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Hsieh AR, Luo YL, Bao BY, Chou TC. Comparative analysis of genetic risk scores for predicting biochemical recurrence in prostate cancer patients after radical prostatectomy. BMC Urol 2024; 24:136. [PMID: 38956663 PMCID: PMC11218119 DOI: 10.1186/s12894-024-01524-6] [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: 12/06/2023] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND In recent years, Genome-Wide Association Studies (GWAS) has identified risk variants related to complex diseases, but most genetic variants have less impact on phenotypes. To solve the above problems, methods that can use variants with low genetic effects, such as genetic risk score (GRS), have been developed to predict disease risk. METHODS As the GRS model with the most incredible prediction power for complex diseases has not been determined, our study used simulation data and prostate cancer data to explore the disease prediction power of three GRS models, including the simple count genetic risk score (SC-GRS), the direct logistic regression genetic risk score (DL-GRS), and the explained variance weighted GRS based on directed logistic regression (EVDL-GRS). RESULTS AND CONCLUSIONS We used 26 SNPs to establish GRS models to predict the risk of biochemical recurrence (BCR) after radical prostatectomy. Combining clinical variables such as age at diagnosis, body mass index, prostate-specific antigen, Gleason score, pathologic T stage, and surgical margin and GRS models has better predictive power for BCR. The results of simulation data (statistical power = 0.707) and prostate cancer data (area under curve = 0.8462) show that DL-GRS has the best prediction performance. The rs455192 was the most relevant locus for BCR (p = 2.496 × 10-6) in our study.
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Affiliation(s)
- Ai-Ru Hsieh
- Department of Statistics, Tamkang University, New Taipei City, 251301, Taiwan.
| | - Yi-Ling Luo
- Department of Public Health, College of Public Health, China Medical University, Taichung, 40402, Taiwan
| | - Bo-Ying Bao
- School of Pharmacy, China Medical University, Taichung, 406040, Taiwan
- Department of Nursing, Asia University, Taichung, 41354, Taiwan
| | - Tzu-Chieh Chou
- Department of Public Health, College of Public Health, China Medical University, Taichung, 40402, Taiwan
- Department of Health Risk Management, College of Public Health, China Medical University, Taichung, 40402, Taiwan
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Sun TH, Wang CC, Liu TY, Lo SC, Huang YX, Chien SY, Chu YD, Tsai FJ, Hsu KC. Utility of polygenic scores across diverse diseases in a hospital cohort for predictive modeling. Nat Commun 2024; 15:3168. [PMID: 38609356 PMCID: PMC11014845 DOI: 10.1038/s41467-024-47472-5] [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: 06/07/2023] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Polygenic scores estimate genetic susceptibility to diseases. We systematically calculated polygenic scores across 457 phenotypes using genotyping array data from China Medical University Hospital. Logistic regression models assessed polygenic scores' ability to predict disease traits. The polygenic score model with the highest accuracy, based on maximal area under the receiver operating characteristic curve (AUC), is provided on the GeneAnaBase website of the hospital. Our findings indicate 49 phenotypes with AUC greater than 0.6, predominantly linked to endocrine and metabolic diseases. Notably, hyperplasia of the prostate exhibited the highest disease prediction ability (P value = 1.01 × 10-19, AUC = 0.874), highlighting the potential of these polygenic scores in preventive medicine and diagnosis. This study offers a comprehensive evaluation of polygenic scores performance across diverse human traits, identifying promising applications for precision medicine and personalized healthcare, thereby inspiring further research and development in this field.
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Affiliation(s)
- Ting-Hsuan Sun
- Artificial Intelligence Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Chia-Chun Wang
- Artificial Intelligence Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Ting-Yuan Liu
- Million-person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Shih-Chang Lo
- Artificial Intelligence Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Yi-Xuan Huang
- Artificial Intelligence Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Shang-Yu Chien
- Artificial Intelligence Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Yu-De Chu
- Artificial Intelligence Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan.
- School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan.
- Division of Pediatric Genetics, Children's Hospital of China Medical University, Taichung, 40447, Taiwan.
- Department of Biotechnology and Bioinformatics, Asia University, Taichung, 41354, Taiwan.
| | - Kai-Cheng Hsu
- Artificial Intelligence Center, China Medical University Hospital, Taichung, 40447, Taiwan.
- Department of Neurology, China Medical University Hospital, Taichung, 40447, Taiwan.
- Department of Medicine, China Medical University, Taichung, 40402, Taiwan.
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Luukkonen PK, Färkkilä M, Jula A, Salomaa V, Männistö S, Lundqvist A, Perola M, Åberg F. Abdominal obesity and alcohol use modify the impact of genetic risk for incident advanced liver disease in the general population. Liver Int 2023; 43:1035-1045. [PMID: 36843445 DOI: 10.1111/liv.15554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 02/28/2023]
Abstract
BACKGROUND & AIMS Genetic variants, abdominal obesity and alcohol use are risk factors for incident liver disease (ILD). We aimed to study whether variants either alone or when aggregated into genetic risk scores (GRSs) associate with ILD, and whether waist-hip ratio (WHR) or alcohol use interacts with this risk. METHODS Our study included 33 770 persons (mean age 50 years, 47% men) who participated in health-examination surveys (FINRISK 1992-2012 or Health 2000) with data on alcohol use, WHR and 63 genotypes associated with liver disease. Data were linked with national health registers for liver-related outcomes (hospitalizations, malignancies and death). Exclusions were baseline clinical liver disease. Mean follow-up time was 12.2 years. Cox regression analyses between variants and ILD were adjusted for age, sex and BMI. RESULTS Variants in PNPLA3, IFNL4, TM6SF2, FDFT1, PPP1R3B, SERPINA1 and HSD17B13 were associated with ILD. GRSs calculated from these variants were not associated with WHR or alcohol use, but were exponentially associated with ILD (up to 25-fold higher risk in high versus low score). The risk of ILD in individuals with high GRS and high WHR or alcohol use compared with those with none of these risk factors was increased by up to 90-fold. GRSs provided new prognostic information particularly in individuals with high WHR. CONCLUSIONS The effect of multiple genetic variants on the risk of ILD is potentiated by abdominal obesity and alcohol use. Simple GRSs may help to identify individuals with adverse lifestyle who are at a particularly high risk of ILD.
