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Schwarzerova J, Hurta M, Barton V, Lexa M, Walther D, Provaznik V, Weckwerth W. A perspective on genetic and polygenic risk scores-advances and limitations and overview of associated tools. Brief Bioinform 2024; 25:bbae240. [PMID: 38770718 PMCID: PMC11106636 DOI: 10.1093/bib/bbae240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 04/14/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Polygenetic Risk Scores are used to evaluate an individual's vulnerability to developing specific diseases or conditions based on their genetic composition, by taking into account numerous genetic variations. This article provides an overview of the concept of Polygenic Risk Scores (PRS). We elucidate the historical advancements of PRS, their advantages and shortcomings in comparison with other predictive methods, and discuss their conceptual limitations in light of the complexity of biological systems. Furthermore, we provide a survey of published tools for computing PRS and associated resources. The various tools and software packages are categorized based on their technical utility for users or prospective developers. Understanding the array of available tools and their limitations is crucial for accurately assessing and predicting disease risks, facilitating early interventions, and guiding personalized healthcare decisions. Additionally, we also identify potential new avenues for future bioinformatic analyzes and advancements related to PRS.
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Affiliation(s)
- Jana Schwarzerova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 10, Brno 61600, Czechia
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna 1010, Austria
| | - Martin Hurta
- Department of Computer Systems, Faculty of Information Technology, Brno University of Technology, Brno 612 00, Czechia
| | - Vojtech Barton
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 10, Brno 61600, Czechia
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno 62500, Czech Republic
| | - Matej Lexa
- Faculty of Informatics, Masaryk University, Botanicka 68a, Brno 60200, Czech Republic
| | - Dirk Walther
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Valentine Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 10, Brno 61600, Czechia
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna 1010, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna 1010, Austria
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2
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Malinowski D, Safranow K, Pawlik A. LPL rs264, PROCR rs867186 and PDGF rs974819 Gene Polymorphisms in Patients with Unstable Angina. J Pers Med 2024; 14:213. [PMID: 38392646 PMCID: PMC10890678 DOI: 10.3390/jpm14020213] [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] [Received: 01/23/2024] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Coronary artery disease is caused by changes in the coronary arteries due to the atherosclerotic process and thrombotic changes. A very important role in the development of the atherosclerotic process in the coronary vessels is played by the inflammatory process and the immune response. Due to the important role of lipids and the coagulation process in the atherosclerotic process, research has also focused on genes affecting lipid metabolism and the coagulation system. Lipoprotein lipase (LPL) is an enzyme that metabolises lipids, hydrolysing triglycerides to produce free fatty acids and glycerol. Protein C (PC) is an essential component of coagulation and fibrinolysis. It is activated on the endothelial surface by the membrane-bound thrombin-thrombomodulin complex. Platelet-derived growth factor (PDGF) has a number of important functions in processes related to fibroblast and smooth muscle cell function. Due to their influence on lipid metabolism and coagulation processes, LPL, PROCR (endothelial cell protein C receptor) and PDGF may affect the atherosclerotic process and, thus, the risk of coronary heart disease. The aim of the study was to examine the associations between the LPL rs264, PROCR rs867186 and PDGF rs974819 gene polymorphisms and the risk of unstable angina and selected clinical parameters. METHODS The study included 232 patients with unstable angina and 144 healthy subjects as the control group. Genotyping was performed using real-time PCR. RESULTS There were no statistically significant differences in the distribution of the polymorphisms tested between the patients with unstable angina and the control subjects. The results showed associations between the PROCR rs867186 and PDGF rs974819 polymorphisms and some clinical parameters in patients with unstable angina. In patients with the PDGF rs974819 CC genotype, there were increased values for cholesterol and LDL serum levels in comparison with patients with the PDGF rs974819 CT and TT genotypes. In patients with the PROCR rs867186 AA genotype, HDL serum levels were lower than in patients with the GA genotype. CONCLUSIONS The results of our study did not show that the LPL rs264, PROCR rs867186 and PDGF rs974819 gene polymorphisms were significant risk factors for unstable angina in our population. The results of the study suggest that PDGF rs974819 and PROCR rs867186 may be associated with some parameters of lipid metabolism.
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Affiliation(s)
- Damian Malinowski
- Department of Pharmacokinetics and Therapeutic Drug Monitoring, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Krzysztof Safranow
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland
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Khan A, Shang N, Nestor JG, Weng C, Hripcsak G, Harris PC, Gharavi AG, Kiryluk K. Polygenic risk alters the penetrance of monogenic kidney disease. Nat Commun 2023; 14:8318. [PMID: 38097619 PMCID: PMC10721887 DOI: 10.1038/s41467-023-43878-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Chronic kidney disease (CKD) is determined by an interplay of monogenic, polygenic, and environmental risks. Autosomal dominant polycystic kidney disease (ADPKD) and COL4A-associated nephropathy (COL4A-AN) represent the most common forms of monogenic kidney diseases. These disorders have incomplete penetrance and variable expressivity, and we hypothesize that polygenic factors explain some of this variability. By combining SNP array, exome/genome sequence, and electronic health record data from the UK Biobank and All-of-Us cohorts, we demonstrate that the genome-wide polygenic score (GPS) significantly predicts CKD among ADPKD monogenic variant carriers. Compared to the middle tertile of the GPS for noncarriers, ADPKD variant carriers in the top tertile have a 54-fold increased risk of CKD, while ADPKD variant carriers in the bottom tertile have only a 3-fold increased risk of CKD. Similarly, the GPS significantly predicts CKD in COL4A-AN carriers. The carriers in the top tertile of the GPS have a 2.5-fold higher risk of CKD, while the risk for carriers in the bottom tertile is not different from the average population risk. These results suggest that accounting for polygenic risk improves risk stratification in monogenic kidney disease.
