101
|
Riddle L, Joseph G, Caruncho M, Koenig BA, James JE. The role of polygenic risk scores in breast cancer risk perception and decision-making. J Community Genet 2023; 14:489-501. [PMID: 37311883 PMCID: PMC10576692 DOI: 10.1007/s12687-023-00655-x] [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: 12/01/2022] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
Polygenic risk scores (PRS) have the potential to improve the accuracy of clinical risk assessments, yet questions about their clinical validity and readiness for clinical implementation persist. Understanding how individuals integrate and act on the information provided by PRS is critical for their effective integration into routine clinical care, yet few studies have examined how individuals respond to the receipt of polygenic risk information. We conducted an embedded Ethical, Legal, and Social Implications (ELSI) study to examine if and how unaffected participants in a US population breast cancer screening trial understood and utilized PRS, as part of a multifactorial risk score combining traditional risk factors with a genetic risk assessment, to make screening and risk-reduction decisions. Semi-structured qualitative interviews were conducted with 24 trial participants who were designated at elevated risk for breast cancer due to their combined risk score. Interviews were analyzed using a grounded theory approach. Participants understood PRS conceptually and accepted it as one of many risk factors to consider, yet the value and meaning they ascribed to this risk estimate varied. Most participants reported financial and insurance barriers to enhanced screening with MRI and were not interested in taking risk-reducing medications. These findings contribute to our understanding of how PRS may be best translated from research to clinical care. Furthermore, they illuminate ethical concerns about identifying risk and making recommendations based on polygenic risk in a population screening context where many may have trouble accessing appropriate care.
Collapse
Affiliation(s)
- Leslie Riddle
- Department of Humanities and Social Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mikaella Caruncho
- Department of Humanities and Social Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Barbara Ann Koenig
- Department of Humanities and Social Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Health and Aging, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer Elyse James
- Institute for Health and Aging, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
102
|
Sarkis-Tannous D, Sukol RB, Sullivan E. Toward more personalized breast cancer risk assessment: The polygenic risk score. JAAPA 2023; 36:37-40. [PMID: 37751256 DOI: 10.1097/01.jaa.0000977692.63075.f3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
ABSTRACT Healthcare providers often are uncertain about how best to assess and manage breast cancer risk. Women at average risk wonder when to start mammography and how often to go. Women at increased risk might inquire about genetic testing, MRI screening, and preventive measures. Patients who carry gene mutations face higher stakes and more complex risk management choices, but only some are aware of their status. This article helps clinicians stratify breast cancer risk and discusses a newer genomic test, the polygenic risk score, that may enable more personalized risk management and decision-making.
Collapse
Affiliation(s)
- Daad Sarkis-Tannous
- At the time this article was written, Daad Sarkis-Tannous, Roxanne B. Sukol, and Erika Sullivan were medical breast specialists at the Cleveland (Ohio) Clinic. Dr. Sukol is now retired. The authors have disclosed no potential conflicts of interest, financial or otherwise
| | | | | |
Collapse
|
103
|
Johansson Å, Andreassen OA, Brunak S, Franks PW, Hedman H, Loos RJ, Meder B, Melén E, Wheelock CE, Jacobsson B. Precision medicine in complex diseases-Molecular subgrouping for improved prediction and treatment stratification. J Intern Med 2023; 294:378-396. [PMID: 37093654 PMCID: PMC10523928 DOI: 10.1111/joim.13640] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Complex diseases are caused by a combination of genetic, lifestyle, and environmental factors and comprise common noncommunicable diseases, including allergies, cardiovascular disease, and psychiatric and metabolic disorders. More than 25% of Europeans suffer from a complex disease, and together these diseases account for 70% of all deaths. The use of genomic, molecular, or imaging data to develop accurate diagnostic tools for treatment recommendations and preventive strategies, and for disease prognosis and prediction, is an important step toward precision medicine. However, for complex diseases, precision medicine is associated with several challenges. There is a significant heterogeneity between patients of a specific disease-both with regards to symptoms and underlying causal mechanisms-and the number of underlying genetic and nongenetic risk factors is often high. Here, we summarize precision medicine approaches for complex diseases and highlight the current breakthroughs as well as the challenges. We conclude that genomic-based precision medicine has been used mainly for patients with highly penetrant monogenic disease forms, such as cardiomyopathies. However, for most complex diseases-including psychiatric disorders and allergies-available polygenic risk scores are more probabilistic than deterministic and have not yet been validated for clinical utility. However, subclassifying patients of a specific disease into discrete homogenous subtypes based on molecular or phenotypic data is a promising strategy for improving diagnosis, prediction, treatment, prevention, and prognosis. The availability of high-throughput molecular technologies, together with large collections of health data and novel data-driven approaches, offers promise toward improved individual health through precision medicine.
