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Koch S, Schmidtke J, Krawczak M, Caliebe A. Clinical utility of polygenic risk scores: a critical 2023 appraisal. J Community Genet 2023; 14:471-487. [PMID: 37133683 PMCID: PMC10576695 DOI: 10.1007/s12687-023-00645-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/31/2023] [Indexed: 05/04/2023] Open
Abstract
Since their first appearance in the context of schizophrenia and bipolar disorder in 2009, polygenic risk scores (PRSs) have been described for a large number of common complex diseases. However, the clinical utility of PRSs in disease risk assessment or therapeutic decision making is likely limited because PRSs usually only account for the heritable component of a trait and ignore the etiological role of environment and lifestyle. We surveyed the current state of PRSs for various diseases, including breast cancer, diabetes, prostate cancer, coronary artery disease, and Parkinson disease, with an extra focus upon the potential improvement of clinical scores by their combination with PRSs. We observed that the diagnostic and prognostic performance of PRSs alone is consistently low, as expected. Moreover, combining a PRS with a clinical score at best led to moderate improvement of the power of either risk marker. Despite the large number of PRSs reported in the scientific literature, prospective studies of their clinical utility, particularly of the PRS-associated improvement of standard screening or therapeutic procedures, are still rare. In conclusion, the benefit to individual patients or the health care system in general of PRS-based extensions of existing diagnostic or treatment regimens is still difficult to judge.
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Affiliation(s)
- Sebastian Koch
- Institut für Medizinische Informatik und Statistik, Christian-Albrechts-Universität zu Kiel, Universitätsklinikum Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Jörg Schmidtke
- Amedes MVZ Wagnerstibbe, Hannover, Germany
- Institut für Humangenetik, Medizinische Hochschule Hannover, Hannover, Germany
| | - Michael Krawczak
- Institut für Medizinische Informatik und Statistik, Christian-Albrechts-Universität zu Kiel, Universitätsklinikum Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Amke Caliebe
- Institut für Medizinische Informatik und Statistik, Christian-Albrechts-Universität zu Kiel, Universitätsklinikum Schleswig-Holstein Campus Kiel, Kiel, Germany.
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Moorthy T, Nguyen H, Chen Y, Austin J, Smoller JW, Hercher L, Sabatello M. How do experts in psychiatric genetics view the clinical utility of polygenic risk scores for schizophrenia? Am J Med Genet B Neuropsychiatr Genet 2023; 192:161-170. [PMID: 37158703 PMCID: PMC10524148 DOI: 10.1002/ajmg.b.32939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 03/02/2023] [Accepted: 04/15/2023] [Indexed: 05/10/2023]
Abstract
Polygenic risk scores (PRS) are promising for identifying common variant-related inheritance for psychiatric conditions but their integration into clinical practice depends on their clinical utility and psychiatrists' understanding of PRS. Our online survey explored these issues with 276 professionals working in psychiatric genetics (RR: 19%). Overall, participants demonstrated knowledge of how to interpret PRS results. Their performance on knowledge-based questions was positively correlated with participants' self-reported familiarity with PRS (r = 0.21, p = 0.0006) although differences were not statistically significant (Wald Chi-square = 3.29, df = 1, p = 0.07). However, only 48.9% of all participants answered all knowledge questions correctly. Many participants (56.5%), especially researchers (42%), indicated having at least occasional conversations about the role of genetics in psychiatric conditions with patients and/or family members. Most participants (62.7%) indicated that PRS are not yet sufficiently robust for assessment of susceptibility to schizophrenia; most significant obstacles were low predictive power and lack of population diversity in available PRS (selected, respectively, by 53.6% and 29.3% of participants). Nevertheless, 89.8% of participants were optimistic about the use of PRS in the next 10 years, suggesting a belief that current shortcomings could be addressed. Our findings inform about the perceptions of psychiatric professionals regarding PRS and the application of PRS in psychiatry.