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Affiliation(s)
- Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Jordan G Nestor
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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Khan A, Shang N, Nestor JG, Weng C, Hripcsak G, Harris PC, Gharavi AG, Kiryluk K. Polygenic risk affects the penetrance of monogenic kidney disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.07.23289614. [PMID: 37214819 PMCID: PMC10197721 DOI: 10.1101/2023.05.07.23289614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Chronic kidney disease (CKD) is a genetically complex disease determined by an interplay of monogenic, polygenic, and environmental risks. Most forms of monogenic kidney diseases have incomplete penetrance and variable expressivity. It is presently unknown if some of the variability in penetrance can be attributed to polygenic factors. Methods Using the UK Biobank (N=469,835 participants) and the All of Us (N=98,622 participants) datasets, we examined two most common forms of monogenic kidney disorders, autosomal dominant polycystic kidney disease (ADPKD) caused by deleterious variants in the PKD1 or PKD2 genes, and COL4A-associated nephropathy (COL4A-AN caused by deleterious variants in COL4A3, COL4A4, or COL4A5 genes). We used the eMERGE-III electronic CKD phenotype to define cases (estimated glomerular filtration rate (eGFR) <60 mL/min/1.73m2 or kidney failure) and controls (eGFR >90 mL/min/1.73m2 in the absence of kidney disease diagnoses). The effects of the genome-wide polygenic score (GPS) for CKD were tested in monogenic variant carriers and non-carriers using logistic regression controlling for age, sex, diabetes, and genetic ancestry. Results As expected, the carriers of known pathogenic and rare predicted loss-of-function variants in PKD1 or PKD2 had a high risk of CKD (ORmeta=17.1, 95% CI: 11.1-26.4, P=1.8E-37). The GPS was comparably predictive of CKD in both ADPKD variant carriers (ORmeta=2.28 per SD, 95%CI: 1.55-3.37, P=2.6E-05) and non-carriers (ORmeta=1.72 per SD, 95% CI=1.69-1.76, P< E-300) independent of age, sex, diabetes, and genetic ancestry. Compared to the middle tertile of the GPS distribution for non-carriers, ADPKD variant carriers in the top tertile had a 54-fold increased risk of CKD, while ADPKD variant carriers in the bottom tertile had only a 3-fold increased risk of CKD. Similarly, the GPS was predictive of CKD in both COL4-AN variant carriers (ORmeta=1.78, 95% CI=1.22-2.58, P=2.38E-03) and non-carriers (ORmeta=1.70, 95%CI: 1.68-1.73 P Conclusions Variable penetrance of kidney disease in ADPKD and COL4-AN is partially explained by differences in polygenic risk profiles. Accounting for polygenic factors has the potential to improve risk stratification in monogenic kidney disease and may have implications for genetic counseling.
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Affiliation(s)
- Atlas Khan
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Ning Shang
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Jordan G. Nestor
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Peter C. Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Ali G. Gharavi
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Krzysztof Kiryluk
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
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Schultz LM, Merikangas AK, Ruparel K, Jacquemont S, Glahn DC, Gur RE, Barzilay R, Almasy L. Stability of polygenic scores across discovery genome-wide association studies. HGG ADVANCES 2022; 3:100091. [PMID: 35199043 PMCID: PMC8841810 DOI: 10.1016/j.xhgg.2022.100091] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 01/18/2022] [Indexed: 01/19/2023] Open
Abstract
Polygenic scores (PGS) are commonly evaluated in terms of their predictive accuracy at the population level by the proportion of phenotypic variance they explain. To be useful for precision medicine applications, they also need to be evaluated at the individual level when phenotypes are not necessarily already known. We investigated the stability of PGS in European American (EUR) and African American (AFR)-ancestry individuals from the Philadelphia Neurodevelopmental Cohort and the Adolescent Brain Cognitive Development study using different discovery genome-wide association study (GWAS) results for post-traumatic stress disorder (PTSD), type 2 diabetes (T2D), and height. We found that pairs of EUR-ancestry GWAS for the same trait had genetic correlations >0.92. However, PGS calculated from pairs of same-ancestry and different-ancestry GWAS had correlations that ranged from <0.01 to 0.74. PGS stability was greater for height than for PTSD or T2D. A series of height GWAS in the UK Biobank suggested that correlation between PGS is strongly dependent on the extent of sample overlap between the discovery GWAS. Focusing on the upper end of the PGS distribution, different discovery GWAS do not consistently identify the same individuals in the upper quantiles, with the best case being 60% of individuals above the 80th percentile of PGS overlapping from one height GWAS to another. The degree of overlap decreases sharply as higher quantiles, less heritable traits, and different-ancestry GWAS are considered. PGS computed from different discovery GWAS have only modest correlation at the individual level, underscoring the need to proceed cautiously with integrating PGS into precision medicine applications.
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Affiliation(s)
- Laura M. Schultz
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA
- Corresponding author
| | - Alison K. Merikangas
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kosha Ruparel
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sébastien Jacquemont
- UHC Sainte-Justine Research Center, Université de Montréal, Montréal, QC H3T 1C5, Canada
- Department of Pediatrics, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - David C. Glahn
- Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Raquel E. Gur
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Child Adolescent Psychiatry and Behavioral Sciences, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ran Barzilay
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Child Adolescent Psychiatry and Behavioral Sciences, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Brunham LR, Trinder M. Polygenic risk scores for the diagnosis and management of dyslipidemia. Curr Opin Endocrinol Diabetes Obes 2022; 29:95-100. [PMID: 35034034 DOI: 10.1097/med.0000000000000708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW To review current progress in the use of polygenic risk scores for lipid traits and their use in the diagnosis and treatment of lipid disorders. RECENT FINDINGS Inherited lipid disorders, including those causing extremes of low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, or triglycerides were initially identified as monogenic traits, in which a single rare variant with large effect size is responsible for the phenotype. More recently, a polygenic basis for many lipid traits has also been identified. Patients with polygenic dyslipidemia can be identified through the use of polygenic risk scores (PRSs), which collapse information from a handful to several million genetic variants into a single metric. SUMMARY PRSs for lipid traits may aid in the identification of the genetic basis for the lipid phenotype in individual patients, may provide additional information regarding the risk of cardiovascular disease, and could help in guiding therapeutic decision making.