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Affiliation(s)
- Panu K Luukkonen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland.,Abdominal Center, Helsinki University Hospital, Helsinki, Finland.,Department of Internal Medicine, University of Helsinki, Helsinki, Finland
| | - Martti Färkkilä
- Clinic of Gastroenterology, Helsinki University, Helsinki University Hospital, Helsinki, Finland
| | - Antti Jula
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Satu Männistö
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Fredrik Åberg
- Transplantation and Liver Surgery Clinic, Helsinki University Hospital, Helsinki University, Helsinki, Finland
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Determining the role of genetic risk scores in symptomatic cancer detection. Br J Gen Pract 2023; 73:106-107. [PMID: 36823064 PMCID: PMC9976822 DOI: 10.3399/bjgp23x732069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
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Mao Z, Gray ALH, Thyagarajan B, Bostick RM. Antioxidant enzyme and DNA base repair genetic risk scores' associations with systemic oxidative stress biomarker in pooled cross-sectional studies. FRONTIERS IN AGING 2023; 4:1000166. [PMID: 37152862 PMCID: PMC10161255 DOI: 10.3389/fragi.2023.1000166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/28/2023] [Indexed: 05/09/2023]
Abstract
Background: Oxidative stress is hypothesized to contribute to the pathogenesis of several chronic diseases. Numerous dietary and lifestyle factors are associated with oxidative stress; however, little is known about associations of genetic factors, individually or jointly with dietary and lifestyle factors, with oxidative stress in humans. Methods: We genotyped 22 haplotype-tagging single nucleotide polymorphisms (SNPs) in 3 antioxidant enzyme (AE) genes and 79 SNPs in 14 DNA base excision repair (BER) genes to develop oxidative stress-specific AE and BER genetic risk scores (GRS) in two pooled cross-sectional studies (n = 245) of 30-74-year-old, White, cancer- and inflammatory bowel disease-free adults. Of the genotypes, based on their associations with a systemic oxidative stress biomarker, plasma F2-isoprostanes (FiP) concentrations, we selected 4 GSTP1 SNPs for an AE GRS, and 12 SNPs of 5 genes (XRCC1, TDG, PNKP, MUTYH, and FEN1) for a BER GRS. We also calculated a previously-reported, validated, questionnaire-based, oxidative stress biomarker-weighted oxidative balance score (OBS) comprising 17 anti- and pro-oxidant dietary and lifestyle exposures, with higher scores representing a higher predominance of antioxidant exposures. We used general linear regression to assess adjusted mean FiP concentrations across GRS and OBS tertiles, separately and jointly. Results: The adjusted mean FiP concentrations among those in the highest relative to the lowest oxidative stress-specific AE and BER GRS tertiles were, proportionately, 11.8% (p = 0.12) and 21.2% (p = 0.002) higher, respectively. In the joint AE/BER GRS analysis, the highest estimated mean FiP concentration was among those with jointly high AE/BER GRS. Mean FiP concentrations across OBS tertiles were similar across AE and BER GRS strata. Conclusion: Our pilot study findings suggest that DNA BER, and possibly AE, genotypes collectively may be associated with systemic oxidative stress in humans, and support further research in larger, general populations.
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Affiliation(s)
- Ziling Mao
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Abigail L. H. Gray
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States
| | - Roberd M. Bostick
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
- *Correspondence: Roberd M. Bostick,
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Dite GS, Spaeth E, Murphy NM, Allman R. A combined clinical and genetic model for predicting risk of ovarian cancer. Eur J Cancer Prev 2023; 32:57-64. [PMID: 36503897 PMCID: PMC9746333 DOI: 10.1097/cej.0000000000000771] [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: 08/18/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Women with a family history of ovarian cancer or a pathogenic or likely pathogenic gene variant are at high risk of the disease, but very few women have these risk factors. We assessed whether a combined polygenic and clinical risk score could predict risk of ovarian cancer in population-based women who would otherwise be considered as being at average risk. METHODS We used the UK Biobank to conduct a prospective cohort study assessing the performance of 10-year ovarian cancer risks based on a polygenic risk score, a clinical risk score and a combined risk score. We used Cox regression to assess association, Harrell's C-index to assess discrimination and Poisson regression to assess calibration. RESULTS The combined risk model performed best and problems with calibration were overcome by recalibrating the model, which then had a hazard ratio per quintile of risk of 1.338 [95% confidence interval (CI), 1.152-1.553], a Harrell's C-index of 0.663 (95% CI, 0.629-0.698) and overall calibration of 1.000 (95% CI, 0.874-1.145). In the refined model with estimates based on the entire dataset, women in the top quintile of 10-year risk were at 1.387 (95% CI, 1.086-1.688) times increased risk, while women in the top quintile of full-lifetime risk were at 1.527 (95% CI, 1.187-1.866) times increased risk compared with the population. CONCLUSION Identification of women who are at high risk of ovarian cancer can allow healthcare providers and patients to engage in joint decision-making discussions around the risks and benefits of screening options or risk-reducing surgery.
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Affiliation(s)
| | - Erika Spaeth
- Phenogen Sciences Inc, Charlotte, North Carolina, USA
| | | | - Richard Allman
- Genetic Technologies Limited, Fitzroy, Victoria, Australia
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Talli I, Dovrolis N, Oulas A, Stavrakaki S, Makedou K, Spyrou GM, Maroulakou I. Novel clinical, molecular and bioinformatics insights into the genetic background of autism. Hum Genomics 2022; 16:39. [PMID: 36117207 PMCID: PMC9482726 DOI: 10.1186/s40246-022-00415-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background Clinical classification of autistic patients based on current WHO criteria provides a valuable but simplified depiction of the true nature of the disorder. Our goal is to determine the biology of the disorder and the ASD-associated genes that lead to differences in the severity and variability of clinical features, which can enhance the ability to predict clinical outcomes. Method Novel Whole Exome Sequencing data from children (n = 33) with ASD were collected along with extended cognitive and linguistic assessments. A machine learning methodology and a literature-based approach took into consideration known effects of genetic variation on the translated proteins, linking them with specific ASD clinical manifestations, namely non-verbal IQ, memory, attention and oral language deficits. Results Linear regression polygenic risk score results included the classification of severe and mild ASD samples with a 81.81% prediction accuracy. The literature-based approach revealed 14 genes present in all sub-phenotypes (independent of severity) and others which seem to impair individual ones, highlighting genetic profiles specific to mild and severe ASD, which concern non-verbal IQ, memory, attention and oral language skills. Conclusions These genes can potentially contribute toward a diagnostic gene-set for determining ASD severity. However, due to the limited number of patients in this study, our classification approach is mostly centered on the prediction and verification of these genes and does not hold a diagnostic nature per se. Substantial further experimentation is required to validate their role as diagnostic markers. The use of these genes as input for functional analysis highlights important biological processes and bridges the gap between genotype and phenotype in ASD.
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Affiliation(s)
- Ioanna Talli
- Department of Italian Language and Literature, School of Philosophy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolas Dovrolis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Anastasis Oulas
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, 2370 Nicosia, Cyprus, P.O. Box 23462, 1683, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, 6 International Airport Avenue, 2370 Nicosia, Cyprus, P.O. Box 23462, 1683, Nicosia, Cyprus
| | - Stavroula Stavrakaki
- Department of Italian Language and Literature, School of Philosophy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kali Makedou
- Laboratory of Biochemistry, School of Medicine, AHEPA General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, 2370 Nicosia, Cyprus, P.O. Box 23462, 1683, Nicosia, Cyprus. .,The Cyprus School of Molecular Medicine, 6 International Airport Avenue, 2370 Nicosia, Cyprus, P.O. Box 23462, 1683, Nicosia, Cyprus.
| | - Ioanna Maroulakou
- Laboratory of Genetics, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece.
