Functional SNPs in Machine Learning Models for the Prediction of Atorvastatin-Induced Myalgia. Front Pharmacol 2021; 12:605764. [PMID: 33967749 PMCID: PMC8100589 DOI: 10.3389/fphar.2021.605764] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Statins can cause muscle symptoms resulting in poor adherence to therapy and increased cardiovascular risk. We hypothesize that combinations of potentially functional SNPs (pfSNPs), rather than individual SNPs, better predict myalgia in patients on atorvastatin. This study assesses the value of potentially functional single nucleotide polymorphisms (pfSNPs) and employs six machine learning algorithms to identify the combination of SNPs that best predict myalgia. Methods: Whole genome sequencing of 183 Chinese, Malay and Indian patients from Singapore was conducted to identify genetic variants associated with atorvastatin induced myalgia. To adjust for confounding factors, demographic and clinical characteristics were also examined for their association with myalgia. The top factor, sex, was then used as a covariate in the whole genome association analyses. Variants that were highly associated with myalgia from this and previous studies were extracted, assessed for potential functionality (pfSNPs) and incorporated into six machine learning models. Predictive performance of a combination of different models and inputs were compared using the average cross validation area under ROC curve (AUC). The minimum combination of SNPs to achieve maximum sensitivity and specificity as determined by AUC, that predict atorvastatin-induced myalgia in most, if not all the six machine learning models was determined. Results: Through whole genome association analyses using sex as a covariate, a larger proportion of pfSNPs compared to non-pf SNPs were found to be highly associated with myalgia. Although none of the individual SNPs achieved genome wide significance in univariate analyses, machine learning models identified a combination of 15 SNPs that predict myalgia with good predictive performance (AUC >0.9). SNPs within genes identified in this study significantly outperformed SNPs within genes previously reported to be associated with myalgia. pfSNPs were found to be more robust in predicting myalgia, outperforming non-pf SNPs in the majority of machine learning models tested. Conclusion: Combinations of pfSNPs that were consistently identified by different machine learning models to have high predictive performance have good potential to be clinically useful for predicting atorvastatin-induced myalgia once validated against an independent cohort of patients.
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Affiliation(s)
- Brandon N S Ooi
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore
| | - Raechell
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore
| | | | - Yong Zher Koh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore
| | - Yu Jin
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Sherman W L Yee
- Department of Medicine, Yong Loo Lin School of Medicine, Cardiovascular Research Institute, National University of Singapore, Singapore, Singapore
| | | | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jack W C Tan
- Department of Cardiology, National Heart Centre Singapore, Singapore, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore, Singapore, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore.,Duke-NUS Graduate School, Singapore, Singapore.,Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Chester L Drum
- Department of Medicine, Yong Loo Lin School of Medicine, Cardiovascular Research Institute, National University of Singapore, Singapore, Singapore.,Translational Laboratory in Genetic Medicine, Singapore, Singapore
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25
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Abreu SC, Tavares V, Carneiro F, Medeiros R. Venous thromboembolism and prostate cancer: what about genetic markers? Pharmacogenomics 2021; 22:365-373. [PMID: 33749329 DOI: 10.2217/pgs-2020-0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim & methods: To review the existing literature concerning the relationship between venous thromboembolism (VTE) and prostate cancer (PC) and explore the putative biological and clinical implications of VTE genetic markers on PC patients by screening the PubMed database. Results: Considering the roles of VTE genome-wide association studies-identified genetic determinants in disease development in the general population, these variants might also underlie the susceptibility for PC-related VTE. Therefore, they could help to identify those with a positive benefit-to-harm ratio for thromboprophylaxis approaches during cancer therapy management, thereby improving patient's prognosis. Conclusion: Future studies are mandatory to explore the relationship between VTE and PC and dissect the predictive value of VTE genome-wide association studies-identified genetic determinants in PC patients, given their clinical implications.
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Affiliation(s)
- Sofia Coelho Abreu
- Oncology Department, Portuguese Institute of Oncology, Porto, 4200 072, Portugal
| | - Valéria Tavares
- Molecular Oncology & Viral Pathology Group, Research Center of Portuguese Institute of Oncology, Porto, 4200 072, Portugal.,Research Department, Portuguese League Against Cancer of Northern Region, Porto, 4200 172, Portugal
| | - Filipa Carneiro
- Oncology Department, Portuguese Institute of Oncology, Porto, 4200 072, Portugal
| | - Rui Medeiros
- Molecular Oncology & Viral Pathology Group, Research Center of Portuguese Institute of Oncology, Porto, 4200 072, Portugal.,Research Department, Portuguese League Against Cancer of Northern Region, Porto, 4200 172, Portugal.,Faculty of Health Sciences, CEBIMED, Fernando Pessoa University, Porto, 4200 150, Portugal
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26
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Cui J, Wang L, Zhong W, Chen Z, Chen J, Yang H, Liu G. Development and Validation of Epigenetic Signature Predict Survival for Patients with Laryngeal Squamous Cell Carcinoma. DNA Cell Biol 2021; 40:247-264. [PMID: 33481663 DOI: 10.1089/dna.2020.5789] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Establishing epigenetic signature to improve the accuracy of survival prediction and optimize therapeutic strategies for laryngeal squamous cell carcinoma (LSCC) by a genome-wide integrated analysis of methylation and the transcriptome. LSCC DNA methylation datasets and RNA sequencing datasets were acquired from the Cancer Genome Atlas (TCGA). MethylMix was applied to detect DNA methylation-driven genes (MDGs), which developed an epigenetic signature. The predictive accuracy and clinical value of the epigenetic signature were evaluated by receiver operating characteristic and decision curve analysis, and compared with tumor-node-metastasis (TNM) stage system. In addition, prognostic value of the epigenetic signature was validated by external Gene Expression Omnibus (GEO) database. According to five MDGs of epigenetic signature, the candidate small molecules for LSCC were screen out by the CMap database. A total of 88 DNA MDGs were identified, five of which (MAGEB2, SUSD1, ZNF382, ZNF418, and ZNF732) were chosen to construct an epigenetic signature. The epigenetic signature can effectively divide patients into high-risk and low-risk group, with the area under curve (AUC) of 0.8 (5-year overall survival [OS]) and AUC of 0.745 (3-year OS). Stratification analysis affirmed that the epigenetic signature was still a significant statistical prognostic model in subsets of patients with different clinical variables. Multivariate Cox regression analysis indicated that the efficacy of epigenetic signature appears independent of other clinicopathological characteristics. In terms of predictive capacity and clinical usefulness, the epigenetic signature was superior to traditional TNM stage. In addition, the epigenetic signature was confirmed in external LSCC cohorts from GEO. Finally, CMap matched the 10 most significant small molecules as promising therapeutic drugs to reverse the LSCC gene expression. An epigenetic signature, with five DNA MDGs, was identified and validated in LSCC patients by integrating multidimensional genomic data, which may offer novel research directions and prospects for individualized treatment of patients with LSCC.