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Affiliation(s)
- Liam R Brunham
- Centre for Heart Lung Innovation
- Department of Medicine
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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Wong CK, Makalic E, Dite GS, Whiting L, Murphy NM, Hopper JL, Allman R. Polygenic risk scores for cardiovascular diseases and type 2 diabetes. PLoS One 2022; 17:e0278764. [PMID: 36459520 PMCID: PMC9718402 DOI: 10.1371/journal.pone.0278764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
Polygenic risk scores (PRSs) are a promising approach to accurately predict an individual's risk of developing disease. The area under the receiver operating characteristic curve (AUC) of PRSs in their population are often only reported for models that are adjusted for age and sex, which are known risk factors for the disease of interest and confound the association between the PRS and the disease. This makes comparison of PRS between studies difficult because the genetic effects cannot be disentangled from effects of age and sex (which have a high AUC without the PRS). In this study, we used data from the UK Biobank and applied the stacked clumping and thresholding method and a variation called maximum clumping and thresholding method to develop PRSs to predict coronary artery disease, hypertension, atrial fibrillation, stroke and type 2 diabetes. We created case-control training datasets in which age and sex were controlled by design. We also excluded prevalent cases to prevent biased estimation of disease risks. The maximum clumping and thresholding PRSs required many fewer single-nucleotide polymorphisms to achieve almost the same discriminatory ability as the stacked clumping and thresholding PRSs. Using the testing datasets, the AUCs for the maximum clumping and thresholding PRSs were 0.599 (95% confidence interval [CI]: 0.585, 0.613) for atrial fibrillation, 0.572 (95% CI: 0.560, 0.584) for coronary artery disease, 0.585 (95% CI: 0.564, 0.605) for type 2 diabetes, 0.559 (95% CI: 0.550, 0.569) for hypertension and 0.514 (95% CI: 0.494, 0.535) for stroke. By developing a PRS using a dataset in which age and sex are controlled by design, we have obtained true estimates of the discriminatory ability of the PRSs alone rather than estimates that include the effects of age and sex.
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Affiliation(s)
- Chi Kuen Wong
- Genetic Technologies Ltd., Fitzroy, Victoria, Australia
- * E-mail:
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gillian S. Dite
- Genetic Technologies Ltd., Fitzroy, Victoria, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | | | | | - John L. Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Richard Allman
- Genetic Technologies Ltd., Fitzroy, Victoria, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
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Workalemahu T, Rahman ML, Ouidir M, Wu J, Zhang C, Tekola-Ayele F. Associations of maternal blood pressure-raising polygenic risk scores with fetal weight. J Hum Hypertens 2022; 36:69-76. [PMID: 33536548 PMCID: PMC8329099 DOI: 10.1038/s41371-021-00483-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 12/12/2020] [Accepted: 01/13/2021] [Indexed: 01/31/2023]
Abstract
Maternal blood pressure (BP) is associated with variations in fetal weight, an important determinant of neonatal and adult health. However, the association of BP-raising genetic risk with fetal weight is unknown. We tested the associations of maternal BP-raising polygenic risk scores (PRS) with estimated fetal weights (EFWs) at 13, 20, 27, and 40 weeks of gestation. This study included 622 White, 637 Black, 568 Hispanic, and 238 Asian pregnant women with genotype data from the NICHD Fetal Growth Studies. PRS of systolic (SBP) and diastolic BP (DBP) were calculated for each participant based on summary statistics from a recent genome-wide association study. Linear regression models were used to compare mean EFW differences between the highest versus lowest tertile of PRS, adjusting for maternal age, education, parity, genetic principal components and fetal sex. Hispanics in the highest DBP PRS tertile, compared to those in the lowest, had 8.1 g (95% CI: -15.1, -1.1), 32.4 g (-58.4, -6.4) and 119.4 g (-218.1, -20.7) lower EFW at 20, 27 and 40 weeks, respectively. Similarly, Asians in the highest DBP PRS tertile had 137.2 g (-263.5, -10.8) lower EFW at week 40, and those in the highest tertile of SBP PRS had 3.2 g (-5.8, -0.7), 12.9 g (-23.5, -2.4), and 39.8 g (-76.9, -2.7) lower EFWs at 13, 20, and 27 weeks. The findings showed that pregnant women's genetic susceptibility to high BP contributes to reduced fetal growth, suggesting a potential future clinical application in perinatal health.
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Affiliation(s)
- Tsegaselassie Workalemahu
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Mohammad L. Rahman
- Harvard Medical School, Department of Population Medicine and Harvard Pilgrim Healthcare Institute, Boston, MA, USA
| | - Marion Ouidir
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jing Wu
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Cuilin Zhang
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Lee J, Kiiskinen T, Mars N, Jukarainen S, Ingelsson E, Neale B, Ripatti S, Natarajan P, Ganna A. Clinical Conditions and Their Impact on Utility of Genetic Scores for Prediction of Acute Coronary Syndrome. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003283. [PMID: 34232692 DOI: 10.1161/circgen.120.003283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Acute coronary syndrome (ACS) is a clinically significant presentation of coronary heart disease. Genetic information has been proposed to improve prediction beyond well-established clinical risk factors. While polygenic scores (PS) can capture an individual's genetic risk for ACS, its prediction performance may vary in the context of diverse correlated clinical conditions. Here, we aimed to test whether clinical conditions impact the association between PS and ACS. METHODS We explored the association between 405 clinical conditions diagnosed before baseline and 9080 incident cases of ACS in 387 832 individuals from the UK Biobank. Results were replicated in 6430 incident cases of ACS in 177 876 individuals from FinnGen. RESULTS We identified 80 conventional (eg, stable angina pectoris and type 2 diabetes) and unconventional (eg, diaphragmatic hernia and inguinal hernia) associations with ACS. The association between PS and ACS was consistent in individuals with and without most clinical conditions. However, a diagnosis of stable angina pectoris yielded a differential association between PS and ACS. PS was associated with a significantly reduced (interaction P=2.87×10-8) risk for ACS in individuals with stable angina pectoris (hazard ratio, 1.163 [95% CI, 1.082-1.251]) compared with individuals without stable angina pectoris (hazard ratio, 1.531 [95% CI, 1.497-1.565]). These findings were replicated in FinnGen (interaction P=1.38×10-6). CONCLUSIONS In summary, while most clinical conditions did not impact utility of PS for prediction of ACS, we found that PS was substantially less predictive of ACS in individuals with prevalent stable coronary heart disease. PS may be more appropriate for prediction of ACS in asymptomatic individuals than symptomatic individuals with clinical suspicion for coronary heart disease.
