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Vaskimo LM, Gomon G, Naamane N, Cordell HJ, Pratt A, Knevel R. The Application of Genetic Risk Scores in Rheumatic Diseases: A Perspective. Genes (Basel) 2023; 14:2167. [PMID: 38136989 PMCID: PMC10743278 DOI: 10.3390/genes14122167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Modest effect sizes have limited the clinical applicability of genetic associations with rheumatic diseases. Genetic risk scores (GRSs) have emerged as a promising solution to translate genetics into useful tools. In this review, we provide an overview of the recent literature on GRSs in rheumatic diseases. We describe six categories for which GRSs are used: (a) disease (outcome) prediction, (b) genetic commonalities between diseases, (c) disease differentiation, (d) interplay between genetics and environmental factors, (e) heritability and transferability, and (f) detecting causal relationships between traits. In our review of the literature, we identified current lacunas and opportunities for future work. First, the shortage of non-European genetic data restricts the application of many GRSs to European populations. Next, many GRSs are tested in settings enriched for cases that limit the transferability to real life. If intended for clinical application, GRSs are ideally tested in the relevant setting. Finally, there is much to elucidate regarding the co-occurrence of clinical traits to identify shared causal paths and elucidate relationships between the diseases. GRSs are useful instruments for this. Overall, the ever-continuing research on GRSs gives a hopeful outlook into the future of GRSs and indicates significant progress in their potential applications.
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Affiliation(s)
- Lotta M. Vaskimo
- Department of Rheumatology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Georgy Gomon
- Department of Rheumatology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Najib Naamane
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Heather J. Cordell
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Arthur Pratt
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Rheumatology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Rachel Knevel
- Department of Rheumatology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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2
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Bui A, Kumar S, Liu J, Orcales F, Gulliver S, Tsoi LC, Gulliver W, Liao W. A partitioned 88-loci psoriasis genetic risk score reveals HLA and non-HLA contributions to clinical phenotypes in a Newfoundland psoriasis cohort. Front Genet 2023; 14:1141010. [PMID: 37323656 PMCID: PMC10265743 DOI: 10.3389/fgene.2023.1141010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Psoriasis is an immune-mediated inflammatory skin disease typically characterized by erythematous and scaly plaques. It affects 3% of the Newfoundland population while only affecting 1.7% of the general Canadian population. Recent genome-wide association studies (GWAS) in psoriasis have identified more than 63 genetic susceptibility loci that individually have modest effects. Prior studies have shown that a genetic risk score (GRS) combining multiple loci can improve psoriasis disease prediction. However, these prior GRS studies have not fully explored the association of GRS with patient clinical characteristics. In this study, we calculated three types of GRS: one using all known GWAS SNPs (GRS-ALL), one using a subset of SNPs from the HLA region (GRS-HLA), and the last using non-HLA SNPs (GRS-noHLA). We examined the relationship between these GRS and a number of psoriasis features within a well characterized Newfoundland psoriasis cohort. We found that both GRS-ALL and GRS-HLA were significantly associated with early age of psoriasis onset, psoriasis severity, first presentation of psoriasis at the elbow or knee, and the total number of body locations affected, while only GRS-ALL was associated with a positive family history of psoriasis. GRS-noHLA was uniquely associated with genital psoriasis. These findings clarify the relationship of the HLA and non-HLA components of GRS with important clinical features of psoriasis.
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Affiliation(s)
- Audrey Bui
- Department of Dermatology, University of California San Francisco, San Francisco, CA, United States
- Lake Erie College of Osteopathic Medicine, Bradenton, FL, United States
| | - Sugandh Kumar
- Department of Dermatology, University of California San Francisco, San Francisco, CA, United States
| | - Jared Liu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, United States
| | - Faye Orcales
- Department of Dermatology, University of California San Francisco, San Francisco, CA, United States
| | | | - Lam C. Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States
| | - Wayne Gulliver
- NewLab Clinical Research Inc, St. John’s, NL, Canada
- Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Wilson Liao
- Department of Dermatology, University of California San Francisco, San Francisco, CA, United States
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3
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Ahmed R, Shi Z, Rifkin AS, Wei J, Lilly Zheng S, Helfand BT, Hulick PJ, Qamar A, Davidson DJ, Billings LK, Xu J. Reclassification of coronary artery disease risk using genetic risk score among subjects with borderline or intermediate clinical risk. Int J Cardiol Heart Vasc 2022; 43:101136. [PMID: 36275420 PMCID: PMC9579501 DOI: 10.1016/j.ijcha.2022.101136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Razina Ahmed
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Andrew S. Rifkin
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Jun Wei
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - S. Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Brian T. Helfand
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA,Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA,University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - Peter J. Hulick
- Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, USA,Department of Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Arman Qamar
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL, USA,Cardiovascular Institute, NorthShore University HealthSystem, Evanston, IL, USA
| | - David J. Davidson
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL, USA,Cardiovascular Institute, NorthShore University HealthSystem, Evanston, IL, USA
| | - Liana K. Billings
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA,Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA,Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, USA,University of Chicago Pritzker School of Medicine, Chicago, IL, USA,Corresponding author.