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Siltari A, Lönnerbro R, Pang K, Shiranov K, Asiimwe A, Evans-Axelsson S, Franks B, Kiran A, Murtola TJ, Schalken J, Steinbeisser C, Bjartell A, Auvinen A, Smith E, N'Dow J, Plass K, Ribal M, Mottet N, Moris L, Lardas M, Van den Broeck T, Willemse PP, Gandaglia G, Campi R, Greco I, Gacci M, Serni S, Briganti A, Crosti D, Meoni M, Garzonio R, Bangma R, Roobol M, Remmers S, Tilki D, Visakorpi T, Talala K, Tammela T, van Hemelrijck M, Bayer K, Lejeune S, Taxiarchopoulou G, van Diggelen F, Senthilkumar K, Schutte S, Byrne S, Fialho L, Cardone A, Gono P, De Vetter M, Ceke K, De Meulder B, Auffray C, Balaur IA, Taibi N, Power S, Kermani NZ, van Bochove K, Cavelaars M, Moinat M, Voss E, Bernini C, Horgan D, Fullwood L, Holtorf M, Lancet D, Bernstein G, Omar I, MacLennan S, Maclennan S, Healey J, Huber J, Wirth M, Froehner M, Brenner B, Borkowetz A, Thomas C, Horn F, Reiche K, Kreux M, Josefsson A, Tandefekt DG, Hugosson J, Huisman H, Hofmacher T, Lindgren P, Andersson E, Fridhammar A, Vizcaya D, Verholen F, Zong J, Butler-Ransohoff JE, Williamson T, Chandrawansa K, Dlamini D, waldeck R, Molnar M, Bruno A, Herrera R, Jiang S, Nevedomskaya E, Fatoba S, Constantinovici N, Maass M, Torremante P, Voss M, Devecseri Z, Cuperus G, Abott T, Dau C, Papineni K, Wang-Silvanto J, Hass S, Snijder R, Doye V, Wang X, Garnham A, Lambrecht M, Wolfinger R, Rogiers S, Servan A, Lefresne F, Caseriego J, Samir M, Lawson J, Pacoe K, Robinson P, Jaton B, Bakkard D, Turunen H, Kilkku O, Pohjanjousi P, Voima O, Nevalaita L, Reich C, Araujo S, Longden-Chapman E, Burke D, Agapow P, Derkits S, Licour M, McCrea C, Payne S, Yong A, Thompson L, Lujan F, Bussmann M, Köhler I. How well do polygenic risk scores identify men at high risk for prostate cancer? Systematic review and meta-analysis. Clin Genitourin Cancer 2022; 21:316.e1-316.e11. [PMID: 36243664 DOI: 10.1016/j.clgc.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Genome-wide association studies have revealed over 200 genetic susceptibility loci for prostate cancer (PCa). By combining them, polygenic risk scores (PRS) can be generated to predict risk of PCa. We summarize the published evidence and conduct meta-analyses of PRS as a predictor of PCa risk in Caucasian men. PATIENTS AND METHODS Data were extracted from 59 studies, with 16 studies including 17 separate analyses used in the main meta-analysis with a total of 20,786 cases and 69,106 controls identified through a systematic search of ten databases. Random effects meta-analysis was used to obtain pooled estimates of area under the receiver-operating characteristic curve (AUC). Meta-regression was used to assess the impact of number of single-nucleotide polymorphisms (SNPs) incorporated in PRS on AUC. Heterogeneity is expressed as I2 scores. Publication bias was evaluated using funnel plots and Egger tests. RESULTS The ability of PRS to identify men with PCa was modest (pooled AUC 0.63, 95% CI 0.62-0.64) with moderate consistency (I2 64%). Combining PRS with clinical variables increased the pooled AUC to 0.74 (0.68-0.81). Meta-regression showed only negligible increase in AUC for adding incremental SNPs. Despite moderate heterogeneity, publication bias was not evident. CONCLUSION Typically, PRS accuracy is comparable to PSA or family history with a pooled AUC value 0.63 indicating mediocre performance for PRS alone.
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Chang EK, Gadzinski AJ, Nyame YA. Blood and urine biomarkers in prostate cancer: Are we ready for reflex testing in men with an elevated prostate-specific antigen? Asian J Urol 2021; 8:343-353. [PMID: 34765442 PMCID: PMC8566358 DOI: 10.1016/j.ajur.2021.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 10/28/2022] Open
Abstract
Objective There is no consensus on the role of biomarkers in determining the utility of prostate biopsy in men with elevated prostate-specific antigen (PSA). There are numerous biomarkers such as prostate health index, 4Kscore, prostate cancer antigen 3, ExoDX, SelectMDx, and Mi-Prostate Score that may be useful in this decision-making process. However, it is unclear whether any of these tests are accurate and cost-effective enough to warrant being a widespread reflex test following an elevated PSA. Our goal was to report on the clinical utility of these blood and urine biomarkers in prostate cancer screening. Methods We performed a systematic review of studies published between January 2000 and October 2020 to report the available parameters and cost-effectiveness of the aforementioned diagnostic tests. We focus on the negative predictive value, the area under the curve, and the decision curve analysis in comparing reflexive tests due to their relevance in evaluating diagnostic screening tests. Results Overall, the biomarkers are roughly equivalent in predictive accuracy. Each test has additional clinical utility to the current diagnostic standard of care, but the added benefit is not substantial to justify using the test reflexively after an elevated PSA. Conclusions Our findings suggest these biomarkers should not be used in binary fashion and should be understood in the context of pre-existing risk predictors, patient's ethnicity, cost of the test, patient life-expectancy, and patient goals. There are more recent diagnostic tools such as multi-parametric magnetic resonance imaging, polygenic single-nucleotide panels, IsoPSA, and miR Sentinel tests that are promising in the realm of prostate cancer screening and need to be investigated further to be considered a consensus reflexive test in the setting of prostate cancer screening.
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Affiliation(s)
- Edward K Chang
- Department of Urology, University of Washington Medical Center, Seattle, WA, USA
| | - Adam J Gadzinski
- Department of Urology, University of Washington Medical Center, Seattle, WA, USA
| | - Yaw A Nyame
- Department of Urology, University of Washington Medical Center, Seattle, WA, USA.,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Abstract
Prostate cancer represents a significant health care burden in the United States due to its incidence, treatment-related morbidity, and cancer-specific mortality. The burden begins with prostate-specific antigen screening, which has been subject to controversy due to concerns of overdiagnosis and overtreatment. Advancements in molecular oncology have provided evidence for the inherited predisposition to prostate cancer, which could improve individualized, risk-adapted approaches to screening and mitigate the harms of routine screening. This review presents the current evidence for the genetic basis of prostate cancer and novel genetically informed, risk-adapted screening strategies for prostate cancer.
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Saunders EJ, Kote-Jarai Z, Eeles RA. Identification of Germline Genetic Variants that Increase Prostate Cancer Risk and Influence Development of Aggressive Disease. Cancers (Basel) 2021; 13:760. [PMID: 33673083 PMCID: PMC7917798 DOI: 10.3390/cancers13040760] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer (PrCa) is a heterogeneous disease, which presents in individual patients across a diverse phenotypic spectrum ranging from indolent to fatal forms. No robust biomarkers are currently available to enable routine screening for PrCa or to distinguish clinically significant forms, therefore late stage identification of advanced disease and overdiagnosis plus overtreatment of insignificant disease both remain areas of concern in healthcare provision. PrCa has a substantial heritable component, and technological advances since the completion of the Human Genome Project have facilitated improved identification of inherited genetic factors influencing susceptibility to development of the disease within families and populations. These genetic markers hold promise to enable improved understanding of the biological mechanisms underpinning PrCa development, facilitate genetically informed PrCa screening programmes and guide appropriate treatment provision. However, insight remains largely lacking regarding many aspects of their manifestation; especially in relation to genes associated with aggressive phenotypes, risk factors in non-European populations and appropriate approaches to enable accurate stratification of higher and lower risk individuals. This review discusses the methodology used in the elucidation of genetic loci, genes and individual causal variants responsible for modulating PrCa susceptibility; the current state of understanding of the allelic spectrum contributing to PrCa risk; and prospective future translational applications of these discoveries in the developing eras of genomics and personalised medicine.
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Affiliation(s)
- Edward J. Saunders
- The Institute of Cancer Research, London SM2 5NG, UK; (Z.K.-J.); (R.A.E.)
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, London SM2 5NG, UK; (Z.K.-J.); (R.A.E.)
| | - Rosalind A. Eeles
- The Institute of Cancer Research, London SM2 5NG, UK; (Z.K.-J.); (R.A.E.)
- Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
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Dorababu A. Report on Recently (2017–20) Designed Quinoline‐Based Human Cancer Cell Growth Inhibitors. ChemistrySelect 2020. [DOI: 10.1002/slct.202003888] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Atukuri Dorababu
- Department of Chemistry SRMPP Govt. First Grade College Huvinahadagali 583219 India
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Black MH, Li S, LaDuca H, Lo M, Chen J, Hoiness R, Gutierrez S, Tippin‐Davis B, Lu H, Gielzak M, Wiley K, Shi Z, Wei J, Zheng SL, Helfand BT, Isaacs W, Xu J. Validation of a prostate cancer polygenic risk score. Prostate 2020; 80:1314-1321. [PMID: 33258481 PMCID: PMC7590110 DOI: 10.1002/pros.24058] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/31/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genome-wide association studies have identified over 100 single-nucleotide polymorphisms (SNPs) associated with prostate cancer (PrCa), and polygenic risk scores (PRS) based on their combined genotypes have been developed for risk stratification. We aimed to assess the contribution of PRS to PrCa risk in a large multisite study. METHODS The sample included 1972 PrCa cases and 1919 unaffected controls. Next-generation sequencing was used to assess pathogenic variants in 14 PrCa-susceptibility genes and 72 validated PrCa-associated SNPs. We constructed a population-standardized PRS and tested its association with PrCa using logistic regression adjusted for age and family history of PrCa. RESULTS The mean age of PrCa cases at diagnosis and age of controls at testing/last clinic visit was 59.5 ± 7.2 and 57.2 ± 13.0 years, respectively. Among 1740 cases with pathology data, 57.4% had Gleason score ≤ 6, while 42.6% had Gleason score ≥ 8. In addition, 39.6% cases and 20.1% controls had a family history of PrCa. The PRS was significantly higher in cases than controls (mean ± SD: 1.42 ± 1.11 vs 1.02 ± 0.76; P < .0001). Compared with men in the 1st quartile of age-adjusted PRS, those in the 2nd, 3rd, and 4th quartile were 1.58 (95% confidence interval [CI]: 1.31-1.90), 2.36 (95% CI: 1.96-2.84), and 3.98 (95% CI: 3.29-4.82) times as likely to have PrCa (all P < .0001). Adjustment for family history yielded similar results. PRS predictive performance was consistent with prior literature (area under the receiver operating curve = 0.64; 95% CI: 0.62-0.66). CONCLUSIONS These data suggest that a 72-SNP PRS is predictive of PrCa, supporting its potential use in clinical risk assessment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Marta Gielzak
- Department of Urology, The James Buchanan Brady Urologic InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Kathleen Wiley
- Department of Urology, The James Buchanan Brady Urologic InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Zhuqing Shi
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - Jun Wei
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - Siqun Lilly Zheng
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - Brian T. Helfand
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - William Isaacs
- Department of Urology, The James Buchanan Brady Urologic InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Jianfeng Xu
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
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15
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New variants in NLRP3 inflammasome genes increase risk for asthma and Blomia tropicalis-induced allergy in a Brazilian population. Cytokine X 2020; 2:100032. [PMID: 33015616 PMCID: PMC7522708 DOI: 10.1016/j.cytox.2020.100032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 02/07/2023] Open
Abstract
Atopic asthma is a chronic lung disease of lower airways caused mainly due to action of T-helper (Th) 2 type cytokines, eosinophilic inflammation, mucus hypersecretion and airway remodelling. Interleukin (IL)-33 increases type 2 immunity polarization in airway playing critical role in eosinophilic asthma. On the other hand, NLRP3 inflammasome activation results in the release of caspase-1 (Casp-1) which, in its turn, promotes IL-33 inactivation. Recent studies have shown associations between NLRP3 variants and inflammatory diseases. However, no study with genes in NLRP3 inflammassome route has been conducted so far with asthma and atopy in any population to date. Blood samples were collected from 1246 asthmatic and non-asthmatic children. Associations were tested for single nucleotide polymorphism (SNP)s in NLRP3 and CASP1 with asthma and markers of atopy and in cultures stimulated with Blomia tropicalis (Bt) mite crude extract. The T allele of rs4925648 (NLRP3) was associated with increased asthma risk (OR 1.50, P = 0.005). In addition, the T allele of rs12130711 polymorphism, whithin the same gene, acted as a protector factor for asthma (OR 0.78, P = 0.038). On the other hand, the C allele of rs4378247 NLRP3 variant was associated with lower levels of IL-13 production when peripheral blood cells were stimulated with Bt (OR 0.39, P = 4E-04). In addition, the greater the number of risk alleles in IL33/NLRP3/CASP1 route the greater was the risk for asthma. The T allele of rs7925706 CASP1 variant was also associated with increased risk for asthma (OR 1.47, P = 0.008). In addition, this same allele increased the eosinophil counts in blood (mm3) in asthmatic individuals compared with non-asthmatic (P = 0.0004). These results suggest that NLRP3 and CASP1 polymorphisms may be associated with susceptibility for asthma and markers of atopy in our population.
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16
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Yanes T, McInerney-Leo AM, Law MH, Cummings S. The emerging field of polygenic risk scores and perspective for use in clinical care. Hum Mol Genet 2020; 29:R165-R176. [DOI: 10.1093/hmg/ddaa136] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
Genetic testing is used widely for diagnostic, carrier and predictive testing in monogenic diseases. Until recently, there were no genetic testing options available for multifactorial complex diseases like heart disease, diabetes and cancer. Genome-wide association studies (GWAS) have been invaluable in identifying single-nucleotide polymorphisms (SNPs) associated with increased or decreased risk for hundreds of complex disorders. For a given disease, SNPs can be combined to generate a cumulative estimation of risk known as a polygenic risk score (PRS). After years of research, PRSs are increasingly used in clinical settings. In this article, we will review the literature on how both genome-wide and restricted PRSs are developed and the relative merit of each. The validation and evaluation of PRSs will also be discussed, including the recognition that PRS validity is intrinsically linked to the methodological and analytical approach of the foundation GWAS together with the ethnic characteristics of that cohort. Specifically, population differences may affect imputation accuracy, risk magnitude and direction. Even as PRSs are being introduced into clinical practice, there is a push to combine them with clinical and demographic risk factors to develop a holistic disease risk. The existing evidence regarding the clinical utility of PRSs is considered across four different domains: informing population screening programs, guiding therapeutic interventions, refining risk for families at high risk, and facilitating diagnosis and predicting prognostic outcomes. The evidence for clinical utility in relation to five well-studied disorders is summarized. The potential ethical, legal and social implications are also highlighted.