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Affiliation(s)
- Jiwoo Lee
- Department of Biomedical Data Science, Stanford University, CA (J.L., E.I.).,Broad Institute of MIT and Harvard, Cambridge (J.L., B.N., S.R., P.N., A.G.).,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston (J.L., B.N., S.R., A.G.).,Finnish Institute for Molecular Medicine, HiLIFE, University of Helsinki, Finland (J.L., T.K., N.M., S.J., S.R., A.G.)
| | - Tuomo Kiiskinen
- Finnish Institute for Molecular Medicine, HiLIFE, University of Helsinki, Finland (J.L., T.K., N.M., S.J., S.R., A.G.)
| | - Nina Mars
- Finnish Institute for Molecular Medicine, HiLIFE, University of Helsinki, Finland (J.L., T.K., N.M., S.J., S.R., A.G.)
| | - Sakari Jukarainen
- Finnish Institute for Molecular Medicine, HiLIFE, University of Helsinki, Finland (J.L., T.K., N.M., S.J., S.R., A.G.)
| | - Erik Ingelsson
- Department of Biomedical Data Science, Stanford University, CA (J.L., E.I.)
| | - Benjamin Neale
- Broad Institute of MIT and Harvard, Cambridge (J.L., B.N., S.R., P.N., A.G.).,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston (J.L., B.N., S.R., A.G.)
| | - Samuli Ripatti
- Broad Institute of MIT and Harvard, Cambridge (J.L., B.N., S.R., P.N., A.G.).,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston (J.L., B.N., S.R., A.G.).,Finnish Institute for Molecular Medicine, HiLIFE, University of Helsinki, Finland (J.L., T.K., N.M., S.J., S.R., A.G.)
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge (J.L., B.N., S.R., P.N., A.G.)
| | - Andrea Ganna
- Broad Institute of MIT and Harvard, Cambridge (J.L., B.N., S.R., P.N., A.G.).,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston (J.L., B.N., S.R., A.G.).,Finnish Institute for Molecular Medicine, HiLIFE, University of Helsinki, Finland (J.L., T.K., N.M., S.J., S.R., A.G.)
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10
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Tayal U, Ware JS, Lakdawala NK, Heymans S, Prasad SK. Understanding the genetics of adult-onset dilated cardiomyopathy: what a clinician needs to know. Eur Heart J 2021; 42:2384-2396. [PMID: 34153989 DOI: 10.1093/eurheartj/ehab286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/10/2021] [Accepted: 05/19/2021] [Indexed: 12/28/2022] Open
Abstract
There is increasing understanding of the genetic basis to dilated cardiomyopathy and in this review, we offer a practical primer for the practising clinician. We aim to help all clinicians involved in the care of patients with dilated cardiomyopathy to understand the clinical relevance of the genetic basis of dilated cardiomyopathy, introduce key genetic concepts, explain which patients and families may benefit from genetic testing, which genetic tests are commonly performed, how to interpret genetic results, and the clinical applications of results. We conclude by reviewing areas for future research in this dynamic field.
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Affiliation(s)
- Upasana Tayal
- National Heart Lung Institute, Imperial College London, UK.,Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals, London, UK
| | - James S Ware
- National Heart Lung Institute, Imperial College London, UK.,Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals, London, UK.,MRC London Institute of Medical Sciences, London, UK
| | - Neal K Lakdawala
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephane Heymans
- Department of Cardiology, CARIM School for Cardiovascular Diseases Faculty of Health, Medicine and Life Sciences, Maastricht University, The Netherlands.,Department of Cardiovascular Sciences, Centre for Molecular and Vascular Biology, Leuven, KU, Belgium.,The Netherlands Heart Institute, Nl-HI, Utrecht, The Netherlands
| | - Sanjay K Prasad
- National Heart Lung Institute, Imperial College London, UK.,Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals, London, UK
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11
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Noto D, Cefalù AB, Martinelli N, Giammanco A, Spina R, Barbagallo CM, Caruso M, Novo S, Sarullo F, Pernice V, Brucato F, Ingrassia V, Fayer F, Altieri GI, Scrimali C, Misiano G, Olivieri O, Girelli D, Averna MR. rs629301 CELSR2 polymorphism confers a ten-year equivalent risk of critical stenosis assessed by coronary angiography. Nutr Metab Cardiovasc Dis 2021; 31:1542-1547. [PMID: 33810964 DOI: 10.1016/j.numecd.2021.01.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND AND AIMS Novel genetic determinants associated with coronary artery disease (CAD) have been discovered by genome wide association studies. Variants encompassing the CELSR2- PSRC1-SORT1 gene cluster have been associated with CAD. This study is aimed to investigate the rs629301 polymorphism association with the extent of CAD evaluated by coronary angiography (CAG), and to evaluate its associations with an extensive panel of lipid and lipoprotein measurements in a large Italian cohort of 2429 patients. METHODS AND RESULTS The patients were collected by four Intensive Care Units located in Palermo and Verona (Italy). Clinical Records were filed, blood samples were collected, lipids and apolipoproteins (apo) were measured in separate laboratories. CAD was defined by the presence of stenotic arteries (>50% lumen diameter) by CAG. The presence of CAD was associated with the rs629301 genotype. Patients with CAD were 78% and 73% (p = 0.007) of the T/T vs. T/G + G/G genotype carriers respectively. T/T genotype was also correlated with the number of stenotic arteries, with a 1.29 (1.04-1.61) risk to have a three-arteries disease. T/T genotype correlated with higher levels of LDL-, non-HDL cholesterol, apoB, apoE and apoCIII, and lower HDL-cholesterol. Logistic Regression confirmed that rs629301was associated with CAD independently from the common risk factors, with a risk similar to that conferred by ten years of age [odds ratios were 1.43 (1.04-1.96) and 1.39 (1.22-1.58) respectively]. CONCLUSIONS rs629301 risk allele was independently associated with the extension and severity of CAD and positively with apoE and apoB containing lipoproteins.