Collapse
Affiliation(s)
- Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala university, Sweden
| | - Ole A. Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopment Research, University of Oslo, Oslo, Norway
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, DK-2200 Copenhagen, Denmark
| | - Paul W. Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Science, Lund University, Sweden
- Novo Nordisk Foundation, Denmark
| | - Harald Hedman
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Ruth J.F. Loos
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Charles Bronfman Institute for Personalized Medicine at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Meder
- Precision Digital Health, Cardiogenetics Center Heidelberg, Department of Cardiology, University Of Heidelberg, Germany
| | - Erik Melén
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm
- Sachś Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Craig E Wheelock
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynaecology, Sahlgrenska University Hospital, Göteborg, Sweden
- Department of Genetics and Bioinformatics, Domain of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| |
Collapse
|
104
|
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.
Collapse
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.
| |
Collapse
|
105
|
Abstract
Multiple tools exist to assess a patient's breast cancer risk. The choice of risk model depends on the patient's risk factors and how the calculation will impact care. High-risk patients-those with a lifetime breast cancer risk of ≥20%-are, for instance, eligible for supplemental screening with breast magnetic resonance imaging. Those with an elevated short-term breast cancer risk (frequently defined as a 5-year risk ≥1.66%) should be offered endocrine prophylaxis. High-risk patients should also receive guidance on modification of lifestyle factors that affect breast cancer risk.
Collapse
Affiliation(s)
- Amy E Cyr
- Department of Medicine, Washington University, Box 8056, 660 South Euclid Avenue, Saint Louis, MO 63110, USA.
| | - Kaitlyn Kennard
- Department of Surgery, Washington University, Box 8051, 660 South Euclid Avenue, Saint louis, MO 63110, USA
| |
Collapse
|
106
|
Letsou W, Wang F, Moon W, Im C, Sapkota Y, Robison LL, Yasui Y. Refining the genetic risk of breast cancer with rare haplotypes and pattern mining. Life Sci Alliance 2023; 6:e202302183. [PMID: 37541849 PMCID: PMC10403637 DOI: 10.26508/lsa.202302183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
Hundreds of common variants have been found to confer small but significant differences in breast cancer risk, supporting the widely accepted polygenic model of inherited predisposition. Using a novel closed-pattern mining algorithm, we provide evidence that rare haplotypes may refine the association of breast cancer risk with common germline alleles. Our method, called Chromosome Overlap, consists in iteratively pairing chromosomes from affected individuals and looking for noncontiguous patterns of shared alleles. We applied Chromosome Overlap to haplotypes of genotyped SNPs from female breast cancer cases from the UK Biobank at four loci containing common breast cancer-risk SNPs. We found two rare (frequency <0.1%) haplotypes bearing a GWAS hit at 11q13 (hazard ratio = 4.21 and 16.7) which replicated in an independent, European ancestry population at P < 0.05, and another at 22q12 (frequency <0.2%, hazard ratio = 2.58) which expanded the risk pool to noncarriers of a GWAS hit. These results suggest that rare haplotypes (or mutations) may underlie the "synthetic association" of breast cancer risk with at least some common variants.