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Affiliation(s)
- Tatiane Yanes
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Aideen M McInerney-Leo
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Matthew H Law
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Herston QLD 4006, Australia
- Faculty of Health, School of Biomedical Sciences, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove QLD 4059, Australia
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17
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Yu H, Shi Z, Lin X, Bao Q, Jia H, Wei J, Helfand BT, Zheng SL, Duggan D, Lu D, Mo Z, Xu J. Broad- and narrow-sense validity performance of three polygenic risk score methods for prostate cancer risk assessment. Prostate 2020; 80:83-87. [PMID: 31634418 DOI: 10.1002/pros.23920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/02/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND Several polygenic risk score (PRS) methods are available for measuring the cumulative effect of multiple risk-associated single nucleotide polymorphisms (SNPs). Their performance in predicting risk at the individual level has not been well studied. METHODS We compared the performance of three PRS methods for prostate cancer risk assessment in a clinical trial cohort, including genetic risk score (GRS), pruning and thresholding (P + T), and linkage disequilibrium prediction (LDpred). Performance was evaluated for score deciles (broad-sense validity) and score values (narrow-sense validity). RESULTS A training process was required to identify the best P + T model (397 SNPs) and LDpred model (3 011 362 SNPs). In contrast, GRS was directly calculated based on 110 established risk-associated SNPs. For broad-sense validity in the testing population, higher deciles were significantly associated with higher observed risk; Ptrend was 7.40 × 10-11 , 7.64 × 10-13 , and 7.51 × 10-10 for GRS, P + T, and LDpred, respectively. For narrow-sense validity, the calibration slope (1 is best) was 1.03, 0.77, and 0.87, and mean bias score (0 is best) was 0.09, 0.21, and 0.10 for GRS, P + T, and LDpred, respectively. CONCLUSIONS The performance of GRS was better than P + T and LDpred. Fewer and well-established SNPs of GRS also make it more feasible and interpretable for genetic testing at the individual level.
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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
| | - Xiaoling Lin
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Quanwa Bao
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Haifei Jia
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jun Wei
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Siqun L Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - David Duggan
- Translational Genomics Research Institute, An Affiliate of City of Hope, Phoenix, Arizona
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
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18
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Na R, Labbate C, Yu H, Shi Z, Fantus RJ, Wang CH, Andriole GL, Isaacs WB, Zheng SL, Helfand BT, Xu J. Single-Nucleotide Polymorphism-Based Genetic Risk Score and Patient Age at Prostate Cancer Diagnosis. JAMA Netw Open 2019; 2:e1918145. [PMID: 31880795 PMCID: PMC6991229 DOI: 10.1001/jamanetworkopen.2019.18145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
IMPORTANCE Few studies have evaluated the association between a single-nucleotide polymorphism-based genetic risk score (GRS) and patient age at prostate cancer (PCa) diagnosis. OBJECTIVES To test the association between a GRS and patient age at PCa diagnosis and to compare the performance of a GRS with that of family history (FH) in PCa risk stratification. DESIGN, SETTING, AND PARTICIPANTS A cohort study of 3225 white men was conducted as a secondary analysis of the Reduction by Dutasteride of Prostate Cancer Events (REDUCE) chemoprevention trial, a 4-year, randomized, double-blind, placebo-controlled multicenter study conducted from March 2003 to April 2009 to evaluate the safety and efficacy of dutasteride in reducing PCa events. Participants were confirmed to be cancer free by prostate biopsy (6-12 cores) within 6 months prior to the study and underwent 10 core biopsies every 2 years per protocol. The dates for performing data analysis were from July 2016 to October 2019. INTERVENTIONS A well-established, population-standardized GRS was calculated for each participant based on 110 known PCa risk-associated single-nucleotide polymorphisms, which is a relative risk compared with the general population. Men were classified into 3 GRS risk groups based on predetermined cutoff values: low (<0.50), average (0.50-1.49), and high (≥1.50). MAIN OUTCOMES AND MEASURES Prostate cancer diagnosis-free survival among men of different risk groups. RESULTS Among 3225 men (median age, 63 years [interquartile range, 58-67 years]) in the study, 683 (21%) were classified as low risk, 1937 (60%) as average risk, and 605 (19%) as high risk based on GRS alone. In comparison, 2789 (86%) were classified as low or average risk and 436 (14%) as high risk based on FH alone. Men in higher GRS risk groups had a PCa diagnosis-free survival rate that was worse than that of those in the lower GRS risk group (χ2 = 53.3; P < .001 for trend) and in participants with a negative FH of PCa (χ2 = 45.5; P < .001 for trend). Combining GRS and FH further stratified overall genetic risk, indicating that 957 men (30%) were at high genetic risk (either high GRS or positive FH), 1667 men (52%) were at average genetic risk (average GRS and negative FH), and 601 men (19%) were at low genetic risk (low GRS and negative FH). The median PCa diagnosis-free survival was 74 years (95% CI, 73-75 years) for men at high genetic risk, 77 years (95% CI, 75 to >80 years) for men at average genetic risk, and more than 80 years (95% CI, >80 to >80 years) for men at low genetic risk. In contrast, the median PCa diagnosis-free survival was 73 years (95% CI, 71-76 years) for men with a positive FH and 77 years (95% CI, 76-79 years) for men with a negative FH. CONCLUSIONS AND RELEVANCE This study suggests that a GRS is significantly associated with patient age at PCa diagnosis. Combining FH and GRS may better stratify inherited risk than FH alone for developing personalized PCa screening strategies.
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Affiliation(s)
- Rong Na
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
- Huashan Hospital, Fudan Institute of Urology, Fudan University, Shanghai, China
- Ruijin Hospital, Department of Urology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Craig Labbate
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
- Section of Urology, University of Chicago Medicine, Chicago, Illinois
| | - Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Richard J. Fantus
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
- Section of Urology, University of Chicago Medicine, Chicago, Illinois
| | - Chi-Hsiung Wang
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Gerald L. Andriole
- Division of Urologic Surgery, Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri
| | - William B. Isaacs
- James Buchanan Brady Urological Institute, Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - S. Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Brian T. Helfand
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
- Huashan Hospital, Fudan Institute of Urology, Fudan University, Shanghai, China
- Section of Urology, University of Chicago Medicine, Chicago, Illinois
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19
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Xu J, Labbate CV, Isaacs WB, Helfand BT. Inherited risk assessment of prostate cancer: it takes three to do it right. Prostate Cancer Prostatic Dis 2019; 23:59-61. [DOI: 10.1038/s41391-019-0165-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 06/12/2019] [Accepted: 06/23/2019] [Indexed: 01/17/2023]
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20
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Prioritization of Variants for Investigation of Genotype-Directed Nutrition in Human Superpopulations. Int J Mol Sci 2019; 20:ijms20143516. [PMID: 31323740 PMCID: PMC6678450 DOI: 10.3390/ijms20143516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/04/2019] [Accepted: 07/16/2019] [Indexed: 01/06/2023] Open
Abstract
Dietary guidelines recommended by key health agencies are generally designed for a global population. However, ethnicity affects human disease and environment-gene interactions, including nutrient intake. Historically, isolated human populations with different genetic backgrounds have adapted to distinct environments with varying food sources. Ethnicity is relevant to the interaction of food intake with genes and disease susceptibility; yet major health agencies generally do not recommend food and nutrients codified by population genotypes and their frequencies. In this paper, we have consolidated published nutrigenetic variants and examine their frequencies in human superpopulations to prioritize these variants for future investigation of population-specific genotype-directed nutrition. The nutrients consumed by individuals interact with their genome and may alter disease risk. Herein, we searched the literature, designed a data model, and manually curated hundreds of papers. The resulting database houses 101 variants that reached significance (p < 0.05), from 35 population studies. Nutrigenetic variants associated with modified nutrient intake have the potential to reduce the risk of colorectal cancer, obesity, metabolic syndrome, type 2 diabetes, and several other diseases. Since many nutrigenetic studies have identified a major variant in some populations, we suggest that superpopulation-specific genotype-directed nutrition modifications be prioritized for future study and evaluation. Genotype-directed nutrition approaches to dietary modification have the potential to reduce disease risk in select human populations.
