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Tisler A, Uusküla A, Ojavee SE, Läll K, Laisk T. Polygenic risk scores for cervical HPV infection, neoplasia and cancer show potential for personalised screening: comparison of two methods. Infect Agent Cancer 2023; 18:82. [PMID: 38057845 DOI: 10.1186/s13027-023-00561-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023] Open
Abstract
The era of precision medicine requires the achievement of accurate risk assessment. Polygenic risk scores (PRSs) have strong potential for increasing the benefits of nationwide cancer screening programs. The current pool of evidence on the role of a PRS as a risk stratification model in actual practice and implementation is limited. To better understand the impact of possible method-induced variance, we constructed and validated two PRSs for cervical cancer (CC) using the Estonian Biobank female population (691 CC cases and 13,820 controls) and evaluated their utility in predicting incident cervical neoplasia (CIN), cancer, and human papillomavirus (HPV) infection using two methods (LDPred and BayesRR-RC). This study demonstrated that two genetic risk scores were significantly associated with CIN, CC, and HPV infection incidence. Independent of the method, we demonstrated that women with elevated PRS values reached the observed cumulative risk levels of CIN or CC much earlier. Our results indicated that the PRS-based discrimination rules could differ substantially when the PRSs contain similar predictive information. In summary, our analysis indicated that PRSs represent a personalized genetic component that could be an additional tool for cervical cancer risk stratification, and earlier detection of abnormalities provides invaluable information for those at high risk.
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Affiliation(s)
- Anna Tisler
- Institute of Family Medicine and Public Health, University of Tartu, Tartu, Estonia.
| | - Anneli Uusküla
- Institute of Family Medicine and Public Health, University of Tartu, Tartu, Estonia
| | - Sven Erik Ojavee
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
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Shieh Y, Roger J, Yau C, Wolf DM, Hirst GL, Swigart LB, Huntsman S, Hu D, Nierenberg JL, Middha P, Heise RS, Shi Y, Kachuri L, Zhu Q, Yao S, Ambrosone CB, Kwan ML, Caan BJ, Witte JS, Kushi LH, 't Veer LV, Esserman LJ, Ziv E. Development and testing of a polygenic risk score for breast cancer aggressiveness. NPJ Precis Oncol 2023; 7:42. [PMID: 37188791 PMCID: PMC10185660 DOI: 10.1038/s41698-023-00382-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 04/28/2023] [Indexed: 05/17/2023] Open
Abstract
Aggressive breast cancers portend a poor prognosis, but current polygenic risk scores (PRSs) for breast cancer do not reliably predict aggressive cancers. Aggressiveness can be effectively recapitulated using tumor gene expression profiling. Thus, we sought to develop a PRS for the risk of recurrence score weighted on proliferation (ROR-P), an established prognostic signature. Using 2363 breast cancers with tumor gene expression data and single nucleotide polymorphism (SNP) genotypes, we examined the associations between ROR-P and known breast cancer susceptibility SNPs using linear regression models. We constructed PRSs based on varying p-value thresholds and selected the optimal PRS based on model r2 in 5-fold cross-validation. We then used Cox proportional hazards regression to test the ROR-P PRS's association with breast cancer-specific survival in two independent cohorts totaling 10,196 breast cancers and 785 events. In meta-analysis of these cohorts, higher ROR-P PRS was associated with worse survival, HR per SD = 1.13 (95% CI 1.06-1.21, p = 4.0 × 10-4). The ROR-P PRS had a similar magnitude of effect on survival as a comparator PRS for estrogen receptor (ER)-negative versus positive cancer risk (PRSER-/ER+). Furthermore, its effect was minimally attenuated when adjusted for PRSER-/ER+, suggesting that the ROR-P PRS provides additional prognostic information beyond ER status. In summary, we used integrated analysis of germline SNP and tumor gene expression data to construct a PRS associated with aggressive tumor biology and worse survival. These findings could potentially enhance risk stratification for breast cancer screening and prevention.
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Affiliation(s)
- Yiwey Shieh
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA.
| | - Jacquelyn Roger
- PhD Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA
| | - Christina Yau
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Denise M Wolf
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Gillian L Hirst
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Lamorna Brown Swigart
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Donglei Hu
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jovia L Nierenberg
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Pooja Middha
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel S Heise
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Yushu Shi
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Marilyn L Kwan
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Bette J Caan
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Laura van 't Veer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Laura J Esserman
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
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Sud A, Horton RH, Hingorani AD, Tzoulaki I, Turnbull C, Houlston RS, Lucassen A. Realistic expectations are key to realising the benefits of polygenic scores. BMJ 2023; 380:e073149. [PMID: 36854461 PMCID: PMC9973128 DOI: 10.1136/bmj-2022-073149] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Haemato-oncology Unit, Royal Marsden Hospital NHS Foundation Trust, Sutton, UK
| | - Rachel H Horton
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
- Clinical Ethics, Law, and Society Group, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Centre for Personalised Medicine, University of Oxford, Oxford, UK
| | - Aroon D Hingorani
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
- Health Data Research UK, London, UK
- University College London, National Institute of Health Research Biomedical Research Centre, London, UK
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, UK
- National Institute for Health Research, Imperial Biomedical Research Centre, Imperial College London, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anneke Lucassen
- Clinical Ethics, Law, and Society Group, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Centre for Personalised Medicine, University of Oxford, Oxford, UK
- Data Health and Society, NIHR Biomedical Research Centre, Southampton, UK
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Brookman-May SD, May M. Re: Prostate Cancer Polygenic Risk Score and Prediction of Lethal Prostate Cancer. Eur Urol 2023; 83:473-474. [PMID: 36710206 DOI: 10.1016/j.eururo.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 01/29/2023]
Affiliation(s)
- Sabine D Brookman-May
- Department of Urology, University Hospital, LMU Munich, Munich, Germany; Janssen Research and Development Oncology, Spring House, PA, USA.
| | - Matthias May
- Department of Urology, St. Elisabeth Hospital, Brothers of Mercy, Straubing, Germany
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