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Vanderlinden LA, Bemis EA, Seifert J, Guthridge JM, Young KA, Demoruelle MK, Feser M, DeJager W, Macwana S, Mikuls TR, O'Dell JR, Weisman MH, Buckner J, Keating RM, Gaffney PM, Kelly JA, Langefeld CD, Deane KD, James JA, Holers VM, Norris JM. Relationship Between a Vitamin D Genetic Risk Score and Autoantibodies Among First-Degree Relatives of Probands With Rheumatoid Arthritis and Systemic Lupus Erythematosus. Front Immunol 2022; 13:881332. [PMID: 35720397 PMCID: PMC9205604 DOI: 10.3389/fimmu.2022.881332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/09/2022] [Indexed: 12/28/2022] Open
Abstract
Objective Higher 25-hydroxyvitamin D (25(OH)D) levels have been associated with reduced risk for autoimmune diseases and are influenced by vitamin D metabolism genes. We estimated genetically-determined vitamin D levels by calculating a genetic risk score (GRS) and investigated whether the vitamin D GRS was associated with the presence of autoantibodies related to rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) in those at increased risk for developing RA and SLE, respectively. Methods In this cross-sectional study, we selected autoantibody positive (aAb+) and autoantibody negative (aAb-) individuals from the Studies of the Etiologies of Rheumatoid Arthritis (SERA), a cohort study of first-degree relatives (FDRs) of individuals with RA (189 RA aAb+, 181 RA aAb-), and the Lupus Family Registry and Repository (LFRR), a cohort study of FDRs of individuals with SLE (157 SLE aAb+, 185 SLE aAb-). Five SNPs known to be associated with serum 25(OH)D levels were analyzed individually as well as in a GRS: rs4588 (GC), rs12785878 (NADSYN1), rs10741657 (CYP2R1), rs6538691 (AMDHD1), and rs8018720 (SEC23A). Results Both cohorts had similar demographic characteristics, with significantly older and a higher proportion of males in the aAb+ FDRs. The vitamin D GRS was inversely associated with RA aAb+ (OR = 0.85, 95% CI = 0.74-0.99), suggesting a possible protective factor for RA aAb positivity in FDRs of RA probands. The vitamin D GRS was not associated with SLE aAb+ in the LFRR (OR = 1.09, 95% CI = 0.94-1.27). The SEC23A SNP was associated with RA aAb+ in SERA (OR = 0.65, 95% CI = 0.43-0.99); this SNP was not associated with SLE aAb+ in LFRR (OR = 1.41, 95% CI = 0.90 - 2.19). Conclusion Genes associated with vitamin D levels may play a protective role in the development of RA aAbs in FDRs of RA probands, perhaps through affecting lifelong vitamin D status. The GRS and the SEC23A SNP may be of interest for future investigation in pre-clinical RA. In contrast, these results do not support a similar association in SLE FDRs, suggesting other mechanisms involved in the relationship between vitamin D and SLE aAbs not assessed in this study.