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Affiliation(s)
- Davide Noto
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy.
| | - Angelo B Cefalù
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Nicola Martinelli
- Department of Medicine, Unit of Internal Medicine, University of Verona, Italy
| | - Antonina Giammanco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Rossella Spina
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Carlo M Barbagallo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Marco Caruso
- Intensive Care Unit, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Italy
| | - Salvatore Novo
- Intensive Care Unit, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Italy
| | - Filippo Sarullo
- Intensive Care Unit, "Buccheri La Ferla" Hospital, Palermo, Italy
| | - Vincenzo Pernice
- Intensive Care Unit, "Villa Maria Eleonora" Hospital, Palermo, Italy
| | - Federica Brucato
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Valeria Ingrassia
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Francesca Fayer
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Grazia I Altieri
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Chiara Scrimali
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Gabriella Misiano
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Oliviero Olivieri
- Department of Medicine, Unit of Internal Medicine, University of Verona, Italy
| | - Domenico Girelli
- Department of Medicine, Unit of Internal Medicine, University of Verona, Italy
| | - Maurizio R Averna
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
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12
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African genetic diversity and adaptation inform a precision medicine agenda. Nat Rev Genet 2021; 22:284-306. [PMID: 33432191 DOI: 10.1038/s41576-020-00306-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 01/29/2023]
Abstract
The deep evolutionary history of African populations, since the emergence of modern humans more than 300,000 years ago, has resulted in high genetic diversity and considerable population structure. Selected genetic variants have increased in frequency due to environmental adaptation, but recent exposures to novel pathogens and changes in lifestyle render some of them with properties leading to present health liabilities. The unique discoverability potential from African genomic studies promises invaluable contributions to understanding the genomic and molecular basis of health and disease. Globally, African populations are understudied, and precision medicine approaches are largely based on data from European and Asian-ancestry populations, which limits the transferability of findings to the continent of Africa. Africa needs innovative precision medicine solutions based on African data that use knowledge and implementation strategies aligned to its climatic, cultural, economic and genomic diversity.
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13
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Vrablik M, Dlouha D, Todorovova V, Stefler D, Hubacek JA. Genetics of Cardiovascular Disease: How Far Are We from Personalized CVD Risk Prediction and Management? Int J Mol Sci 2021; 22:4182. [PMID: 33920733 PMCID: PMC8074003 DOI: 10.3390/ijms22084182] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
Despite the rapid progress in diagnosis and treatment of cardiovascular disease (CVD), this disease remains a major cause of mortality and morbidity. Recent progress over the last two decades in the field of molecular genetics, especially with new tools such as genome-wide association studies, has helped to identify new genes and their variants, which can be used for calculations of risk, prediction of treatment efficacy, or detection of subjects prone to drug side effects. Although the use of genetic risk scores further improves CVD prediction, the significance is not unambiguous, and some subjects at risk remain undetected. Further research directions should focus on the "second level" of genetic information, namely, regulatory molecules (miRNAs) and epigenetic changes, predominantly DNA methylation and gene-environment interactions.
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Affiliation(s)
- Michal Vrablik
- 3rd Department of Internal Medicine, General University Hospital and 1st Faculty of Medicine, Charles University, 11636 Prague, Czech Republic; (V.T.); (J.A.H.)
| | - Dana Dlouha
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic;
| | - Veronika Todorovova
- 3rd Department of Internal Medicine, General University Hospital and 1st Faculty of Medicine, Charles University, 11636 Prague, Czech Republic; (V.T.); (J.A.H.)
| | - Denes Stefler
- Department of Epidemiology and Public Health, Institute of Epidemiology and Health Care, University College London, London WC1E 7HB, UK;
| | - Jaroslav A. Hubacek
- 3rd Department of Internal Medicine, General University Hospital and 1st Faculty of Medicine, Charles University, 11636 Prague, Czech Republic; (V.T.); (J.A.H.)
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic;
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14
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Ragia G, Manolopoulos VG. Assessing COVID-19 susceptibility through analysis of the genetic and epigenetic diversity of ACE2-mediated SARS-CoV-2 entry. Pharmacogenomics 2020; 21:1311-1329. [PMID: 33243086 PMCID: PMC7694444 DOI: 10.2217/pgs-2020-0092] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
There is considerable variation in disease course among individuals infected with SARS-CoV-2. Many of them do not exhibit any symptoms, while some others proceed to develop COVID-19; however, severity of COVID-19 symptoms greatly differs among individuals. Focusing on the early events related to SARS-CoV-2 entry to cells through the ACE2 pathway, we describe how variability in (epi)genetic factors can conceivably explain variability in disease course. We specifically focus on variations in ACE2, TMPRSS2 and FURIN genes, as central components for SARS-CoV-2 infection, and on other molecules that modulate their expression such as CALM, ADAM-17, AR and ESRs. We propose a genetic classifier for predicting SARS-CoV-2 infectivity potential as a preliminary tool for identifying the at-risk-population. This tool can serve as a dynamic scaffold being updated and adapted to validated (epi)genetic data. Overall, the proposed approach holds potential for better personalization of COVID-19 handling.