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Affiliation(s)
- Tiahna Moorthy
- NYC Health + Hospitals/Jacobi Medical Center, Bronx, NY, USA
| | | | - Ying Chen
- New York State Psychiatric Institute, New York City, NY, USA
| | - Jehannine Austin
- Psychiatry and Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jordan W Smoller
- Psychiatry, Harvard Medical School, Boston, MA, USA
- Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Precision Psychiatry and Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Laura Hercher
- Sarah Lawrence College Joan H. Marks Graduate Program in Human Genetics, Bronxville, NY, USA
| | - Maya Sabatello
- Medical Sciences (in Medicine), Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York City, NY, USA
- Medical Sciences (in Medical Humanities and Ethics), Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York City, NY, USA
- Precision Medicine: Ethics, Politics and Culture Project, Columbia University, New York City, NY, USA
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Le T, Rojas PS, Fakunle M, Huang FW. Racial disparity in the genomics of precision oncology of prostate cancer. Cancer Rep (Hoboken) 2023; 6 Suppl 1:e1867. [PMID: 37565547 PMCID: PMC10440844 DOI: 10.1002/cnr2.1867] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Significant racial disparities in prostate cancer incidence and mortality have been reported between African American Men (AAM), who are at increased risk for prostate cancer, and European American Men (EAM). In most of the studies carried out on prostate cancer, this population is underrepresented. With the advancement of genome-wide association studies, several genetic predictor models of prostate cancer risk have been elaborated, as well as numerous studies that identify both germline and somatic mutations with clinical utility. RECENT FINDINGS Despite significant advances, the AAM population continues to be underrepresented in genomic studies, which can limit generalizability and potentially widen disparities. Here we outline racial disparities in currently available genomic applications that are used to estimate the risk of individuals developing prostate cancer and to identify personalized oncology treatment strategies. While the incidence and mortality of prostate cancer are different between AAM and EAM, samples from AAM remain to be unrepresented in different studies. CONCLUSION This disparity impacts the available genomic data on prostate cancer. As a result, the disparity can limit the predictive utility of the genomic applications and may lead to the widening of the existing disparities. More studies with substantially higher recruitment and engagement of African American patients are necessary to overcome this disparity.
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Affiliation(s)
- Tu Le
- Division of Hematology and Oncology, Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Division of Hematology and Oncology, Department of MedicineSan Francisco Veterans Affairs Medical CenterSan FranciscoCaliforniaUSA
| | - Pilar Soto Rojas
- Division of Hematology and Oncology, Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of OncologyHospital Universitario Virgen MacarenaSevilleSpain
| | - Mary Fakunle
- Department of UrologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Franklin W. Huang
- Division of Hematology and Oncology, Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Division of Hematology and Oncology, Department of MedicineSan Francisco Veterans Affairs Medical CenterSan FranciscoCaliforniaUSA
- Department of UrologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Chan Zuckerberg BiohubSan FranciscoCaliforniaUSA
- Institute for Human GeneticsUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Bakar Computational Health Sciences InstituteUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Benioff Initiative for Prostate Cancer ResearchUniversity of California San FranciscoSan FranciscoCaliforniaUSA
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Shortall J, Vasquez Osorio E, Green A, McWilliam A, Elumalai T, Reeves K, Johnson-Hart C, Beasley W, Hoskin P, Choudhury A, van Herk M. Dose outside of the prostate is associated with improved outcomes for high-risk prostate cancer patients treated with brachytherapy boost. Front Oncol 2023; 13:1200676. [PMID: 37397380 PMCID: PMC10311256 DOI: 10.3389/fonc.2023.1200676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Background One in three high-risk prostate cancer patients treated with radiotherapy recur. Detection of lymph node metastasis and microscopic disease spread using conventional imaging is poor, and many patients are under-treated due to suboptimal seminal vesicle or lymph node irradiation. We use Image Based Data Mining (IBDM) to investigate association between dose distributions, and prognostic variables and biochemical recurrence (BCR) in prostate cancer patients treated with radiotherapy. We further test whether including dose information in risk-stratification models improves performance. Method Planning CTs, dose distributions and clinical information were collected for 612 high-risk prostate cancer patients treated with conformal hypo-fractionated radiotherapy, intensity modulated radiotherapy (IMRT), or IMRT plus a single fraction high dose rate (HDR) brachytherapy boost. Dose distributions (including HDR boost) of all studied patients were mapped to a reference anatomy using the prostate delineations. Regions where dose distributions significantly differed between patients that did and did-not experience BCR were assessed voxel-wise using 1) a binary endpoint of BCR at four-years (dose only) and 2) Cox-IBDM (dose and prognostic variables). Regions where dose was associated with outcome were identified. Cox proportional-hazard models with and without region dose information were produced and the Akaike Information Criterion (AIC) was used to assess model performance. Results No significant regions were observed for patients treated with hypo-fractionated radiotherapy or IMRT. Regions outside the target where higher dose was associated with lower BCR were observed for patients treated with brachytherapy boost. Cox-IBDM revealed that dose response was influenced by age and T-stage. A region at the seminal vesicle tips was identified in binary- and Cox-IBDM. Including the mean dose in this region in a risk-stratification model (hazard ratio=0.84, p=0.005) significantly reduced AIC values (p=0.019), indicating superior performance, compared with prognostic variables only. The region dose was lower in the brachytherapy boost patients compared with the external beam cohorts supporting the occurrence of marginal misses. Conclusion Association was identified between BCR and dose outside of the target region in high-risk prostate cancer patients treated with IMRT plus brachytherapy boost. We show, for the first-time, that the importance of irradiating this region is linked to prognostic variables.