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Affiliation(s)
- Lauren A Vanderlinden
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Elizabeth A Bemis
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jennifer Seifert
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Joel M Guthridge
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Kendra A Young
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Mary Kristen Demoruelle
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Marie Feser
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Wade DeJager
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Susan Macwana
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Ted R Mikuls
- Division of Rheumatology and Immunology, University of Nebraska Medical Center and VA Nebraska-Western Iowa Health Care System, Omaha, NE, United States
| | - James R O'Dell
- Division of Rheumatology and Immunology, University of Nebraska Medical Center and VA Nebraska-Western Iowa Health Care System, Omaha, NE, United States
| | - Michael H Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jane Buckner
- Center for Translational Immunology, Benaroya Research Institute (BRI) at Virginia Mason, Seattle, WA, United States
| | - Richard M Keating
- Division of Rheumatology, Scripps Health, La Jolla, CA, United States
| | - Patrick M Gaffney
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Jennifer A Kelly
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston Salem, NC, United States.,Center for Precision Medicine, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Kevin D Deane
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Judith A James
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Vernon Michael Holers
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jill M Norris
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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Gkouskou KK, Grammatikopoulou MG, Lazou E, Sanoudou D, Goulis DG, Eliopoulos AG. Genetically-Guided Medical Nutrition Therapy in Type 2 Diabetes Mellitus and Pre-diabetes: A Series of n-of-1 Superiority Trials. Front Nutr 2022; 9:772243. [PMID: 35265654 PMCID: PMC8899711 DOI: 10.3389/fnut.2022.772243] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/12/2022] [Indexed: 12/12/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a heterogeneous metabolic disorder of multifactorial etiology that includes genetic and dietary influences. By addressing the latter, medical nutrition therapy (MNT) contributes to the management of T2DM or pre-diabetes toward achieving glycaemic control and improved insulin sensitivity. However, the clinical outcomes of MNT vary and may further benefit from personalized nutritional plans that take into consideration genetic variations associated with individual responses to macronutrients. The aim of the present series of n-of-1 trials was to assess the effects of genetically-guided vs. conventional MNT on patients with pre-diabetes or T2DM. A quasi-experimental, cross-over design was adopted in three Caucasian adult men with either diagnosis. Complete diet, bioclinical and anthropometric assessment was performed and a conventional MNT, based on the clinical practice guidelines was applied for 8 weeks. After a week of “wash-out,” a precision MNT was prescribed for an additional 8-week period, based on the genetic characteristics of each patient. Outcomes of interest included changes in body weight (BW), fasting plasma glucose (FPG), and blood pressure (BP). Collectively, the trials indicated improvements in BW, FPG, BP, and glycosylated hemoglobin (HbA1c) following the genetically-guided precision MNT intervention. Moreover, both patients with pre-diabetes experienced remission of the condition. We conclude that improved BW loss and glycemic control can be achieved in patients with pre-diabetes/T2DM, by coupling MNT to their genetic makeup, guiding optimal diet, macronutrient composition, exercise and oral nutrient supplementation in a personalized manner.
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Affiliation(s)
- Kalliopi K Gkouskou
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Embiodiagnostics Biology Research Company, Heraklion, Greece
| | - Maria G Grammatikopoulou
- Unit of Reproductive Endocrinology, First Department of Obstetrics and Gynecology, Faculty of Health Sciences, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Department of Nutritional Sciences and Dietetics, Faculty of Health Sciences, International Hellenic University, Thessaloniki, Greece
| | - Evgenia Lazou
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Despina Sanoudou
- Clinical Genomics and Pharmacogenomics Unit, Fourth Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Dimitrios G Goulis
- Unit of Reproductive Endocrinology, First Department of Obstetrics and Gynecology, Faculty of Health Sciences, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Aristides G Eliopoulos
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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Chen M, Tsai CW, Chang WS, Xu J, Xu Y, Bau DT, Gu J. Prognostic value of leukocyte telomere length in renal cell carcinoma patients. Am J Cancer Res 2020; 10:3428-3439. [PMID: 33163281 PMCID: PMC7642657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023] Open
Abstract
Telomeres play important roles in cancer initiation and progression. Leukocyte telomere length (LTL) can modulate cancer risk and outcome. We hypothesize that genetically predicted short LTL is associated with worse prognosis in renal cell carcinoma (RCC). A total of 1,086 histologically confirmed RCC patients were included in this study. A weighted genetic risk score (GRS) predictive of LTL was constructed using 10 confirmed LTL-associated single nucleotide polymorphisms (SNPs). The associations of individual SNPs and GRS with recurrence and survival were determined by multivariate Cox proportional hazards analysis. In individual SNP analysis, long LTL-associated allele of rs7675998 in NAF1 gene at chromosome 4 was significantly associated with a reduced risk of recurrence (HR=0.85, 95% CI, 0.73-0.99, P=0.043), while the long LTL-associated allele of rs10936599 in TERC at chromosome 3 conferred a reduced risk of death (HR=0.85, 95% CI, 0.73-1.00, P=0.047). More importantly, genetically predicted LTL was associated with both recurrence and survival. Dichotomized at the median value of GRS, patients with low GRS (indicating short LTL) exhibited significantly increased risks of recurrence (HR=1.26, 95% CI, 1.03-1.54, P=0.025) and death (HR=1.23, 95% CI, 1.00-1.50, P=0.045). Hence, we concluded that genetically predicted short LTL is associated with worse prognosis in RCC patients.