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Affiliation(s)
- Jie Cui
- Department of Head and Neck Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, PR China
| | - Liping Wang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou, PR China
| | - Waisheng Zhong
- Department of Head Neck Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China
| | - Zhen Chen
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, PR China
| | - Jie Chen
- Department of Head Neck Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China
| | - Hong Yang
- Department of Head and Neck Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, PR China
| | - Genglong Liu
- Department of Pathology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, PR China
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27
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Zietz M, Zucker J, Tatonetti NP. Associations between blood type and COVID-19 infection, intubation, and death. Nat Commun 2020; 11:5761. [PMID: 33188185 PMCID: PMC7666188 DOI: 10.1038/s41467-020-19623-x] [Citation(s) in RCA: 219] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/16/2020] [Indexed: 01/06/2023] Open
Abstract
The rapid global spread of the novel coronavirus SARS-CoV-2 has strained healthcare and testing resources, making the identification and prioritization of individuals most at-risk a critical challenge. Recent evidence suggests blood type may affect risk of severe COVID-19. Here, we use observational healthcare data on 14,112 individuals tested for SARS-CoV-2 with known blood type in the New York Presbyterian (NYP) hospital system to assess the association between ABO and Rh blood types and infection, intubation, and death. We find slightly increased infection prevalence among non-O types. Risk of intubation was decreased among A and increased among AB and B types, compared with type O, while risk of death was increased for type AB and decreased for types A and B. We estimate Rh-negative blood type to have a protective effect for all three outcomes. Our results add to the growing body of evidence suggesting blood type may play a role in COVID-19. Recent evidence has suggested that blood type may be associated with severe COVID-19. Here, the authors use data from ~14,000 individuals tested for SARS-CoV-2 at a New York City hospital, and find that certain ABO and Rh blood types are associated with infection, intubation, and death.
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Affiliation(s)
- Michael Zietz
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jason Zucker
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA. .,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA. .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA. .,Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.
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Skille H, Paulsen B, Hveem K, Gabrielsen ME, Brumpton B, Hindberg K, Gran OV, Rosendaal FR, Braekkan SK, Hansen JB. Combined effects of five prothrombotic genotypes and cancer on the risk of a first venous thromboembolic event. J Thromb Haemost 2020; 18:2861-2869. [PMID: 32671915 DOI: 10.1111/jth.15011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/08/2020] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND The role of combined prothrombotic genotypes in cancer-related venous thromboembolism (VTE) is scarcely studied. We aimed to investigate the impact of a 5-single nucleotide polymorphism (SNP) score on the risk of VTE in patients with and without cancer using a population-based case-cohort. METHODS Cases with a first VTE (n = 1493) and a subcohort (n = 13 072) were derived from the Tromsø Study (1994-2012) and the Nord-Trøndelag Health Study (1995-2008). Five SNPs previously reported as a risk score were genotyped: ABO (rs8176719), F5 (rs6025), F2 (rs1799963), FGG (rs2066865), and F11 (rs2036914). Hazard ratios (HRs) for VTE were estimated according to cancer status and the number of risk alleles in the 5-SNP score (0-1, 2-3, and ≥4 alleles). RESULTS During a median follow-up of 12.3 years, 1496 individuals were diagnosed with cancer, of whom 232 experienced VTE. The VTE risk increased with the number of risk alleles in the 5-SNP score among subjects without and with cancer. In cancer-free subjects, the HR was 2.17 (95% confidence interval [CI] 1.79-2.62) for ≥4 versus 0-1 risk alleles. In cancer patients, the corresponding HR was 1.93 (95% CI 1.28-2.91). The combination of cancer and ≥4 risk alleles yielded a 17-fold (HR 17.1, 95% CI 12.5-23.4) higher risk of VTE compared with cancer-free subjects with 0-1 risk alleles. CONCLUSION The risk of VTE increases with the number of prothrombotic risk alleles in subjects with and without cancer, and the combination of prothrombotic risk alleles and cancer leads to a highly elevated risk of VTE.
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Affiliation(s)
- Hanne Skille
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Benedikte Paulsen
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
| | - Ben Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
| | - Kristian Hindberg
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Olga V Gran
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Frits R Rosendaal
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT-The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sigrid K Braekkan
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT-The Arctic University of Norway, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - John-Bjarne Hansen
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT-The Arctic University of Norway, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
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Meißner L, Schürmann P, Dörk T, Hagemeier L, Klintschar M. Genetic association study of fatal pulmonary embolism. Int J Legal Med 2020; 135:143-151. [PMID: 33128086 PMCID: PMC7782449 DOI: 10.1007/s00414-020-02441-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/07/2020] [Indexed: 01/10/2023]
Abstract
Pulmonary embolism (PE) is a complex multi-factorial disease and represents one manifestation of venous thromboembolism (VTE). Most commonly PE constitutes a complication of VTE’s other clinical presentation deep vein thrombosis (DVT). The majority of studies concerning risk factors do not distinguish between PE and DVT. The risk factors are often estimated to be alike, but the prevalence and the risk associated with the major genetic factor Factor V Leiden differ between the two disease states. We have investigated the association of 22 SNPs with PE in 185 PE case and 375 healthy control subjects. At p = 0.05, eight SNPs presented with nominally significant evidence of association (EOA), although no significantly different genotype distributions remained between cases and controls after Bonferroni correction. Three of these variants (rs1800790, rs3813948, rs6025) showed EOA in the main analysis, and five variants (rs169713, rs1801131, rs4524, rs5985 and rs8176592) demonstrated EOAs in subgroups. Genomic variation modulating Factor V, Factor XIII, Beta fibrinogen (FGB), TFPI or HIVEP1 should be worth to be followed in subsequent studies. The findings of this study support the view that PE represents a complex disease with many factors contributing relatively small effects. Larger sample sizes will be required to reliably detect these small effects.
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Affiliation(s)
- Lisa Meißner
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany
| | - Peter Schürmann
- Gynaecology Research Unit, Department of Obstetrics and Gynaecology, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany
| | - Thilo Dörk
- Gynaecology Research Unit, Department of Obstetrics and Gynaecology, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany
| | - Lars Hagemeier
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany
| | - Michael Klintschar
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany.