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Prediction model for the efficacy of folic acid therapy on hyperhomocysteinaemia based on genetic risk score methods. Br J Nutr 2019; 122:39-46. [PMID: 30935434 DOI: 10.1017/s0007114519000783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
No risk assessment tools for the efficacy of folic acid treatment for hyperhomocysteinaemia (HHcy) have been developed. We aimed to use two common genetic risk score (GRS) methods to construct prediction models for the efficacy of folic acid therapy on HHcy, and the best gene-environment prediction model was screened out. A prospective cohort study enrolling 638 HHcy patients was performed. We used a logistic regression model to estimate the associations of two GRS methods with the efficacy. Performances were compared using area under the receiver operating characteristic curve (AUC). The simple count genetic risk score (SC-GRS) and weighted genetic risk score (wGRS) were found to be independently associated with the efficacy of folic acid treatment for HHcy. Using the SC-GRS, per risk allele increased with a 1·46-fold increased failure risk (P < 0·001) after adjustment for traditional risk factors, including age, sex, BMI, smoking, alcohol consumption, history of diabetes, history of hypertension, history of hyperlipidaemia, history of stroke and history of CHD. When used the wGRS, the association was strengthened (OR = 2·08, P < 0·001). Addition of the SC-GRS and wGRS to the traditional risk model significantly improved the predictive ability by AUC (0·859). A precise gene-environment predictive model with good performance was developed for predicting the treatment failure rate of folic acid therapy for HHcy.
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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] [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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Shi Z, Yu H, Wu Y, Lin X, Bao Q, Jia H, Perschon C, Duggan D, Helfand BT, Zheng SL, Xu J. Systematic evaluation of cancer-specific genetic risk score for 11 types of cancer in The Cancer Genome Atlas and Electronic Medical Records and Genomics cohorts. Cancer Med 2019; 8:3196-3205. [PMID: 30968590 PMCID: PMC6558466 DOI: 10.1002/cam4.2143] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/01/2019] [Accepted: 03/18/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Genetic risk score (GRS) is an odds ratio (OR)-weighted and population-standardized method for measuring cumulative effect of multiple risk-associated single nucleotide polymorphisms (SNPs). We hypothesize that GRS is a valid tool for risk assessment of most common cancers. METHODS Utilizing genotype and phenotype data from The Cancer Genome Atlas (TCGA) and Electronic Medical Records and Genomics (eMERGE), we tested 11 cancer-specific GRSs (bladder, breast, colorectal, glioma, lung, melanoma, ovarian, pancreatic, prostate, renal, and thyroid cancer) for association with the respective cancer type. Cancer-specific GRSs were calculated, for the first time in these cohorts, based on previously published risk-associated SNPs using the Caucasian subjects in these two cohorts. RESULTS Mean cancer-specific GRS in the population controls of eMERGE approximated the expected value of 1.00 (between 0.98 and 1.02) for all 11 types of cancer. Mean cancer-specific GRS was consistently higher in respective cancer patients than controls for all 11 types of cancer (P < 0.05). When subjects were categorized into low-, average-, and high-risk groups based on cancer-specific GRS (<0.5, 0.5-1.5, and >1.5, respectively), significant dose-response associations of higher cancer-specific GRS with higher OR of respective type of cancer were found for nine types of cancer (P-trend < 0.05). More than 64% subjects in the population controls of eMERGE can be classified as high risk for at least one type of these cancers. CONCLUSION Validity of GRS for predicting cancer risk is demonstrated for most types of cancer. If confirmed in larger studies, cancer-specific GRS may have the potential for developing personalized cancer screening strategy.
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Affiliation(s)
- 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
| | - Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Yishuo Wu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - 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
| | - Quanwa Bao
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Haifei Jia
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chelsea Perschon
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Siqun L Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - 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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24
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Selecting variants of unknown significance through network-based gene-association significantly improves risk prediction for disease-control cohorts. Sci Rep 2019; 9:3266. [PMID: 30824863 PMCID: PMC6397233 DOI: 10.1038/s41598-019-39796-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 01/31/2019] [Indexed: 12/12/2022] Open
Abstract
Variants of unknown/uncertain significance (VUS) pose a huge dilemma in current genetic variation screening methods and genetic counselling. Driven by methods of next generation sequencing (NGS) such as whole exome sequencing (WES), a plethora of VUS are being detected in research laboratories as well as in the health sector. Motivated by this overabundance of VUS, we propose a novel computational methodology, termed VariantClassifier (VarClass), which utilizes gene-association networks and polygenic risk prediction models to shed light into this grey area of genetic variation in association with disease. VarClass has been evaluated using numerous validation steps and proves to be very successful in assigning significance to VUS in association with specific diseases of interest. Notably, using VUS that are deemed significant by VarClass, we improved risk prediction accuracy in four large case-studies involving disease-control cohorts from GWAS as well as WES, when compared to traditional odds ratio analysis. Biological interpretation of selected high scoring VUS revealed interesting biological themes relevant to the diseases under investigation. VarClass is available as a standalone tool for large-scale data analyses, as well as a web-server with additional functionalities through a user-friendly graphical interface.
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25
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Shi Z, Yu H, Wu Y, Ford M, Perschon C, Wang C, Zheng SL, Xu J. Genetic risk score modifies the effect of APOE on risk and age onset of Alzheimer's disease. Clin Genet 2018; 95:302-309. [PMID: 30460685 DOI: 10.1111/cge.13479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/25/2018] [Accepted: 11/14/2018] [Indexed: 01/08/2023]
Abstract
Single nucleotide polymorphism (SNP)-based genetic risk score (GRS) and APOE genotype are both important in risk prediction of Alzheimer's disease (AD); however, the interaction between GRS and APOE has not been extensively investigated. Our objective was to determine whether GRS modifies the APOE effect on AD risk and age at onset (AAO). The study included 774 AD cases and 767 controls of European descent. Population standardized GRS was calculated based on 17 previously implicated AD risk-associated SNPs. Association was analyzed using logistic regression, Cox proportional hazards model and Kaplan-Meier curve. We found that GRS was significantly associated with AD risk and the association was stronger among APOE ε4 carriers. Compared to ε4 non-carriers, the Odds Ratio (OR) for AD was 8.09 (95% Confidence Interval [CI]: 4.98-13.63) for ε4 carriers with high-GRS (≥1.5). In contrast, the OR was 2.55 (95% CI: 1.46-4.49) for ε4 carriers with low-GRS (<0.6). In conclusion, these results suggest SNP-based GRS may supplement APOE for better assessment of inherited risk and age of onset of AD.
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Affiliation(s)
- Zhuqing Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Yishuo Wu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Madison Ford
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Chelsea Perschon
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Chihsiung Wang
- Center for Biomedical Research Informatics, NorthShore University Health System, Evanston, Illinois
| | - Siqun L Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Jianfeng Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
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26
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Fantus RJ, Helfand BT. Germline Genetics of Prostate Cancer: Time to Incorporate Genetics into Early Detection Tools. Clin Chem 2018; 65:74-79. [PMID: 30459162 DOI: 10.1373/clinchem.2018.286658] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/12/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Prostate cancer (PCa) remains the most common solid malignancy in men, and its prevalence makes understanding its heritability of paramount importance. To date, the most common factors used to estimate a man's risk of developing PCa are age, race, and family history. Despite recent advances in its utility in multiple malignancies (e.g., breast and colon cancer), genetic testing is still relatively underutilized in PCa. CONTENT Multiple highly penetrant genes (HPGs) and single-nucleotide polymorphisms (SNPs) have been show to increase a patient's risk of developing PCa. Mutations in the former, like DNA damage repair genes, can confer a 2- to 3-fold increased risk of developing PCa and can increase the risk of aggressive disease. Similarly, PCa-risk SNPs can be used to create risk scores (e.g., genetic or polygenic risk scores) that can be used to further stratify an individual's disease susceptibility. Specifically, these genetic risk scores can provide more specific estimates of a man's lifetime risk ranging up to >6-fold higher risk of PCa. SUMMARY It is becoming increasingly evident that in addition to the standard family history and race information, it is necessary to obtain genetic testing (including an assessment of HPG mutation status and genetic risk score) to provide a full risk assessment. The additional information derived thereby will improve current practices in PCa screening by risk-stratifying patients before initial prostate-specific antigen testing, determining a patient's frequency of visits, and even help identify potentially at-risk family members.