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Affiliation(s)
- Georgia Ragia
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, 68100, Greece
| | - Vangelis G Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, 68100, Greece.,Clinical Pharmacology & Pharmacogenetics Unit, Academic General Hospital of Alexandroupolis, Alexandroupolis, 68100, Greece
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15
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Shrivastava A, Haase T, Zeller T, Schulte C. Biomarkers for Heart Failure Prognosis: Proteins, Genetic Scores and Non-coding RNAs. Front Cardiovasc Med 2020; 7:601364. [PMID: 33330662 PMCID: PMC7719677 DOI: 10.3389/fcvm.2020.601364] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Heart failure (HF) is a complex disease in which cardiomyocyte injury leads to a cascade of inflammatory and fibrosis pathway activation, thereby causing decrease in cardiac function. As a result, several biomolecules are released which can be identified easily in circulating body fluids. The complex biological processes involved in the development and worsening of HF require an early treatment strategy to stop deterioration of cardiac function. Circulating biomarkers provide not only an ideal platform to detect subclinical changes, their clinical application also offers the opportunity to monitor disease treatment. Many of these biomarkers can be quantified with high sensitivity; allowing their clinical application to be evaluated beyond diagnostic purposes as potential tools for HF prognosis. Though the field of biomarkers is dominated by protein molecules, non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) are novel and promising biomarker candidates that encompass several ideal characteristics required in the biomarker field. The application of genetic biomarkers as genetic risk scores in disease prognosis, albeit in its infancy, holds promise to improve disease risk estimation. Despite the multitude of biomarkers that have been available and identified, the majority of novel biomarker candidates are not cardiac-specific, and instead may simply be a readout of systemic inflammation or other pathological processes. Thus, the true value of novel biomarker candidates in HF prognostication remains unclear. In this article, we discuss the current state of application of protein, genetic as well as non-coding RNA biomarkers in HF risk prognosis.
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Affiliation(s)
- Apurva Shrivastava
- Clinic for Cardiology, University Heart and Vascular Center, University Medical Center Eppendorf, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Luebeck, University Medical Center Eppendorf, Hamburg, Germany
| | - Tina Haase
- Clinic for Cardiology, University Heart and Vascular Center, University Medical Center Eppendorf, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Luebeck, University Medical Center Eppendorf, Hamburg, Germany
| | - Tanja Zeller
- Clinic for Cardiology, University Heart and Vascular Center, University Medical Center Eppendorf, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Luebeck, University Medical Center Eppendorf, Hamburg, Germany
| | - Christian Schulte
- Clinic for Cardiology, University Heart and Vascular Center, University Medical Center Eppendorf, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Luebeck, University Medical Center Eppendorf, Hamburg, Germany.,King's British Heart Foundation Centre, King's College London, London, United Kingdom
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16
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Figtree GA, Vernon ST, Nicholls SJ. Taking the next steps to implement polygenic risk scoring for improved risk stratification and primary prevention of coronary artery disease. Eur J Prev Cardiol 2020; 29:580-587. [DOI: 10.1093/eurjpc/zwaa030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/30/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022]
Abstract
Abstract
Coronary artery disease (CAD) remains the leading cause of death worldwide. The role of hypertension, cholesterol, diabetes mellitus, and smoking in driving disease has been well recognized at a population level and has been the target of primary prevention strategies for over 50 years with substantial impact. However, in many cases, these factors alone do not provide enough precision at the individual level to allow physicians and patients to take appropriate preventive measures and many patients continue to suffer acute coronary syndromes in the absence of these risk factors. Recent advances in user-friendly chip designs, high speed throughput, and economic efficiency of genome-wide association studies complemented by advances in statistical analytical approaches have facilitated the rapid development of polygenic risk scores (PRSs). The latest PRSs combine data regarding hundreds of thousands of single-nucleotide polymorphisms to predict chronic diseases including CAD. Novel CAD PRSs are strong predictors of risk and may have application, in a complementary manner with existing risk prediction algorithms. However, there remain substantial controversies, and ultimately, we need to move forward from observational studies to prospectively and rigorously assess the potential impact if widespread implementation is to be aspired to. Consideration needs to be made of ethnicity, sex, as well as age, and risk estimate based on existing non-genomic algorithms. We provide an overview and commentary on the important advances in deriving and validating PRSs, as well as pragmatic considerations that will be required for implementation of the new knowledge into clinical practice.
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Affiliation(s)
| | - Stephen Thomas Vernon
- Cardiothoracic and Vascular Health, Level 12, Kolling Institute of Medical Research, Northern Sydney Local Health District, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2050, Australia
| | - Stephen James Nicholls
- Monash Heart, 246 Clayton Road, Clayton, Victoria, 3168, Australia
- Monash Health, Monash University, Melbourne, Clayton, Victoria, 3800, Australia
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17
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Qoronfleh MW, Chouchane L, Mifsud B, Al Emadi M, Ismail S. THE FUTURE OF MEDICINE, healthcare innovation through precision medicine: policy case study of Qatar. LIFE SCIENCES, SOCIETY AND POLICY 2020; 16:12. [PMID: 33129349 PMCID: PMC7603723 DOI: 10.1186/s40504-020-00107-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
In 2016, the World Innovation Summit for Health (WISH) published its Forum Report on precision medicine "PRECISION MEDICINE - A GLOBAL ACTION PLAN FOR IMPACT". Healthcare is undergoing a transformation, and it is imperative to leverage new technologies to generate new data and support the advent of precision medicine (PM). Recent scientific breakthroughs and technological advancements have improved our disease knowledge and altered diagnosis and treatment approaches resulting in a more precise, predictive, preventative and personalized health care that is customized for the individual patient. Consequently, the big data revolution has provided an opportunity to apply artificial intelligence and machine learning algorithms to mine such a vast data set. Additionally, personalized medicine promises to revolutionize healthcare, with its key goal of providing the right treatment to the right patient at the right time and dose, and thus the potential of improving quality of life and helping to bring down healthcare costs.This policy briefing will look in detail at the issues surrounding continued development, sustained investment, risk factors, testing and approval of innovations for better strategy and faster process. The paper will serve as a policy bridge that is required to enhance a conscious decision among the powers-that-be in Qatar in order to find a way to harmonize multiple strands of activity and responsibility in the health arena. The end goal will be for Qatar to enhance public awareness and engagement and to integrate effectively the incredible advances in research into healthcare systems, for the benefit of all patients.The PM policy briefing provides concrete recommendations on moving forward with PM initiatives in Qatar and internationally. Equally important, integration of PM within a primary care setting, building a coalition of community champions through awareness and advocacy, finally, communicating PM value, patient engagement/empowerment and education/continued professional development programs of the healthcare workforce.Key recommendations for implementation of precision medicine inside and outside Qatar: 1. Create Community Awareness and PM Education Programs 2. Engage and Empower Patients 3. Communicate PM Value 4. Develop appropriate Infrastructure and Information Management Systems 5. Integrate PM into standard Healthcare System and Ensure Access to Care PM is no longer futuristic. It is here. Implementing PM in routine clinical care does require some investment and infrastructure development. Invariably, cost and lack of expertise are cited as barriers to PM implementation. Equally consequential, are the curriculum and professional development of medical care experts.Policymakers need to lead and coordinate effort among stakeholders and consider cultural and faith perspectives to ensure success. It is essential that policymakers integrate PM approaches into national strategies to improve health and health care for all, and to drive towards the future of medicine precision health.