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Zietz M, Zucker J, Tatonetti NP. Testing the association between blood type and COVID-19 infection, intubation, and death. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.04.08.20058073. [PMID: 32511586 PMCID: PMC7276013 DOI: 10.1101/2020.04.08.20058073] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The rapid global spread of the novel coronavirus SARS-CoV-2 has strained healthcare and testing resources, making the identification and prioritization of individuals most at-risk a critical challenge. Recent evidence suggests blood type may affect risk of severe COVID-19. We used observational healthcare data on 14,112 individuals tested for SARS-CoV-2 with known blood type in the New York Presbyterian (NYP) hospital system to assess the association between ABO and Rh blood types and infection, intubation, and death. We found slightly increased infection prevalence among non-O types. Risk of intubation was decreased among A and increased among AB and B types, compared with type O, while risk of death was increased for type AB and decreased for types A and B. We estimated Rh-negative blood type to have a protective effect for all three outcomes. Our results add to the growing body of evidence suggesting blood type may play a role in COVID-19.
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Affiliation(s)
- Michael Zietz
- Department of Biomedical Informatics, Columbia University Irving Medical Center
| | - Jason Zucker
- Department of Medicine, Columbia University Irving Medical Center
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Desch KC, Ozel AB, Halvorsen M, Jacobi PM, Golden K, Underwood M, Germain M, Tregouet DA, Reitsma PH, Kearon C, Mokry L, Richards JB, Williams F, Li JZ, Goldstein D, Ginsburg D. Whole-exome sequencing identifies rare variants in STAB2 associated with venous thromboembolic disease. Blood 2020; 136:533-541. [PMID: 32457982 PMCID: PMC7393257 DOI: 10.1182/blood.2019004161] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/12/2020] [Indexed: 12/13/2022] Open
Abstract
Deep vein thrombosis and pulmonary embolism, collectively defined as venous thromboembolism (VTE), are the third leading cause of cardiovascular death in the United States. Common genetic variants conferring increased varying degrees of VTE risk have been identified by genome-wide association studies (GWAS). Rare mutations in the anticoagulant genes PROC, PROS1 and SERPINC1 result in perinatal lethal thrombosis in homozygotes and markedly increased VTE risk in heterozygotes. However, currently described VTE variants account for an insufficient portion of risk to be routinely used for clinical decision making. To identify new rare VTE risk variants, we performed a whole-exome study of 393 individuals with unprovoked VTE and 6114 controls. This study identified 4 genes harboring an excess number of rare damaging variants in patients with VTE: PROS1, STAB2, PROC, and SERPINC1. At STAB2, 7.8% of VTE cases and 2.4% of controls had a qualifying rare variant. In cell culture, VTE-associated variants of STAB2 had a reduced surface expression compared with reference STAB2. Common variants in STAB2 have been previously associated with plasma von Willebrand factor and coagulation factor VIII levels in GWAS, suggesting that haploinsufficiency of stabilin-2 may increase VTE risk through elevated levels of these procoagulants. In an independent cohort, we found higher von Willebrand factor levels and equivalent propeptide levels in individuals with rare STAB2 variants compared with controls. Taken together, this study demonstrates the utility of gene-based collapsing analyses to identify loci harboring an excess of rare variants with functional connections to a complex thrombotic disease.
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Affiliation(s)
| | - Ayse B Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Matt Halvorsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Marine Germain
- INSERM UMR_S 1219, Bordeaux Population Health Research Center, University of Bordeaux, Bordeaux, France
| | - David-Alexandre Tregouet
- INSERM UMR_S 1219, Bordeaux Population Health Research Center, University of Bordeaux, Bordeaux, France
| | - Pieter H Reitsma
- Einthoven Laboratory for Experimental Vascular and Regenerative Medicine, Leiden, The Netherlands
| | - Clive Kearon
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Lauren Mokry
- Department of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montreal, QC, Canada
| | - J Brent Richards
- Department of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montreal, QC, Canada
| | - Frances Williams
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, United Kingdom
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - David Goldstein
- Columbia University, Institute for Genomic Medicine, New York, NY; and
| | - David Ginsburg
- Department of Pediatrics and
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI
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Predicting the Risk of Recurrent Venous Thromboembolism: Current Challenges and Future Opportunities. J Clin Med 2020; 9:jcm9051582. [PMID: 32456008 PMCID: PMC7290951 DOI: 10.3390/jcm9051582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 05/19/2020] [Indexed: 12/11/2022] Open
Abstract
Acute venous thromboembolism (VTE) is a commonly diagnosed condition and requires treatment with anticoagulation to reduce the risk of embolisation as well as recurrent venous thrombotic events. In many cases, cessation of anticoagulation is associated with an unacceptably high risk of recurrent VTE, precipitating the use of indefinite anticoagulation. In contrast, however, continuing anticoagulation is associated with increased major bleeding events. As a consequence, it is essential to accurately predict the subgroup of patients who have the highest probability of experiencing recurrent VTE, so that treatment can be appropriately tailored to each individual. To this end, the development of clinical prediction models has aided in calculating the risk of recurrent thrombotic events; however, there are several limitations with regards to routine use for all patients with acute VTE. More recently, focus has shifted towards the utility of novel biomarkers in the understanding of disease pathogenesis as well as their application in predicting recurrent VTE. Below, we review the current strategies used to predict the development of recurrent VTE, with emphasis on the application of several promising novel biomarkers in this field.
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Genomic and transcriptomic association studies identify 16 novel susceptibility loci for venous thromboembolism. Blood 2020; 134:1645-1657. [PMID: 31420334 DOI: 10.1182/blood.2019000435] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 07/17/2019] [Indexed: 12/29/2022] Open
Abstract
Venous thromboembolism (VTE) is a significant contributor to morbidity and mortality. To advance our understanding of the biology contributing to VTE, we conducted a genome-wide association study (GWAS) of VTE and a transcriptome-wide association study (TWAS) based on imputed gene expression from whole blood and liver. We meta-analyzed GWAS data from 18 studies for 30 234 VTE cases and 172 122 controls and assessed the association between 12 923 718 genetic variants and VTE. We generated variant prediction scores of gene expression from whole blood and liver tissue and assessed them for association with VTE. Mendelian randomization analyses were conducted for traits genetically associated with novel VTE loci. We identified 34 independent genetic signals for VTE risk from GWAS meta-analysis, of which 14 are newly reported associations. This included 11 newly associated genetic loci (C1orf198, PLEK, OSMR-AS1, NUGGC/SCARA5, GRK5, MPHOSPH9, ARID4A, PLCG2, SMG6, EIF5A, and STX10) of which 6 replicated, and 3 new independent signals in 3 known genes. Further, TWAS identified 5 additional genetic loci with imputed gene expression levels differing between cases and controls in whole blood (SH2B3, SPSB1, RP11-747H7.3, RP4-737E23.2) and in liver (ERAP1). At some GWAS loci, we found suggestive evidence that the VTE association signal for novel and previously known regions colocalized with expression quantitative trait locus signals. Mendelian randomization analyses suggested that blood traits may contribute to the underlying risk of VTE. To conclude, we identified 16 novel susceptibility loci for VTE; for some loci, the association signals are likely mediated through gene expression of nearby genes.