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Affiliation(s)
- Richard J Fantus
- Section of Urology, Department of Surgery, University of Chicago Medicine, Chicago, IL
| | - Brian T Helfand
- Division of Urology, Department of Surgery, NorthShore University Health System, Evanston, IL.
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27
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Current progress and questions in germline genetics of prostate cancer. Asian J Urol 2018; 6:3-9. [PMID: 30775244 PMCID: PMC6363602 DOI: 10.1016/j.ajur.2018.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/07/2018] [Indexed: 12/31/2022] Open
Abstract
Dramatic progress has been made in the area of germline genetics of prostate cancer (PCa) in the past decade. Both common and rare genetic variants with effects on risk ranging from barely detectable to outright practice-changing have been identified. For men with high risk PCa, the application of genetic testing for inherited pathogenic mutations is becoming standard of care. A major question exists about which additional populations of men to test, as men at all risk levels can potentially benefit by knowing their unique genetic profile of germline susceptibility variants. This article will provide a brief overview of some current issues in understanding inherited susceptibility for PCa.
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28
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A multiparametric approach to improve upon existing prostate cancer screening and biopsy recommendations. Curr Opin Urol 2018; 27:475-480. [PMID: 28614085 DOI: 10.1097/mou.0000000000000418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW To provide an overview of how genetic, serum, and urine biomarkers can help identify men at high risk for prostate cancer (PCa) and aggressive disease and men who would benefit from prostate biopsy. RECENT FINDINGS Screening for PCa is controversial because of concerns about overdiagnosis and overtreatment of nonlife-threatening tumors. Therefore, an approach to screening that includes a detailed family history with genetic testing of risk single nucleotide polymorphisms and high-penetrance genetic variants should be considered. After an elevated serum prostate-specific antigen (PSA) level has been confirmed, obtaining additional information (family history, biomarkers, and imaging) should be considered before recommending a prostate biopsy. SUMMARY There are now genetic tests that can help identify men who would benefit from PSA testing. Additional biomarker and imaging tests should be offered to those men who are confirmed to have elevated PSA values. These new biomarkers and imaging tests can improve the specificity of PSA testing while missing a small percentage of high-grade tumors. The path forward involves a multiparametric risk assessment based on clinical data and these new tests.
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Chen H, Ewing CM, Zheng S, Grindedaal EM, Cooney KA, Wiley K, Djurovic S, Andreassen OA, Axcrona K, Mills IG, Xu J, Maehle L, Fosså SD, Isaacs WB. Genetic factors influencing prostate cancer risk in Norwegian men. Prostate 2018; 78:186-192. [PMID: 29181843 DOI: 10.1002/pros.23453] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 10/18/2017] [Indexed: 11/09/2022]
Abstract
Norway has one of the highest rates of death due to prostate cancer (PCa) in the world. To assess the contribution of both common and rare single nucleotide variants (SNPs) to the prostate cancer burden in Norway, we assessed the frequency of the established prostate cancer susceptibility allele, HOXB13 G84E, as well as a series of validated, common PCa risk SNPs in a Norwegian PCa population of 779 patients. The G84E allele was observed in 2.3% of patients compared to 0.7% of control individuals, OR = 3.8, P = 1 × 10-4. While there was a trend toward an earlier age at diagnosis, overall the clinicopathologic features of PCa were not significantly different in G84E carriers and non-carriers. Evaluation of 32 established common risk alleles revealed significant associations of risk alleles at 13 loci, including SNPs at 8q24, and near TET2, SLC22A3, NKX3-1, CASC8, MYC, DAP2IP, MSMB, HNF1B, PPP1R14A, and KLK2/3. When the data for each SNP are combined into a genetic risk score (GRS), Norwegian men within the top decile of GRS have over 5-fold greater risk to be diagnosed with PCa than men with GRS in the lowest decile. These results indicate that risk alleles of HOXB13 and common variant SNPs are important components of inherited PCa risk in the Norwegian population, although these factors appear to contribute little to the malignancy's aggressiveness.
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Affiliation(s)
- Haitao Chen
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Charles M Ewing
- Brady Urological Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Sigun Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Eli M Grindedaal
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Kathleen A Cooney
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Kathleen Wiley
- Brady Urological Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Srdjan Djurovic
- NORMENT, KG Jebsen Centre for Psychosis Research and Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ole A Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Karol Axcrona
- Department of Urology, Akershus University Hospital, Lørenskog, Norway
| | - Ian G Mills
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, Oslo, Norway
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- PCUK Movember Centre of Excellence, Centre for Cancer Research and Cell Biology (CCRCB), Queen's University, Northern Ireland, United Kingdom
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Lovise Maehle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Sophie D Fosså
- Department of Oncology, Faculty of Medicine, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - William B Isaacs
- Brady Urological Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
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Chen H, Na R, Packiam VT, Conran CA, Jiang D, Tao S, Yu H, Lin X, Meng W, Zheng SL, Brendler CB, Helfand BT, Xu J. Reclassification of prostate cancer risk using sequentially identified SNPs: Results from the REDUCE trial. Prostate 2017; 77:1179-1186. [PMID: 28670847 PMCID: PMC6949015 DOI: 10.1002/pros.23369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 04/28/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUND Although the clinical validity of risk-associated single nucleotide polymorphisms (SNPs) for assessment of disease susceptibility has been consistently established, risk reclassification from increasing numbers of implicated risk-associated SNPs raises concern that it is premature for clinical use. Our objective is to assess the degree and impact of risk reclassification with the increasing number of SNPs. METHODS A total of 3239 patients from the Reduction by Dutasteride of Prostate Cancer Events (REDUCE) trial were included. Four genetic risk scores (GRSs) were calculated based on sets of sequentially discovered prostate cancer (PCa) risk-associated SNPs (17, 34, 51, and 68 SNPs). RESULTS Pair-wise correlation coefficients between sets of GRSs increased as more SNPs were included in the GRS: 0.80, 0.86, and 0.95 for 17 versus 34 SNPs, 34 versus 51 SNPs, and 51 versus 68 SNPs, respectively. Using a GRS of 1.5 as a cutoff for higher versus lower risk, reclassification rates of PCa risk decreased: 14.11%, 12.04%, and 8.15% for 17 versus 34 SNPs, 34 versus 51 SNPs, and 51 versus 68 SNPs, respectively. Evolving GRSs, nevertheless, provide a tool for further refining risk assessment. When all four sequential GRSs were considered, the detection rates of PCa for men whose GRSs were consistently <1.5, reclassified, and consistently ≥1.5 were 20.8%, 29.67%, and 39.26%, respectively (Ptrend = 1.12 × 10-8 ). In comparison, the detection rates of PCa in men with negative or positive family history were 23.75% and 31.78%, respectively. CONCLUSIONS Risk assessment using currently available SNPs is justified. Multiple GRS values from evolving sets of SNPs provide a valuable tool for better refining risk.