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Affiliation(s)
- M. Walid Qoronfleh
- Research & Policy Department, World Innovation Summit for Health (WISH), Qatar Foundation, P.O. Box 5825, Doha, Qatar
| | - Lotfi Chouchane
- Departments of Genetic Medicine and Microbiology and Immunology, Weill Cornell Medicine, Qatar, Doha, Qatar
| | - Borbala Mifsud
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Maryam Al Emadi
- Clinical Operations, Primary Health Corporation (PHCC), Doha, Qatar
| | - Said Ismail
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
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18
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Carlsson B, Lindén D, Brolén G, Liljeblad M, Bjursell M, Romeo S, Loomba R. Review article: the emerging role of genetics in precision medicine for patients with non-alcoholic steatohepatitis. Aliment Pharmacol Ther 2020; 51:1305-1320. [PMID: 32383295 PMCID: PMC7318322 DOI: 10.1111/apt.15738] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/13/2020] [Accepted: 03/29/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Non-alcoholic steatohepatitis (NASH) is a severe form of non-alcoholic fatty liver disease (NAFLD) characterised by liver fat accumulation, inflammation and progressive fibrosis. Emerging data indicate that genetic susceptibility increases risks of NAFLD, NASH and NASH-related cirrhosis. AIMS To review NASH genetics and discuss the potential for precision medicine approaches to treatment. METHOD PubMed search and inclusion of relevant literature. RESULTS Single-nucleotide polymorphisms in PNPLA3, TM6SF2, GCKR, MBOAT7 and HSD17B13 are clearly associated with NASH development or progression. These genetic variants are common and have moderate-to-large effect sizes for development of NAFLD, NASH and hepatocellular carcinoma (HCC). The genes play roles in lipid remodelling in lipid droplets, hepatic very low-density lipoprotein (VLDL) secretion and de novo lipogenesis. The PNPLA3 I148M variant (rs738409) has large effects, with approximately twofold increased odds of NAFLD and threefold increased odds of NASH and HCC per allele. Obesity interacts with PNPLA3 I148M to elevate liver fat content and increase rates of NASH. Although the isoleucine-to-methionine substitution at amino acid position 148 of the PNPLA3 enzyme inactivates its lipid remodelling activity, the effect of PNPLA3 I148M results from trans-repression of another lipase (ATGL/PNPLA2) by sequestration of a shared cofactor (CGI-58/ABHD5), leading to decreased hepatic lipolysis and VLDL secretion. In homozygous Pnpla3 I148M knock-in rodent models of NAFLD, targeted PNPLA3 mRNA knockdown reduces hepatic steatosis, inflammation and fibrosis. CONCLUSION The emerging genetic and molecular understanding of NASH paves the way for novel interventions, including precision medicines that can modulate the activity of specific genes associated with NASH.
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Affiliation(s)
- Björn Carlsson
- Research and Early DevelopmentCardiovascular, Renal and MetabolismBioPharmaceuticals R&DAstraZenecaGothenburgSweden
| | - Daniel Lindén
- Research and Early DevelopmentCardiovascular, Renal and MetabolismBioPharmaceuticals R&DAstraZenecaGothenburgSweden,Division of EndocrinologyDepartment of Neuroscience and PhysiologySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Gabriella Brolén
- Precision MedicineCardiovascular, Renal and MetabolismR&DAstraZenecaGothenburgSweden
| | - Mathias Liljeblad
- Research and Early DevelopmentCardiovascular, Renal and MetabolismBioPharmaceuticals R&DAstraZenecaGothenburgSweden
| | - Mikael Bjursell
- Research and Early DevelopmentCardiovascular, Renal and MetabolismBioPharmaceuticals R&DAstraZenecaGothenburgSweden
| | - Stefano Romeo
- Department of Molecular and Clinical MedicineUniversity of GothenburgGothenburgSweden,Clinical Nutrition UnitDepartment of Medical and Surgical SciencesMagna Graecia UniversityCatanzaroItaly,Cardiology DepartmentSahlgrenska University HospitalGothenburgSweden
| | - Rohit Loomba
- NAFLD Research CenterDivision of GastroenterologyUniversity of California San DiegoSan DiegoCAUSA
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19
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Lu T, Forgetta V, Yu OHY, Mokry L, Gregory M, Thanassoulis G, Greenwood CMT, Richards JB. Polygenic risk for coronary heart disease acts through atherosclerosis in type 2 diabetes. Cardiovasc Diabetol 2020; 19:12. [PMID: 32000781 PMCID: PMC6993460 DOI: 10.1186/s12933-020-0988-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/14/2020] [Indexed: 12/25/2022] Open
Abstract
Background Type 2 diabetes increases the risk of coronary heart disease (CHD), yet the mechanisms involved remain poorly described. Polygenic risk scores (PRS) provide an opportunity to understand risk factors since they reflect etiologic pathways from the entire genome. We therefore tested whether a PRS for CHD influenced risk of CHD in individuals with type 2 diabetes and which risk factors were associated with this PRS. Methods We tested the association of a CHD PRS with CHD and its traditional clinical risk factors amongst individuals with type 2 diabetes in UK Biobank (N = 21,102). We next tested the association of the CHD PRS with atherosclerotic burden in a cohort of 352 genome-wide genotyped participants with type 2 diabetes who had undergone coronary angiograms. Results In the UK Biobank we found that the CHD PRS was strongly associated with CHD amongst individuals with type 2 diabetes (OR per standard deviation increase = 1.50; p = 1.5 × 10− 59). But this CHD PRS was, at best, only weakly associated with traditional clinical risk factors, such as hypertension, hyperlipidemia, glycemic control, obesity and smoking. Conversely, in the angiographic cohort, the CHD PRS was strongly associated with multivessel stenosis (OR = 1.65; p = 4.9 × 10− 4) and increased number of major stenotic lesions (OR = 1.35; p = 9.4 × 10− 3). Conclusions Polygenic predisposition to CHD is strongly associated with atherosclerotic burden in individuals with type 2 diabetes and this effect is largely independent of traditional clinical risk factors. This suggests that genetic risk for CHD acts through atherosclerosis with little effect on most traditional risk factors, providing the opportunity to explore new biological pathways.