Collapse
Affiliation(s)
- William Letsou
- Department of Biological & Chemical Sciences, New York Institute of Technology, Old Westbury, NY, USA
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Fan Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wonjong Moon
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cindy Im
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- School of Public Health, University of Alberta, Edmonton, Canada
| | - Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yutaka Yasui
- Department of Biological & Chemical Sciences, New York Institute of Technology, Old Westbury, NY, USA
- School of Public Health, University of Alberta, Edmonton, Canada
| |
Collapse
|
107
|
Zattarin E, Taglialatela I, Lobefaro R, Leporati R, Fucà G, Ligorio F, Sposetti C, Provenzano L, Azzollini J, Vingiani A, Ferraris C, Martelli G, Manoukian S, Pruneri G, de Braud F, Vernieri C. Breast cancers arising in subjects with germline BRCA1 or BRCA2 mutations: Different biological and clinical entities with potentially diverse therapeutic opportunities. Crit Rev Oncol Hematol 2023; 190:104109. [PMID: 37643668 DOI: 10.1016/j.critrevonc.2023.104109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/11/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023] Open
Abstract
Breast cancers (BCs) arising in carriers of germline BRCA1 and BRCA2 pathogenic variants (PVs) have long been considered as indistinguishable biological and clinical entities. However, the loss of function of BRCA1 or BRCA2 proteins has different consequences in terms of tumor cell reliance on estrogen receptor signaling and tumor microenvironment composition. Here, we review accumulating preclinical and clinical data indicating that BRCA1 or BRCA2 inactivation may differentially affect BC sensitivity to standard systemic therapies. Based on a different crosstalk between BRCA1 or BRCA2 and the ER pathway, BRCA2-mutated Hormone Receptor-positive, HER2-negative advanced BC may be less sensitive to endocrine therapy (ET) plus CDK 4/6 inhibitors (CDK 4/6i), whereas BRCA2-mutated triple-negative breast cancer (TNBC) may be especially sensitive to immune checkpoint inhibitors. If validated in future prospective studies, these data may have relevant clinical implications, thus establishing different treatment paths in patients with BRCA1 or BRCA2 PVs.
Collapse
Affiliation(s)
- Emma Zattarin
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ida Taglialatela
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Riccardo Lobefaro
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rita Leporati
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giovanni Fucà
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Ligorio
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Caterina Sposetti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Leonardo Provenzano
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Vingiani
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Pathology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Cristina Ferraris
- Breast Unit, Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Gabriele Martelli
- Breast Unit, Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giancarlo Pruneri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Pathology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo de Braud
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Claudio Vernieri
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy.
| |
Collapse
|
108
|
Tao LR, Ye Y, Zhao H. Early breast cancer risk detection: a novel framework leveraging polygenic risk scores and machine learning. J Med Genet 2023; 60:960-964. [PMID: 37055164 DOI: 10.1136/jmg-2022-108582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 03/27/2023] [Indexed: 04/15/2023]
Abstract
BACKGROUND Breast cancer (BC) is the most common cancer and the second leading cause of cancer death in women; an estimated one in eight women in the USA will develop BC during her lifetime. However, current methods of BC screening, including clinical breast exams, mammograms, biopsies and others, are often underused due to limited access, expense and a lack of risk awareness, causing 30% (up to 80% in low-income and middle-income countries) of patients with BC to miss the precious early detection phase. METHODS This study creates a key step to supplement the current BC diagnostic pipeline: a prescreening platform, prior to traditional detection and diagnostic steps. We have developed BREast CAncer Risk Detection Application (BRECARDA), a novel framework that personalises BC risk assessment using artificial intelligence neural networks to incorporate relevant genetic and non-genetic risk factors. A polygenic risk score (PRS) was enhanced by employing AnnoPred and validated by fivefolds cross-validation, outperforming three existing state-of-the-art PRS methods. RESULTS We used data from 97 597 female participants of the UK BioBank to train our algorithm. Using the enhanced PRS thus trained together with non-genetic information, BRECARDA was evaluated in a testing dataset with 48 074 UK Biobank female participants and achieved a high accuracy of 94.28% and area under the curve of 0.7861. Our optimised AnnoPred outperformed other state-of-the-art methods on quantifying genetic risk, indicating its potential for supplementing the current BC detection tests, population screening and risk evaluation. CONCLUSION BRECARDA can enhance disease risk prediction, identify high-risk individuals for BC screening, facilitate disease diagnosis and improve population-level screening efficiency. It can serve as a valuable and supplemental platform to assist doctors in BC diagnosis and evaluation.