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Affiliation(s)
- Meng Chen
- Department of Clinical Laboratory, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
- Department of Epidemiology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Chia-Wen Tsai
- Department of Epidemiology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
- Terry Fox Cancer Research Laboratory, China Medical University HospitalTaichung, Taiwan
| | - Wen-Shin Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
- Terry Fox Cancer Research Laboratory, China Medical University HospitalTaichung, Taiwan
| | - Junfeng Xu
- Department of Epidemiology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Yifan Xu
- Department of Epidemiology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Da-Tian Bau
- Terry Fox Cancer Research Laboratory, China Medical University HospitalTaichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia UniversityTaichung, Taiwan
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
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Manco L, Bento C, Relvas L, Cunha E, Pereira J, Moreira V, Alvarez M, Maia T, Ribeiro ML. Multi-Locus Models to Address Hb F Variability in Portuguese β-Thalassemia Carriers. Hemoglobin 2020; 44:113-117. [PMID: 32319326 DOI: 10.1080/03630269.2020.1753766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Hb F production is under the influence of major quantitative trait loci (QTL). The present study aims: i) to replicate the association with Hb F for representative genetic variants in the three major Hb F QTLs in a Portuguese sample of β-thalassemia (β-thal) carriers; and ii) to test different genetic multi-locus models to account for the genetic component of Hb F variation. A population sample of 79 Portuguese β-thal carriers (39 males, 40 females), aged between 2 to 70 years old, were genotyped for polymorphisms in the locus control region (LCR)-5' hypersensitive site 4 (5'HS4) rs16912979, XmnI-HBG2 rs7482144, BCL11A rs1427407 and HMIP rs66650371, using standard biomolecular procedures. Univariate linear regression models were used to test for genetic associations with Hb F. The minor alleles of the individual variants BCL11A rs1427407 (T) (0.165), HMIP rs66650371 (3 bp del) (0.247) and XmnI-HBG2 rs7482144 (T) (0.196), were found to be significantly associated with increased levels of Hb F (p = 0.029, p = 0.002 and p = 0.0004, respectively), explaining about 6.0, 12.0 and 15.0% of Hb F variation, respectively. In a multiple linear regression approach, the three loci accounted for about 30.0% of Hb F variance. Two genetic risk scores (GRS), rationalizing the number of minor alleles into a single genetic variable, explained about 30.0 and 32.0% of the Hb F variation. In conclusion, we replicated in β-thal carriers previously reported associations with Hb F. Multi-locus models combining three representative variants of Hb F influencing QTLs can explain a larger amount of Hb F variability.
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Affiliation(s)
- Licínio Manco
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,Department of Haematology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Celeste Bento
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,Department of Haematology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Luís Relvas
- Department of Haematology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Elisabete Cunha
- Department of Haematology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Janet Pereira
- Department of Haematology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Valeria Moreira
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Manuela Alvarez
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Tabita Maia
- Department of Haematology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - M Letícia Ribeiro
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,Department of Haematology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
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8
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Wu Q, Xiao X, Xu Y. Performance of FRAX in Predicting Fractures in US Postmenopausal Women with Varied Race and Genetic Profiles. J Clin Med 2020; 9:E285. [PMID: 31968614 PMCID: PMC7019759 DOI: 10.3390/jcm9010285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/06/2020] [Accepted: 01/14/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Whether the Fracture Risk Assessment Tool (FRAX) performed differently in estimating the 10-year fracture probability in women of different genetic profiling and race remained unclear. METHODS The genomic data in the Women's Health Initiative (WHI) study was analyzed (n = 23,981). The genetic risk score (GRS) was calculated from 14 fracture-associated single nucleotide polymorphisms (SNPs) for each participant. FRAX without bone mineral density (BMD) was used to estimate fracture probability. RESULTS FRAX significantly overestimated the risk of major osteoporotic fracture (MOF) in the WHI study. The most significant overestimation was observed in women with low GRS (predicted/observed ratio (POR): 1.61, 95% CI: 1.45-1.79) specifically Asian women (POR: 3.5, 95% CI 2.48-4.81) and in African American women (POR: 2.59, 95% CI: 2.33-2.87). Compared to the low GRS group, the 10-year probability of MOF adjusted for the FRAX score was 21% and 30% higher in the median GRS group and high GRS group, respectively. Asian, African American, and Hispanic women respectively had a 78%, 76%, and 56% lower hazard than Caucasian women after the FRAX score was adjusted. The results were similar for hip fractures. CONCLUSIONS Our study suggested the FRAX performance varies significantly by both genetic profile and race in postmenopausal women.