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Tavares V, Pinto R, Assis J, Pereira D, Medeiros R. Venous thromboembolism GWAS reported genetic makeup and the hallmarks of cancer: Linkage to ovarian tumour behaviour. Biochim Biophys Acta Rev Cancer 2020; 1873:188331. [DOI: 10.1016/j.bbcan.2019.188331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022]
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35
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Pang H, Zong Z, Hao L, Cao Q. ABO blood group influences risk of venous thromboembolism and myocardial infarction. J Thromb Thrombolysis 2019; 50:430-438. [DOI: 10.1007/s11239-019-02012-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Klarin D, Busenkell E, Judy R, Lynch J, Levin M, Haessler J, Aragam K, Chaffin M, Haas M, Lindström S, Assimes TL, Huang J, Min Lee K, Shao Q, Huffman JE, Kabrhel C, Huang Y, Sun YV, Vujkovic M, Saleheen D, Miller DR, Reaven P, DuVall S, Boden WE, Pyarajan S, Reiner AP, Trégouët DA, Henke P, Kooperberg C, Gaziano JM, Concato J, Rader DJ, Cho K, Chang KM, Wilson PWF, Smith NL, O'Donnell CJ, Tsao PS, Kathiresan S, Obi A, Damrauer SM, Natarajan P. Genome-wide association analysis of venous thromboembolism identifies new risk loci and genetic overlap with arterial vascular disease. Nat Genet 2019; 51:1574-1579. [PMID: 31676865 PMCID: PMC6858581 DOI: 10.1038/s41588-019-0519-3] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/24/2019] [Indexed: 12/22/2022]
Abstract
Venous thromboembolism is a significant cause of mortality1, yet its genetic determinants are incompletely defined. We performed a discovery genome-wide association study in the Million Veteran Program and UK Biobank, with testing of approximately 13 million DNA sequence variants for association with venous thromboembolism (26,066 cases and 624,053 controls) and meta-analyzed both studies, followed by independent replication with up to 17,672 venous thromboembolism cases and 167,295 controls. We identified 22 previously unknown loci, bringing the total number of venous thromboembolism-associated loci to 33, and subsequently fine-mapped these associations. We developed a genome-wide polygenic risk score for venous thromboembolism that identifies 5% of the population at an equivalent incident venous thromboembolism risk to carriers of the established factor V Leiden p.R506Q and prothrombin G20210A mutations. Our data provide mechanistic insights into the genetic epidemiology of venous thromboembolism and suggest a greater overlap among venous and arterial cardiovascular disease than previously thought.
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Affiliation(s)
- Derek Klarin
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Vascular Surgery and Endovascular Therapy, University of Florida School of Medicine, Gainesville, FL, USA
| | - Emma Busenkell
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Renae Judy
- Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Julie Lynch
- Veterans Affairs Informatics and Computing Infrastructure, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, UT, USA
- University of Massachusetts College of Nursing & Health Sciences, Boston, MA, USA
| | - Michael Levin
- Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeffery Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Krishna Aragam
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Chaffin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mary Haas
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara Lindström
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Themistocles L Assimes
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jie Huang
- Massachusetts Veterans Epidemiology Research and Information Center, Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Kyung Min Lee
- Veterans Affairs Informatics and Computing Infrastructure, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, UT, USA
- Center for Healthcare Organization and Implementation Research, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, USA
- Boston University School of Public Health, Department of Health Law, Policy & Management, Boston, MA, USA
| | - Qing Shao
- Center for Healthcare Organization and Implementation Research, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, USA
| | - Jennifer E Huffman
- Massachusetts Veterans Epidemiology Research and Information Center, Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Christopher Kabrhel
- Center for Vascular Emergencies, Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yunfeng Huang
- Department of Epidemiology, Emory University Rollins School of Public Health, Department of Biomedical Informatics Emory University School of Medicine, Atlanta, GA, USA
- Atlanta Veterans Affairs Health Care System, Decatur, GA, USA
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Department of Biomedical Informatics Emory University School of Medicine, Atlanta, GA, USA
- Atlanta Veterans Affairs Health Care System, Decatur, GA, USA
| | - Marijana Vujkovic
- Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, Philadelphia, PA, USA
| | - Danish Saleheen
- Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, Philadelphia, PA, USA
| | - Donald R Miller
- Center for Healthcare Organization and Implementation Research, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, USA
- Boston University School of Public Health, Department of Health Law, Policy & Management, Boston, MA, USA
| | - Peter Reaven
- Phoenix Veterans Affairs Health Care System, Phoenix, AZ, USA
| | - Scott DuVall
- Veterans Affairs Informatics and Computing Infrastructure, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, UT, USA
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - William E Boden
- Massachusetts Veterans Epidemiology Research and Information Center, Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Saiju Pyarajan
- Massachusetts Veterans Epidemiology Research and Information Center, Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David-Alexandre Trégouët
- Bordeaux Population Health Research Center (INSERM UMR S 1219), University of Bordeaux, Bordeaux, France
| | - Peter Henke
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center, Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - John Concato
- Clinical Epidemiology Research Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel J Rader
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center, Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kyong-Mi Chang
- Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter W F Wilson
- Atlanta Veterans Affairs Health Care System, Decatur, GA, USA
- Emory Clinical Cardiovascular Research Institute, Atlanta, GA, USA
| | - Nicholas L Smith
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Christopher J O'Donnell
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Massachusetts Veterans Epidemiology Research and Information Center, Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Cardiovascular Medicine Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Philip S Tsao
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sekar Kathiresan
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Verve Therapeutics, Cambridge, MA, USA
| | - Andrea Obi
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Scott M Damrauer
- Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pradeep Natarajan
- Veterans Affairs Boston Healthcare System, Boston, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Wang Y, Bromberg Y. Identifying mutation-driven changes in gene functionality that lead to venous thromboembolism. Hum Mutat 2019; 40:1321-1329. [PMID: 31144782 PMCID: PMC6745089 DOI: 10.1002/humu.23824] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/26/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022]
Abstract
Venous thromboembolism (VTE) is a common hematological disorder. VTE affects millions of people around the world each year and can be fatal. Earlier studies have revealed the possible VTE genetic risk factors in Europeans. The 2018 Critical Assessment of Genome Interpretation (CAGI) challenge had asked participants to distinguish between 66 VTE and 37 non-VTE African American (AA) individuals based on their exome sequencing data. We used variants from AA VTE association studies and VTE genes from DisGeNET database to evaluate VTE risk via four different approaches; two of these methods were most successful at the task. Our best performing method represented each exome as a vector of predicted functional effect scores of variants within the known genes. These exome vectors were then clustered with k-means. This approach achieved 70.8% precision and 69.7% recall in identifying VTE patients. Our second-best ranked method had collapsed the variant effect scores into gene-level function changes, using the same vector clustering approach for patient/control identification. These results show predictability of VTE risk in AA population and highlight the importance of variant-driven gene functional changes in judging disease status. Of course, more in-depth understanding of AA VTE pathogenicity is still needed for more precise predictions.