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Affiliation(s)
- Haitao Chen
- Center for Genomic Translational Medicine and Prevention, School of Public Health, Fudan University, 130 Dongan Road, Shanghai, China PR 200032
| | - Rong Na
- Fudan Institute of Urology, Huashan Hospital, Fudan University, 12 Mid-Wulumuqi Road, Shanghai, China PR 200040
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL, USA 60201
| | - Vignesh T. Packiam
- Section of Urology, University of Chicago Medical Center, 5841 S Maryland Ave, Chicago, IL, USA 60637
| | - Carly A. Conran
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL, USA 60201
| | - Deke Jiang
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL, USA 60201
| | - Sha Tao
- Center for Genomic Translational Medicine and Prevention, School of Public Health, Fudan University, 130 Dongan Road, Shanghai, China PR 200032
| | - Hongjie Yu
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL, USA 60201
| | - Xiaoling Lin
- Fudan Institute of Urology, Huashan Hospital, Fudan University, 12 Mid-Wulumuqi Road, Shanghai, China PR 200040
| | - Wei Meng
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China PR 200032
| | - S. Lilly Zheng
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL, USA 60201
| | - Charles B. Brendler
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL, USA 60201
| | - Brian T. Helfand
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL, USA 60201
| | - Jianfeng Xu
- Center for Genomic Translational Medicine and Prevention, School of Public Health, Fudan University, 130 Dongan Road, Shanghai, China PR 200032
- Fudan Institute of Urology, Huashan Hospital, Fudan University, 12 Mid-Wulumuqi Road, Shanghai, China PR 200040
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL, USA 60201
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31
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Congrès l’association américaine de recherche contre le cancer — AACR 2017. ONCOLOGIE 2017. [DOI: 10.1007/s10269-017-2720-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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32
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Oh JJ, Park S, Lee SE, Hong SK, Lee S, Kim TJ, Lee IJ, Ho JN, Yoon S, Byun SS. Genetic risk score to predict biochemical recurrence after radical prostatectomy in prostate cancer: prospective cohort study. Oncotarget 2017; 8:75979-75988. [PMID: 29100285 PMCID: PMC5652679 DOI: 10.18632/oncotarget.18275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/07/2017] [Indexed: 12/28/2022] Open
Abstract
Purpose To investigate the genetic risk score (GRS) from a large-scale exome-wide association study as a tool of prediction for biochemical recurrence (BCR) after radical prostatectomy (RP) in prostate cancer (PCa). Results The 16 SNPs were selected as significant predictors of BCR. The GRS in men experiencing BCR was -1.21, significantly higher than in non-BCR patients (–2.43) (p < 0.001). The 10-year BCR-free survival rate was 46.3% vs. 81.8% in the high-versus low GRS group, respectively (p < 0.001). The GRS was a significant factor after adjusting for other variables in Cox proportional hazard models (HR:1.630, p < 0.001). The predictive ability of the multivariate model without GRS was 84.4%, increased significantly to 88.0% when GRS was included (p = 0.0026). Materials and Methods Total 912 PCa patients were enrolled who had received RP and genotype analysis using Exome chip (HumanExome BeadChip). Genetic results were obtained by the methods of logistic regression analysis which measured the odds ratio (OR) to BCR. The GRS was calculated by the sum of each weighted-risk allele count multiplied by the natural logarithm of the respective ORs. Survival analyses were performed using the GRS. We compared the accuracy of separate multivariate models incorporating clinicopathological factors that either included or excluded the GRS. Conclusions GRS had additional predictive gain of BCR after RP in PCa. The addition of personally calculated GRS significantly increased the BCR prediction rate. After validation of these results, GRS of BCR could be potential biomarker to predict clinical outcomes.
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Affiliation(s)
- Jong Jin Oh
- Department of Urology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seunghyun Park
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Korea.,School of Electrical Engineering, Korea University, Seoul, Korea
| | - Sang Eun Lee
- Department of Urology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sung Kyu Hong
- Department of Urology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sangchul Lee
- Department of Urology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Tae Jin Kim
- Department of Urology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - In Jae Lee
- Department of Urology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jin-Nyoung Ho
- Department of Urology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Biomedical Research Institute, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sungroh Yoon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Korea
| | - Seok-Soo Byun
- Department of Urology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
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Associations between single nucleotide polymorphisms in RYBP and the prognosis of hepatocellular carcinoma in a Chinese population. Carcinogenesis 2017; 38:532-540. [DOI: 10.1093/carcin/bgx031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/20/2017] [Indexed: 12/13/2022] Open
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34
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Helfand BT, Kearns J, Conran C, Xu J. Clinical validity and utility of genetic risk scores in prostate cancer. Asian J Androl 2017; 18:509-14. [PMID: 27297129 PMCID: PMC4955171 DOI: 10.4103/1008-682x.182981] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Current issues related to prostate cancer (PCa) clinical care (e.g., over-screening, over-diagnosis, and over-treatment of nonaggressive PCa) call for risk assessment tools that can be combined with family history (FH) to stratify disease risk among men in the general population. Since 2007, genome-wide association studies (GWASs) have identified more than 100 SNPs associated with PCa susceptibility. In this review, we discuss (1) the validity of these PCa risk-associated SNPs, individually and collectively; (2) the various methods used for measuring the cumulative effect of multiple SNPs, including genetic risk score (GRS); (3) the adequate number of SNPs needed for risk assessment; (4) reclassification of risk based on evolving numbers of SNPs used to calculate genetic risk, (5) risk assessment for men from various racial groups, and (6) the clinical utility of genetic risk assessment. In conclusion, data available to date support the clinical validity of PCa risk-associated SNPs and GRS in risk assessment among men with or without FH. PCa risk-associated SNPs are not intended for diagnostic use; rather, they should be used the same way as FH. Combining GRS and FH can significantly improve the performance of risk assessment. Improved risk assessment may have important clinical utility in targeted PCa testing. However, clinical trials are urgently needed to evaluate this clinical utility as well as the acceptance of GRS by patients and physicians.
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Affiliation(s)
- Brian T Helfand
- Department of Surgery, NorthShore University HealthSystem, Program for Personalized Cancer Care, Evanston, IL 60201, USA
| | - James Kearns
- Department of Surgery, NorthShore University HealthSystem, Program for Personalized Cancer Care, Evanston, IL 60201, USA
| | - Carly Conran
- Department of Surgery, NorthShore University HealthSystem, Program for Personalized Cancer Care, Evanston, IL 60201, USA
| | - Jianfeng Xu
- Department of Surgery, NorthShore University HealthSystem, Program for Personalized Cancer Care, Evanston, IL 60201, USA
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35
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Liu W, Xu J. Translation of genomics and epigenomics in prostate cancer: progress and promising directions. Asian J Androl 2016; 18:503-4. [PMID: 27270344 PMCID: PMC4955169 DOI: 10.4103/1008-682x.182820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
During the last several years, exciting discoveries have been made in prostate cancer (PCa) as a result of significant advances in genomic technology and information. For example, using genome-wide association studies, more than 100 inherited genetic variants associated with PCa risk have been identified. Similarly, with the use of next-generation sequencing, various types of recurrent somatic DNA alterations in prostate tumors have been revealed. Some of these discoveries have potential clinical application to supplement existing tools for better decision-making regarding the need for screening, biopsy, and treatment of PCa. However, because of the complexity of these genomic findings and incomplete understanding of the genetics of this multifactorial disease, this potential has not yet been fully realized.
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Affiliation(s)
- Wennuan Liu
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL 60201, USA
| | - Jianfeng Xu
- NorthShore University HealthSystem, Program for Personalized Cancer Care, 1001 University Place, Evanston, IL 60201, USA
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