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Affiliation(s)
- Qing Wu
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA; (X.X.); (Y.X.)
- Department of Environmental and Occupational Health, School of Public Health, University of Nevada Las Vegas, NV 89154, USA
| | - Xiangxue Xiao
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA; (X.X.); (Y.X.)
- Department of Environmental and Occupational Health, School of Public Health, University of Nevada Las Vegas, NV 89154, USA
| | - Yingke Xu
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA; (X.X.); (Y.X.)
- Department of Environmental and Occupational Health, School of Public Health, University of Nevada Las Vegas, NV 89154, USA
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9
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Yu H, Shi Z, Wu Y, Wang CH, Lin X, Perschon C, Isaacs WB, Helfand BT, Lilly Zheng S, Duggan D, Mo Z, Lu D, Xu J. Concept and benchmarks for assessing narrow-sense validity of genetic risk score values. Prostate 2019; 79:1099-1105. [PMID: 31037745 DOI: 10.1002/pros.23821] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/08/2019] [Accepted: 04/12/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND While higher genetic risk score (GRS) has been statistically associated with increased disease risk (broad-sense validity), the concept and tools for assessing the validity of reported GRS values from tests (narrow-sense validity) are underdeveloped. METHODS We propose two benchmarks for assessing the narrow-sense validity of GRS. The baseline benchmark requires that the mean GRS value in a general population approximates 1.0. The calibration benchmark assesses the agreement between observed risks and estimated risks (GRS values). We assessed benchmark performance for three prostate cancer (PCa) GRS tests, derived from three SNP panels with increasing stringency of selection criteria, in a PCa chemoprevention trial where 714 of 3225 men were diagnosed with PCa during the 4-year follow-up. RESULTS GRS from Panels 1, 2, and 3 were all statistically associated with PCa risk; P = 5.58 × 10-3 , P = 1 × 10-3 , and P = 1.5 × 10-13 , respectively (broad-sense validity). For narrow-sense validity, the mean GRS value among men without PCa was 1.33, 1.09, and 0.98 for Panels 1, 2, and 3, respectively (baseline benchmark). For assessing the calibration benchmark, observed risks were calculated for seven groups of men with GRS values <0.3, 0.3-0.79, 0.8-1.19, 1.2-1.49, 1.5-1.99, 2-2.99, and ≥3. The calibration slope (higher is better) was 0.15, 0.12, and 0.60, and the bias score (lower is better) between the observed risks and GRS values was 0.08, 0.08, and 0.02 for Panels 1, 2, and 3, respectively. CONCLUSION Performance differed considerably among GRS tests. We recommend that all GRS tests be evaluated using the two benchmarks before clinical implementation for individual risk assessment.