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Affiliation(s)
- Yanran Wang
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
- Department of Genetics, Rutgers University, New Brunswick, New Jersey
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Katsonis P, Lichtarge O. CAGI5: Objective performance assessments of predictions based on the Evolutionary Action equation. Hum Mutat 2019; 40:1436-1454. [PMID: 31317604 PMCID: PMC6900054 DOI: 10.1002/humu.23873] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/02/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022]
Abstract
Many computational approaches estimate the effect of coding variants, but their predictions often disagree with each other. These contradictions confound users and raise questions regarding reliability. Performance assessments can indicate the expected accuracy for each method and highlight advantages and limitations. The Critical Assessment of Genome Interpretation (CAGI) community aims to organize objective and systematic assessments: They challenge predictors on unpublished experimental and clinical data and assign independent assessors to evaluate the submissions. We participated in CAGI experiments as predictors, using the Evolutionary Action (EA) method to estimate the fitness effect of coding mutations. EA is untrained, uses homology information, and relies on a formal equation: The fitness effect equals the functional sensitivity to residue changes multiplied by the magnitude of the substitution. In previous CAGI experiments (between 2011 and 2016), our submissions aimed to predict the protein activity of single mutants. In 2018 (CAGI5), we also submitted predictions regarding clinical associations, folding stability, and matching genomic data with phenotype. For all these diverse challenges, we used EA to predict the fitness effect of variants, adjusted to specifically address each question. Our submissions had consistently good performance, suggesting that EA predicts reliably the effects of genetic variants.
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Affiliation(s)
- Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas.,Department of Pharmacology, Baylor College of Medicine, Houston, Texas.,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas
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Pujol-Moix N, Martinez-Perez A, Sabater-Lleal M, Llobet D, Vilalta N, Hamsten A, Souto JC, Soria JM. Influence of ABO Locus on PFA-100 Collagen-ADP Closure Time Is Not Totally Dependent on the Von Willebrand Factor. Results of a GWAS on GAIT-2 Project Phenotypes. Int J Mol Sci 2019; 20:ijms20133221. [PMID: 31262040 PMCID: PMC6651679 DOI: 10.3390/ijms20133221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/24/2019] [Accepted: 06/27/2019] [Indexed: 01/05/2023] Open
Abstract
(1) Background: In a previous study, we found that two phenotypes related to platelet reactivity, measured with the PFA-100 system, were highly heritable. The aim of the present study was to identify genetic determinants that influence the variability of these phenotypes: closure time of collagen-ADP (Col-ADP) and of collagen-epinephrine (Col-Epi). (2) Methods: As part of the GAIT-2 (Genetic Analysis of Idiopathic Thrombophilia (2) Project, 935 individuals from 35 large Spanish families were studied. A genome-wide association study (GWAS) with ≈ 10 M single nucleotide polymorphisms (SNPs) was carried out with Col-ADP and Col-Epi phenotypes. (3) Results: The study yielded significant genetic signals that mapped to the ABO locus. After adjusting both phenotypes for the ABO genotype, these signals disappeared. After adjusting for von Willebrand factor (VWF) or for coagulation factor VIII (FVIII), the significant signals disappeared totally for Col-Epi phenotype but only partially for Col-ADP phenotype. (4) Conclusion: Our results suggest that the ABO locus exerts the main genetic influence on PFA-100 phenotypes. However, while the effect of the ABO locus on Col-Epi phenotype is mediated through VWF and/or FVIII, the effect of the ABO locus on Col-ADP phenotype is partly produced through VWF and/or FVIII, and partly through other mechanisms.
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Affiliation(s)
- Núria Pujol-Moix
- Thrombosis and Hemostasis Research Group, Institute of Biomedical Research (IIB-Sant Pau), 08025 Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain
| | - Angel Martinez-Perez
- Unit of Genomics of Complex Diseases, Institute of Biomedical Research (IIB-Sant Pau), 08025 Barcelona, Spain
| | - Maria Sabater-Lleal
- Unit of Genomics of Complex Diseases, Institute of Biomedical Research (IIB-Sant Pau), 08025 Barcelona, Spain
- Cardiovascular Medicine Unit, Department of Medicine, Center of Molecular Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Dolors Llobet
- Thrombosis and Hemostasis Research Group, Institute of Biomedical Research (IIB-Sant Pau), 08025 Barcelona, Spain
- Unit of Hemostasis and Thrombosis, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
| | - Noèlia Vilalta
- Thrombosis and Hemostasis Research Group, Institute of Biomedical Research (IIB-Sant Pau), 08025 Barcelona, Spain
- Unit of Hemostasis and Thrombosis, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
| | - Anders Hamsten
- Cardiovascular Medicine Unit, Department of Medicine, Center of Molecular Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Joan Carles Souto
- Thrombosis and Hemostasis Research Group, Institute of Biomedical Research (IIB-Sant Pau), 08025 Barcelona, Spain.