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Affiliation(s)
- Tianyuan Lu
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Quantitative Life Sciences Program, McGill University, Montreal, QC, Canada
| | - Vincenzo Forgetta
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Oriana H Y Yu
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Endocrinology, Jewish General Hospital, Montreal, QC, Canada
| | - Lauren Mokry
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Madeline Gregory
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - George Thanassoulis
- Department of Medicine, McGill University, Montreal, QC, Canada.,Preventive and Genomic Cardiology, McGill University Health Centre and Research Institute, Montreal, QC, Canada
| | - Celia M T Greenwood
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.,Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, QC, Canada
| | - J Brent Richards
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada. .,Department of Twin Research and Genetic Epidemiology, King's College London, Strand, London, UK. .,Jewish General Hospital, Room H-413, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.
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20
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Schulte C, Zeller T. Biomarkers in primary prevention : Meaningful diagnosis based on biomarker scores? Herz 2019; 45:10-16. [PMID: 31807790 DOI: 10.1007/s00059-019-04874-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cardiovascular (CV) risk assessment is based on the utilization of risk scores, enabling clinicians to estimate an individual's risk to develop CV pathologies and events. Such risk scores comprise classic CV risk factors such as smoking, diabetes, hypertension, and blood cholesterol levels. Recently, other CV biomarkers such as cardiac troponins have been suggested and evaluated as alternative biomarkers not only in the acute diagnostic setting of myocardial infarction, but also as markers for risk stratification in the general population. In this review, we summarize the current knowledge on biomarkers in the field of primary prevention in cardiovascular disease (CVD). Furthermore, we present potential alternative biomarker-based strategies for CV risk assessment. In this respect we provide an outlook on the potential use of genomic variation as well as circulating non-coding RNAs to complement current risk assessment strategies so as to further personalize risk stratification in CVD.
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Affiliation(s)
- Christian Schulte
- Klinik für Kardiologie, Universitäres Herz- und Gefäßzentrum Hamburg, Martinistraße 52, 20246, Hamburg, Germany.,Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), Standort Hamburg/Lübeck/Kiel, Hamburg, Germany
| | - Tanja Zeller
- Klinik für Kardiologie, Universitäres Herz- und Gefäßzentrum Hamburg, Martinistraße 52, 20246, Hamburg, Germany. .,Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), Standort Hamburg/Lübeck/Kiel, Hamburg, Germany.
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21
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Affiliation(s)
- Nisha Nair
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK.
| | - Anthony G Wilson
- University College Dublin Centre for Arthritis Research, Conway Institute, University College Dublin, Dublin, Ireland.
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22
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Genetic Testing in Inherited Heart Diseases. Heart Lung Circ 2019; 29:505-511. [PMID: 31813745 DOI: 10.1016/j.hlc.2019.10.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/02/2019] [Accepted: 10/13/2019] [Indexed: 12/19/2022]
Abstract
Inherited heart diseases include numerous conditions, from the more prevalent hypertrophic cardiomyopathy (HCM) and familial hypercholesterolaemia (FH), to the comparatively less common inherited arrhythmia syndromes, such as long QT syndrome (LQTS), catecholaminergic polymorphic ventricular tachycardia (CPVT) and Brugada syndrome (BrS). Genetic testing has evolved rapidly over the last decade and is now considered a mainstream component of clinical management of inherited heart diseases. Cardiac manifestations can also be part of wider syndromes, and genetic testing can play a critical role in clarifying the underlying aetiological basis of disease in some cases. The greatest utility of a genetic diagnosis, however, comes from the ability to elucidate disease risk amongst asymptomatic at-risk family members. Given the nuances and challenges, cardiac genetic testing is best performed in a multidisciplinary specialised clinic with access to cardiac genetic counselling.
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23
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Sinha A, Lloyd-Jones DM, Khan SS. Risk assessment to prevent heart failure. Aging (Albany NY) 2019; 11:9227-9228. [PMID: 31727868 PMCID: PMC6874428 DOI: 10.18632/aging.102444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 10/24/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Arjun Sinha
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Division of Cardiology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Division of Cardiology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sadiya S Khan
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Division of Cardiology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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24
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Harel T, Peshes-Yaloz N, Bacharach E, Gat-Viks I. Predicting Phenotypic Diversity from Molecular and Genetic Data. Genetics 2019; 213:297-311. [PMID: 31352366 PMCID: PMC6727812 DOI: 10.1534/genetics.119.302463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/04/2019] [Indexed: 01/03/2023] Open
Abstract
Despite the importance of complex phenotypes, an in-depth understanding of the combined molecular and genetic effects on a phenotype has yet to be achieved. Here, we introduce InPhenotype, a novel computational approach for complex phenotype prediction, where gene-expression data and genotyping data are integrated to yield quantitative predictions of complex physiological traits. Unlike existing computational methods, InPhenotype makes it possible to model potential regulatory interactions between gene expression and genomic loci without compromising the continuous nature of the molecular data. We applied InPhenotype to synthetic data, exemplifying its utility for different data parameters, as well as its superiority compared to current methods in both prediction quality and the ability to detect regulatory interactions of genes and genomic loci. Finally, we show that InPhenotype can provide biological insights into both mouse and yeast datasets.
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Affiliation(s)
- Tom Harel
- School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801 Israe
| | - Naama Peshes-Yaloz
- School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801 Israe
| | - Eran Bacharach
- School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801 Israe
| | - Irit Gat-Viks
- School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801 Israe
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25
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