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Affiliation(s)
- Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Yishuo Wu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chi-Hsiung Wang
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Xiaoling Lin
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chelsea Perschon
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - William B Isaacs
- Department of Urology and the James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - S Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - David Duggan
- Genetic Basis of Human Disease Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
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Zhang J, Ye X, Wu C, Fu H, Xu W, Hu P. Modeling Gene-Environment Interaction for the Risk of Non-hodgkin Lymphoma. Front Oncol 2019; 8:657. [PMID: 30693270 PMCID: PMC6340069 DOI: 10.3389/fonc.2018.00657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/12/2018] [Indexed: 01/06/2023] Open
Abstract
Background: Non-hodgkin lymphoma (NHL) is one of the most common and deadly cancers. There is limited analysis of gene-environment interactions for the risk of NHL. This study intends to explore the interactions between genetic variants and environmental factors, and how they contribute to NHL risk. Methods: A case-control study was performed in Shanghai, China. The cases were diagnosed between 2003 and 2008 with patients aged 18 years or older. Samples and SNPs which did not satisfy quality control were excluded from the analysis. Weighted and unweighted genetic risk scores (GRS) and environmental risk scores were generated using clustering analysis algorithm. Univariate and multivariable logistic regression analyses were conducted. Moreover, genetics and environment interactions (G × E) were tested on the NHL cases and controls. Results: After quality control, there are 22 SNPs, 11 environmental variables and 5 demographical variables to be explored. For logistic regression analyses, 5 SNPs (rs1800893, rs4251961, rs1800630, rs13306698, rs1799931) and environmental tobacco smoking showed statistically significant associations with the risk of NHL. Odds ratio (OR) and 95% confidence interval (CI) was 10.82 (4.34–28.88) for rs13306698, 2.84 (1.66–4.95) for rs1800893, and 2.54 (1.43–4.58) for rs4251961. For G × E analysis, the interaction between smoking and dichotomized weighted GRS showed statistically significant association with NHL (OR = 0.23, 95% CI = [0.09, 0.61]). Conclusions: Several genetic and environmental risk factors and their interactions associated with the risk of NHL have been identified. Replication in other cohorts is needed to validate the results.
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Affiliation(s)
- Jiahui Zhang
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Xibiao Ye
- Department of Community Health Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Cuie Wu
- School of Public Health, Fudan University, Shanghai, China
| | - Hua Fu
- School of Public Health, Fudan University, Shanghai, China
| | - Wei Xu
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.,Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Pingzhao Hu
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry and Medical Genetics, Faculty of Health Sciences, College of Medicine, University of Manitoba, Winnipeg, MB, Canada.,Research Institute in Oncology and Hematology, Winnipeg, MB, Canada
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11
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Goldstein BA, Knowles JW, Salfati E, Ioannidis JPA, Assimes TL. Corrigendum: Simple, standardized incorporation of genetic risk into non-genetic risk prediction tools for complex traits: coronary heart disease as an example. Front Genet 2015. [PMID: 26217377 PMCID: PMC4493401 DOI: 10.3389/fgene.2015.00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Benjamin A Goldstein
- Department of Biostatistics and Bioinformatics, Center for Predictive Medicine, Duke Clinical Research Institute, Duke University Durham, NC, USA
| | - Joshua W Knowles
- Division of Cardiovascular Medicine, Stanford University Stanford, CA, USA
| | - Elias Salfati
- Division of Cardiovascular Medicine, Stanford University Stanford, CA, USA
| | - John P A Ioannidis
- Department of Medicine, Stanford Prevention Research Center, Stanford University Stanford, CA, USA
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12
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Shi J, Li L, Hong J, Qi L, Cui B, Gu W, Zhang Y, Miao L, Wang R, Wang W, Ning G. Genetic variants determining body fat distribution and sex hormone-binding globulin among Chinese female young adults. J Diabetes 2014; 6:514-8. [PMID: 24628818 DOI: 10.1111/1753-0407.12146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 03/01/2014] [Accepted: 03/03/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Measures of body fat distribution (i.e. waist : hip ratio [WHR]) are major risk factors for diabetes, independent of overall adiposity. The genetic variants related to body fat distribution show sexual dimorphism and particularly affect females. Substantial literature supports a role for sex hormone-binding globulin (SHBG) in the maintenance of glucose homeostasis. The aim of the present study was to examine the association of the genetic risk score of body fat distribution with SHBG levels and insulin resistance in young (14-30 years) Chinese females. METHODS In all, 675 young Chinese females were evaluated in the present study. A genetic risk score (GRS) was calculated on the basis of 12 established variants associated with body fat distribution. The main outcome variable was serum SHBG levels and homeostasis model assessment of insulin resistance (HOMA-IR). RESULTS The GRS of body fat distribution was significantly associated with decreasing serum SHBG levels (P = 0.018), independent of body mass index and WHR. In addition, the GRS and SHBG showed additive effects on HOMA-IR (P = 0.004). CONCLUSIONS The GRS of body fat distribution reflects serum SHBG levels, and the GRS and SHBG jointly influence the risk of insulin resistance.