- Unit of Hemostasis and Thrombosis, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain.
| | - José Manuel Soria
- Unit of Genomics of Complex Diseases, Institute of Biomedical Research (IIB-Sant Pau), 08025 Barcelona, Spain
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Khanshour AM, Kou I, Fan Y, Einarsdottir E, Makki N, Kidane YH, Kere J, Grauers A, Johnson TA, Paria N, Patel C, Singhania R, Kamiya N, Takeda K, Otomo N, Watanabe K, Luk KDK, Cheung KMC, Herring JA, Rios JJ, Ahituv N, Gerdhem P, Gurnett CA, Song YQ, Ikegawa S, Wise CA. Genome-wide meta-analysis and replication studies in multiple ethnicities identify novel adolescent idiopathic scoliosis susceptibility loci. Hum Mol Genet 2019; 27:3986-3998. [PMID: 30395268 DOI: 10.1093/hmg/ddy306] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is the most common musculoskeletal disorder of childhood development. The genetic architecture of AIS is complex, and the great majority of risk factors are undiscovered. To identify new AIS susceptibility loci, we conducted the first genome-wide meta-analysis of AIS genome-wide association studies, including 7956 cases and 88 459 controls from 3 ancestral groups. Three novel loci that surpassed genome-wide significance were uncovered in intragenic regions of the CDH13 (P-value_rs4513093 = 1.7E-15), ABO (P-value_ rs687621 = 7.3E-10) and SOX6 (P-value_rs1455114 = 2.98E-08) genes. Restricting the analysis to females improved the associations at multiple loci, most notably with variants within CDH13 despite the reduction in sample size. Genome-wide gene-functional enrichment analysis identified significant perturbation of pathways involving cartilage and connective tissue development. Expression of both SOX6 and CDH13 was detected in cartilage chondrocytes and chromatin immunoprecipitation sequencing experiments in that tissue revealed multiple HeK27ac-positive peaks overlapping associated loci. Our results further define the genetic architecture of AIS and highlight the importance of vertebral cartilage development in its pathogenesis.
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Affiliation(s)
- Anas M Khanshour
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Ikuyo Kou
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Yanhui Fan
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, University of Helsinki, 00014 University of Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, 00014 University of Helsinki, Finland.,Department of Biosciences & Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Nadja Makki
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yared H Kidane
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Juha Kere
- Folkhälsan Institute of Genetics, University of Helsinki, 00014 University of Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, 00014 University of Helsinki, Finland.,Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK.,Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden
| | - Anna Grauers
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden.,Department of Orthopedics, Sundsvall and Härnösand County Hospital, Sundsvall, Sweden
| | - Todd A Johnson
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Nandina Paria
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Chandreshkumar Patel
- McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Richa Singhania
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | | | - Kazuki Takeda
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Nao Otomo
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kota Watanabe
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Keith D K Luk
- Department of Orthopaedics & Traumatology, The University of Hong Kong, Hong Kong, China
| | - Kenneth M C Cheung
- Department of Orthopaedics & Traumatology, The University of Hong Kong, Hong Kong, China
| | - John A Herring
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan J Rios
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nadav Ahituv
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Gerdhem
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden.,Department of Orthopedics, Karolinska University Hospital, K54 Huddinge, Stockholm, Sweden
| | - Christina A Gurnett
- Department of Neurology, School of Medicine, Washington University, St. Louis, MO, USA
| | - You-Qiang Song
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Shiro Ikegawa
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Carol A Wise
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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41
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Benincasa G, Costa D, Infante T, Lucchese R, Donatelli F, Napoli C. Interplay between genetics and epigenetics in modulating the risk of venous thromboembolism: A new challenge for personalized therapy. Thromb Res 2019; 177:145-153. [DOI: 10.1016/j.thromres.2019.03.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/12/2019] [Accepted: 03/13/2019] [Indexed: 02/09/2023]
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Rohmann JL, de Haan HG, Algra A, Vossen CY, Rosendaal FR, Siegerink B. Genetic determinants of activity and antigen levels of contact system factors. J Thromb Haemost 2019; 17:157-168. [PMID: 30288888 DOI: 10.1111/jth.14307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 09/17/2018] [Indexed: 11/27/2022]
Abstract
Essentials Genetic variation may provide valuable insight into the role of the contact system in thrombosis. Explored associations of genetic variants with activity, antigen, and disease in RATIO study. Two novel loci were identified: KLKB1 rs4253243 for prekallikrein; KNG1 rs5029980 for HMWK levels. Contact system variants and haplotypes were not associated with myocardial infarction or stroke. SUMMARY: Background The complex, interdependent contact activation system has been implicated in thrombotic disease, although few genetic determinants of levels of proteins from this system are known. Objectives Our primary aim was to study the influence of common F11, F12, KLKB1, and KNG1 variants on factor (F) XI activity and FXI, FXII, prekallikrein (PK) and high-molecular-weight kininogen (HMWK) antigen levels, as well as the risk of myocardial infarction and ischemic stroke. Patients/methods We analyzed samples from all 630 healthy participants, 182 ischemic stroke patients and 216 myocardial infarction patients in the RATIO case-control study of women aged < 50 years. Forty-three tagging single nucleotide variants (SNVs) were genotyped to represent common genetic variation in the contact system genes. Antigen and activity levels were measured with sandwich-ELISA-based and one-stage clotting assays. We performed single variant, age-adjusted, linear regression analyses per trait and disease phenotype, assuming additive inheritance and determined conditionally independent associations. Haplotypes based on the lead SNV and all conditionally independent SNVs were tested for association with traits and disease. Results We identified two novel associations of KLKB1 SNV rs4253243 with PK antigen (βconditional = -12.38; 95% CI, -20.07 to -4.69) and KNG1 SNV rs5029980 with HMWK antigen (βconditional = 5.86; 95% CI, 2.40-9.32) and replicated previously reported associations in a single study. Further analyses probed whether the observed associations were indicative of linkage, pleiotropic effects or mediation. No individual SNVs or haplotypes were associated with the disease outcomes. Conclusion This study adds to current knowledge of how genetic variation influences contact system protein levels and clarifies interdependencies.