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Affiliation(s)
- Jane Shortall
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Eliana Vasquez Osorio
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Andrew Green
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Alan McWilliam
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, United Kingdom
| | - Thriaviyam Elumalai
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, United Kingdom
| | - Kimberley Reeves
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Corinne Johnson-Hart
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, United Kingdom
| | - William Beasley
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, United Kingdom
| | - Peter Hoskin
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, United Kingdom
| | - Ananya Choudhury
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, United Kingdom
| | - Marcel van Herk
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
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The Combined Effect of Polygenic Risk Score and Prostate Health Index in Chinese Men Undergoing Prostate Biopsy. J Clin Med 2023; 12:jcm12041343. [PMID: 36835879 PMCID: PMC9960699 DOI: 10.3390/jcm12041343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/02/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
To date, the combined effect of polygenic risk score (PRS) and prostate health index (phi) on PCa diagnosis in men undergoing prostate biopsy has never been investigated. A total of 3166 patients who underwent initial prostate biopsy in three tertiary medical centers from August 2013 to March 2019 were included. PRS was calculated on the basis of the genotype of 102 reported East-Asian-specific risk variants. It was then evaluated in the univariable or multivariable logistic regression models that were internally validated using repeated 10-fold cross-validation. Discriminative performance was assessed by area under the receiver operating curve (AUC) and net reclassification improvement (NRI) index. Compared with men in the first quintile of age and family history adjusted PRS, those in the second, third, fourth, and fifth quintiles were 1.86 (odds ratio, 95% confidence interval (CI): 1.34-2.56), 2.07 (95%CI: 1.50-2.84), 3.26 (95%CI: 2.36-4.48), and 5.06 (95%CI: 3.68-6.97) times as likely to develop PCa (all p < 0.001). Adjustment for other clinical parameters yielded similar results. Among patients with prostate-specific antigen (PSA) at 2-10 ng/mL or 2-20 ng/mL, PRS still had an observable ability to differentiate PCa in the group of prostate health index (phi) at 27-36 (Ptrend < 0.05) or >36 (Ptrend ≤ 0.001). Notably, men with moderate phi (27-36) but highest PRS (top 20% percentile) would have a comparable risk of PCa (positive rate: 26.7% or 31.3%) than men with high phi (>36) but lowest PRS (bottom 20% percentile positive rate: 27.4% or 34.2%). The combined model of PRS, phi, and other clinical risk factors provided significantly better performance (AUC: 0.904, 95%CI: 0.887-0.921) than models without PRS. Adding PRS to clinical risk models could provide significant net benefit (NRI, from 8.6% to 27.6%), especially in those early onset patients (NRI, from 29.2% to 44.9%). PRS may provide additional predictive value over phi for PCa. The combination of PRS and phi that effectively captured both clinical and genetic PCa risk is clinically practical, even in patients with gray-zone PSA.
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Abstract
PURPOSE OF REVIEW This study was conducted in order to review the outcomes regarding polygenic risk score (PRS) in prediction of prostate cancer (PCa). With the increasing proficiency of genetic analysis, assessment of PRS for prediction of PCa has been performed in numerous studies. Genetic risk prediction models for PCa that include hundreds to thousands of independent risk-associated variants are under development. For estimation of additive effect of multiple variants, the number of risk alleles carried by an individual is summed, and each variant is weighted according to its estimated effect size for generation of a PRS. RECENT FINDINGS Currently, regarding the accuracy of PRS alone, PCa detection rate ranged from 0.56 to 0.67. A higher rate of accuracy of 0.866-0.880 was observed for other models combining PRS with established clinical markers. The results of PRS from Asian populations showed a level of accuracy that is somewhat low compared with values from Western populations (0.63-0.67); however, recent results from Asian cohorts were similar to that of Western counterparts. Here, we review current PRS literature and examine the clinical utility of PRS for prediction of PCa. SUMMARY Emerging data from several studies regarding PRS in PCa could be the solution to adding predictive value to PCa risk estimation. Although commercial markers are available, development of a large-scale, well validated PRS model should be undertaken in the near future, in order to translate hypothetical scenarios to actual clinical practice.
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Mighton C, Lerner‐Ellis J. Principles of molecular testing for hereditary cancer. Genes Chromosomes Cancer 2022; 61:356-381. [DOI: 10.1002/gcc.23048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Chloe Mighton
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Genomics Health Services Research Program Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto Toronto ON Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health University of Toronto Toronto ON Canada
| | - Jordan Lerner‐Ellis
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
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