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Affiliation(s)
- Juan Shi
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrinology and Metabolism, Endocrine and Metabolic E-Institutes of Shanghai Universities (EISU) and Key Laboratory for Endocrinology and Metabolism of Chinese Health Ministry, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
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Che R, Motsinger-Reif AA. Evaluation of genetic risk score models in the presence of interaction and linkage disequilibrium. Front Genet 2013; 4:138. [PMID: 23888168 PMCID: PMC3719135 DOI: 10.3389/fgene.2013.00138] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 07/01/2013] [Indexed: 01/16/2023] Open
Abstract
In the area of genetic epidemiology, genetic risk predictive modeling is becoming an important area of translational success. As an increasing number of genetic variants are successfully discovered, the use of multiple genetic variants in constructing a genetic risk score (GRS) for modeling has been widely applied using a variety of approaches. Previously, we compared the performance of a simple, additive GRS with weighted GRS approaches, but our initial simulation experiment assumed very simple models without many of the complications found in real genetic studies. In particular, interactions between variants and linkage disequilibrium (LD) (indirect mapping) remain important and challenging problems for GRS modeling. In the present study, we applied two simulation strategies to mimic various types of epistasis to evaluate their impact on the performance of the GRS models. We simulated a range of models demonstrating statistical interaction and linkage disequilibrium. Three genetic risk models were compared in terms of power, type I error, C-statistic and AIC, including a simple count GRS (SC-GRS), an odds ratio weighted GRS (OR-GRS) and an explained variance weighted GRS (EV-GRS). Simulation factors of interest included allele frequencies, effect sizes, strengths of interaction, degrees of LD and heritability. We extensively examined the extent to how these interactions could influence the performance of genetic risk models. Our results show that the weighted methods outperform simple count method in general even if interaction or LD is present, with well controlled type I error.
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Affiliation(s)
- Ronglin Che
- Department of Statistics, Bioinformatics Research Center, North Carolina State University Raleigh, NC, USA
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Jo J, Nam CM, Sull JW, Yun JE, Kim SY, Lee SJ, Kim YN, Park EJ, Kimm H, Jee SH. Prediction of Colorectal Cancer Risk Using a Genetic Risk Score: The Korean Cancer Prevention Study-II (KCPS-II). Genomics Inform 2012; 10:175-83. [PMID: 23166528 PMCID: PMC3492653 DOI: 10.5808/gi.2012.10.3.175] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 08/21/2012] [Accepted: 08/23/2012] [Indexed: 01/07/2023] Open
Abstract
Colorectal cancer (CRC) is among the leading causes of cancer deaths and can be caused by environmental factors as well as genetic factors. Therefore, we developed a prediction model of CRC using genetic risk scores (GRS) and evaluated the effects of conventional risk factors, including family history of CRC, in combination with GRS on the risk of CRC in Koreans. This study included 187 cases (men, 133; women, 54) and 976 controls (men, 554; women, 422). GRS were calculated with most significantly associated single-nucleotide polymorphism with CRC through a genomewide association study. The area under the curve (AUC) increased by 0.5% to 5.2% when either counted or weighted GRS was added to a prediction model consisting of age alone (AUC 0.687 for men, 0.598 for women) or age and family history of CRC (AUC 0.692 for men, 0.603 for women) for both men and women. Furthermore, the risk of CRC significantly increased for individuals with a family history of CRC in the highest quartile of GRS when compared to subjects without a family history of CRC in the lowest quartile of GRS (counted GRS odds ratio [OR], 47.9; 95% confidence interval [CI], 4.9 to 471.8 for men; OR, 22.3; 95% CI, 1.4 to 344.2 for women) (weighted GRS OR, 35.9; 95% CI, 5.9 to 218.2 for men; OR, 18.1, 95% CI, 3.7 to 88.1 for women). Our findings suggest that in Koreans, especially in Korean men, GRS improve the prediction of CRC when considered in conjunction with age and family history of CRC.
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Affiliation(s)
- Jaeseong Jo
- Institute for Health Promotion and Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul 120-752, Korea. ; Department of Public Health, Graduate School of Yonsei University, Seoul 120-752, Korea
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