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Affiliation(s)
- J L Rohmann
- Center for Stroke Research Berlin, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute of Public Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - H G de Haan
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - A Algra
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Neurology and Neurosurgery, Brain Center Rudolph Magnus, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
- Julius Centre for Health Sciences and Primary Care, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - C Y Vossen
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - F R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - B Siegerink
- Center for Stroke Research Berlin, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
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43
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Jiang X, Zeleznik OA, Lindström S, Lasky‐Su J, Hagan K, Clish CB, Eliassen AH, Kraft P, Kabrhel C. Metabolites Associated With the Risk of Incident Venous Thromboembolism: A Metabolomic Analysis. J Am Heart Assoc 2018; 7:e010317. [PMID: 30571496 PMCID: PMC6404443 DOI: 10.1161/jaha.118.010317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Background Venous thromboembolism ( VTE ) is a complex thrombotic disorder that constitutes a major source of mortality and morbidity. To improve understanding of the cause of VTE , we conducted a metabolomic analysis in a case-control study including 240 incident VTE cases and 6963 controls nested within 3 large prospective population-based cohorts, the Nurses' Health Study, the Nurses' Health Study II , and the Health Professionals Follow-Up Study. Methods and Results For each individual, we measured 211 metabolites and collected detailed information on lifestyle factors. We performed logistic regression and enrichment analysis to identify metabolites and biological categories associated with incident VTE risk, accounting for key confounders, such as age, sex, smoking, alcohol consumption, body mass index, and comorbid diseases (eg, cancers). We performed analyses of all VTEs and separate analyses of pulmonary embolism. Using the basic model controlling for age, sex, and primary disease, we identified 60 nominally significant VTE - or pulmonary embolism-associated metabolites ( P<0.05). These metabolites were enriched for diacylglycerols ( Ppermutation<0.05). However, after controlling for multiple testing, only 1 metabolite (C5 carnitine; odds ratio, 1.25; 95% confidence interval, 1.10-1.41; Pcorrected=0.03) remained significantly associated with VTE . After further adjustment for body mass index, no metabolites were significantly associated with disease after accounting for multiple testing, and no metabolite classes were enriched for nominally significant associations. Conclusions Although our findings suggest that circulating metabolites may influence the risk of incident VTE , the associations we observed were confounded by body mass index. Larger studies involving additional individuals and with broader metabolomics coverage are needed to confirm our findings.
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Affiliation(s)
- Xia Jiang
- Program in Genetic Epidemiology and Statistical GeneticsHarvard T.H. Chan School of Public HealthBostonMA
- Unit of Cardiovascular EpidemiologyInstitute of Environmental MedicineKarolinska InstitutetStockholmSweden
| | - Oana A. Zeleznik
- Channing Division of Network MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA
- Department of MedicineHarvard Medical SchoolBostonMA
| | - Sara Lindström
- EpidemiologyUniversity of WashingtonSeattleWA
- Public Health SciencesFred Hutchinson Cancer Research CenterSeattleWA
| | - Jessica Lasky‐Su
- Channing Division of Network MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA
| | - Kaitlin Hagan
- Channing Division of Network MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA
- Department of MedicineHarvard Medical SchoolBostonMA
| | | | | | - Peter Kraft
- Program in Genetic Epidemiology and Statistical GeneticsHarvard T.H. Chan School of Public HealthBostonMA
| | - Christopher Kabrhel
- Channing Division of Network MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA
- Department of Emergency MedicineCenter for Vascular EmergenciesMassachusetts General HospitalBostonMA
- Department of Emergency MedicineHarvard Medical SchoolBostonMA
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Phenome-wide association studies across large population cohorts support drug target validation. Nat Commun 2018; 9:4285. [PMID: 30327483 PMCID: PMC6191429 DOI: 10.1038/s41467-018-06540-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
Phenome-wide association studies (PheWAS) have been proposed as a possible aid in drug development through elucidating mechanisms of action, identifying alternative indications, or predicting adverse drug events (ADEs). Here, we select 25 single nucleotide polymorphisms (SNPs) linked through genome-wide association studies (GWAS) to 19 candidate drug targets for common disease indications. We interrogate these SNPs by PheWAS in four large cohorts with extensive health information (23andMe, UK Biobank, FINRISK, CHOP) for association with 1683 binary endpoints in up to 697,815 individuals and conduct meta-analyses for 145 mapped disease endpoints. Our analyses replicate 75% of known GWAS associations (P < 0.05) and identify nine study-wide significant novel associations (of 71 with FDR < 0.1). We describe associations that may predict ADEs, e.g., acne, high cholesterol, gout, and gallstones with rs738409 (p.I148M) in PNPLA3 and asthma with rs1990760 (p.T946A) in IFIH1. Our results demonstrate PheWAS as a powerful addition to the toolkit for drug discovery. Testing the association between genetic variants and a range of phenotypes can assist drug development. Here, in a phenome-wide association study in up to 697,815 individuals, Diogo et al. identify genotype–phenotype associations predicting efficacy, alternative indications or adverse drug effects.
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45
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Yue Y, Sun Q, Man C, Fu Y. Association of the CYP4V2 polymorphism rs13146272 with venous thromboembolism in a Chinese population. Clin Exp Med 2018; 19:159-166. [PMID: 30276487 PMCID: PMC6394589 DOI: 10.1007/s10238-018-0529-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/22/2018] [Indexed: 12/28/2022]
Abstract
Genome-wide association studies have identified the CYP4V2 polymorphism (rs13146272) as a risk factor associated with venous thromboembolism (VTE). However, due to the small sample size and variance in genetic analysis models, the relationship between VTE and rs13146272 remains unclear. Here, we performed a case-control study to analyse the associations between rs13146272 and VTE in a Chinese population and to compare the differences among various ethnicities. In this study, 226 VTE patients and 205 healthy controls were recruited, and the allele frequency of variant rs13146272 was analysed by a MassARRAY SNP genotyping assay. In addition, 9 case-control cohorts from 5 studies involving 6667 VTE-affected individuals and 8716 control subjects were included in this meta-analysis. Pooled ORs and 95% CIs were calculated to assess the association between rs13146272 and VTE by using different genetic models. Our case-control study results showed that there was no significant association between VTE and rs13146272 under the additive model (OR = 0.92, 95% CIs: 0.70-1.21, p = 0.55) in this Chinese population. However, the results of the meta-analysis performed by merging all cohorts showed that rs13146272 was significantly associated with VTE under the additive model, recessive model and dominant model. In the additive and recessive models, the association reached the threshold for genome-wide significance (p < 5.0e-08). In conclusion, our pooled systematic study results indicated that individuals with the A allele had a higher risk of developing VTE than those with the C allele of the rs13146272 variant, but the risk was inconsistent among different ethnicities. Further validation of this association with larger sample sizes and multiple ethnicities is warranted.
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Affiliation(s)
- Yongjian Yue
- Institute of Shenzhen Respiratory Diseases, Department of Respiratory and Critical Medicine, The Second Clinical Medical College (Shenzhen People's Hospital) of Jinan University, No. 1017 Dongmen North Road, Luohu District, Shenzhen, 518020, Guangdong, China
| | - Qing Sun
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, China
| | - Chiwai Man
- Department of Orthopaedics and Traumatology, Faculty of Medicine, The Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong, HKSAR, China
| | - Yingyun Fu
- Institute of Shenzhen Respiratory Diseases, Department of Respiratory and Critical Medicine, The Second Clinical Medical College (Shenzhen People's Hospital) of Jinan University, No. 1017 Dongmen North Road, Luohu District, Shenzhen, 518020, Guangdong, China.
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Lobach I, Sampson J, Alekseyenko A, Lobach S, Zhang L. Case-control studies of gene-environment interactions. When a case might not be the case. PLoS One 2018; 13:e0201140. [PMID: 30133451 PMCID: PMC6104951 DOI: 10.1371/journal.pone.0201140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/08/2018] [Indexed: 01/01/2023] Open
Abstract
Case-control Genome-Wide Association Studies (GWAS) provide a rich resource for studying the genetic architecture of complex diseases. A key is to elucidate how the genetic effects vary by the environment, what is traditionally defined by Gene-Environment interactions (GxE). The overlooked complication is that multiple, distinct pathophysiologic mechanisms may lead to the same clinical diagnosis and often these mechanisms have distinct genetic bases. In this paper, we first show that using the clinically diagnosed status can lead to severely biased estimates of GxE interactions in situations when the frequency of the pathologic diagnosis of interest, as compared to other diagnoses, depends on the environment. We then propose a pseudo-likelihood solution to correct the bias. Finally, we demonstrate our method in extensive simulations and in a GWAS of Alzheimer's disease.
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Affiliation(s)
- Iryna Lobach
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
| | - Joshua Sampson
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Alexander Alekseyenko
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States of America
| | - Siarhei Lobach
- Applied Mathematics and Computer Science Department, Belarusian State University, Minsk, Belarus
| | - Li Zhang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
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47
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Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nat Genet 2018; 50:1171-1179. [PMID: 30013180 PMCID: PMC6094955 DOI: 10.1038/s41588-018-0160-6] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
Abstract
Key challenges for human genetics, precision medicine and evolutionary biology include deciphering the regulatory code of gene expression and understanding the transcriptional effects of genome variation. However, this is extremely difficult because of the enormous scale of the noncoding mutation space. We developed a deep learning-based framework, ExPecto, that can accurately predict, ab initio from a DNA sequence, the tissue-specific transcriptional effects of mutations, including those that are rare or that have not been observed. We prioritized causal variants within disease- or trait-associated loci from all publicly available genome-wide association studies and experimentally validated predictions for four immune-related diseases. By exploiting the scalability of ExPecto, we characterized the regulatory mutation space for human RNA polymerase II-transcribed genes by in silico saturation mutagenesis and profiled > 140 million promoter-proximal mutations. This enables probing of evolutionary constraints on gene expression and ab initio prediction of mutation disease effects, making ExPecto an end-to-end computational framework for the in silico prediction of expression and disease risk.
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Affiliation(s)
- Jian Zhou
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Chandra L Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kevin Yao
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | | | - Aaron K Wong
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Olga G Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Flatiron Institute, Simons Foundation, New York, NY, USA.
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
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48
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Gran OV, Brækkan SK, Hansen JB. Prothrombotic genotypes and risk of venous thromboembolism in cancer. Thromb Res 2018; 164 Suppl 1:S12-S18. [DOI: 10.1016/j.thromres.2017.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/29/2017] [Indexed: 12/21/2022]
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49
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Allyn-Feuer A, Ade A, Luzum JA, Higgins GA, Athey BD. The pharmacoepigenomics informatics pipeline defines a pathway of novel and known warfarin pharmacogenomics variants. Pharmacogenomics 2018; 19:413-434. [PMID: 29400612 PMCID: PMC6021929 DOI: 10.2217/pgs-2017-0186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/16/2018] [Indexed: 12/21/2022] Open
Abstract
AIM 'Pharmacoepigenomics' methods informed by omics datasets and pre-existing knowledge have yielded discoveries in neuropsychiatric pharmacogenomics. Now we evaluate the generality of these methods by discovering an extended warfarin pharmacogenomics pathway. MATERIALS & METHODS We developed the pharmacoepigenomics informatics pipeline, a scalable multi-omics variant screening pipeline for pharmacogenomics, and conducted an experiment in the genomics of warfarin. RESULTS We discovered known and novel pharmacogenomics variants and genes, both coding and regulatory, for warfarin response, including adverse events. Such genes and variants cluster in a warfarin response pathway consolidating known and novel warfarin response variants and genes. CONCLUSION These results can inform a new warfarin test. The pharmacoepigenomics informatics pipeline may be able to discover new pharmacogenomics markers in other drug-disease systems.
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Affiliation(s)
- Ari Allyn-Feuer
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alex Ade
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jasmine A Luzum
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gerald A Higgins
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brian D Athey
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI 48109, USA
- Department of Psychiatry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Michigan Institute for Data Science, University of Michigan Office of Research, Ann Arbor, MI 48109, USA
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50
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Steri M, Idda ML, Whalen MB, Orrù V. Genetic variants in mRNA untranslated regions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1474. [PMID: 29582564 DOI: 10.1002/wrna.1474] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/05/2018] [Accepted: 02/11/2018] [Indexed: 12/24/2022]
Abstract
Genome Wide Association Studies (GWAS) have mapped thousands of genetic variants associated with complex disease risk and regulating quantitative traits, thus exploiting an unprecedented high-resolution genetic characterization of the human genome. A small fraction (3.7%) of the identified associations is located in untranslated regions (UTRs), and the molecular mechanism has been elucidated for few of them. Genetic variations at UTRs may modify regulatory elements affecting the interaction of the UTRs with proteins and microRNAs. The overall functional consequences include modulation of messenger RNA (mRNA) transcription, secondary structure, stability, localization, translation, and access to regulators like microRNAs (miRNAs) and RNA-binding proteins (RBPs). Alterations of these regulatory mechanisms are known to modify molecular pathways and cellular processes, potentially leading to disease processes. Here, we analyze some examples of genetic risk variants mapping in the UTR regulatory elements. We describe a recently identified genetic variant localized in the 3'UTR of the TNFSF13B gene, associated with autoimmunity risk and responsible of an increased stability and translation of TNFSF13B mRNA. We discuss how the correct use and interpretation of public GWAS repositories could lead to a better understanding of etiopathogenetic mechanisms and the generation of robust biological hypothesis as starting point for further functional studies. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Evolution and Genomics > Computational Analyses of RNA RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - M Laura Idda
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institute of Health, Baltimore, Maryland
| | - Michael B Whalen
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Trento, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
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