Collapse
Affiliation(s)
- Lynn Rose Tao
- Thomas Jefferson High School for Science and Technology, Alexandria, Virginia, USA
| | - Yixuan Ye
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| |
Collapse
|
109
|
Allard-Chamard H, Li Q, Rahman P. Emerging Concepts in Precision Medicine in Axial Spondyloarthritis. Curr Rheumatol Rep 2023; 25:204-212. [PMID: 37505349 DOI: 10.1007/s11926-023-01113-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2023] [Indexed: 07/29/2023]
Abstract
PURPOSE OF REVIEW Axial spondyloarthritis (AxSpA) is among the rheumatology's most heritable complex diseases, yet precision medicine at clinics still needs to be explored. We reviewed the emerging concepts and recent developments in polygenic risk scores, Mendelian randomization, pharmacogenomics, single-cell sequencing, and spatial transcriptomics. RECENT FINDINGS Polygenic risk score has resulted in encouraging results with potential diagnostic utility as it appears to outperform current diagnostic tools. Its performance and generalizability vary with ethnicity. Mendelian randomization has elucidated multiple causal associations, particularly between inflammatory bowel disease and AxSpA. Single-cell transcriptomics (particularly scRNA-seq and scATAC-seq) has identified numerous cell types, including synovial and blood immunological cells, to understand the contribution of both innate and adaptative immunity in AxSpA. Current molecular tools provide an exciting opportunity to advance precision medicine for AxSpA patients. However, extensive research and implementation strategies are still required before they can have an impact in the clinic.
Collapse
Affiliation(s)
- Hugues Allard-Chamard
- Division of Rheumatology, Faculté de Médecine Et Des Sciences de La Santé de L'Université de Sherbrooke Et Centre de Recherche du CHUS, Sherbrooke, QC, J1K 2R1, Canada
| | - Quan Li
- Department of Medicine, Memorial University, St. John's, NL, Canada
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Proton Rahman
- Department of Medicine, Division of Rheumatology, Memorial University of Newfoundland, 154 LeMarchant Rd, St. John's, Newfoundland, A1C-5B8, Canada.
| |
Collapse
|
110
|
Zhang H, Zhan J, Jin J, Zhang J, Lu W, Zhao R, Ahearn TU, Yu Z, O'Connell J, Jiang Y, Chen T, Okuhara D, Garcia-Closas M, Lin X, Koelsch BL, Chatterjee N. A new method for multiancestry polygenic prediction improves performance across diverse populations. Nat Genet 2023; 55:1757-1768. [PMID: 37749244 PMCID: PMC10923245 DOI: 10.1038/s41588-023-01501-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/16/2023] [Indexed: 09/27/2023]
Abstract
Polygenic risk scores (PRSs) increasingly predict complex traits; however, suboptimal performance in non-European populations raise concerns about clinical applications and health inequities. We developed CT-SLEB, a powerful and scalable method to calculate PRSs, using ancestry-specific genome-wide association study summary statistics from multiancestry training samples, integrating clumping and thresholding, empirical Bayes and superlearning. We evaluated CT-SLEB and nine alternative methods with large-scale simulated genome-wide association studies (~19 million common variants) and datasets from 23andMe, Inc., the Global Lipids Genetics Consortium, All of Us and UK Biobank, involving 5.1 million individuals of diverse ancestry, with 1.18 million individuals from four non-European populations across 13 complex traits. Results demonstrated that CT-SLEB significantly improves PRS performance in non-European populations compared with simple alternatives, with comparable or superior performance to a recent, computationally intensive method. Moreover, our simulation studies offered insights into sample size requirements and SNP density effects on multiancestry risk prediction.
Collapse
Affiliation(s)
- Haoyu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | | | - Jin Jin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jingning Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wenxuan Lu
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA
| | - Ruzhang Zhao
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Zhi Yu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tony Chen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | | | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
111
|
Ho PJ, Lim EH, Hartman M, Wong FY, Li J. Breast cancer risk stratification using genetic and non-genetic risk assessment tools for 246,142 women in the UK Biobank. Genet Med 2023; 25:100917. [PMID: 37334786 DOI: 10.1016/j.gim.2023.100917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023] Open
Abstract
PURPOSE The benefit of using individual risk prediction tools to identify high-risk individuals for breast cancer (BC) screening is uncertain, despite the personalized approach of risk-based screening. METHODS We studied the overlap of predicted high-risk individuals among 246,142 women enrolled in the UK Biobank. Risk predictors assessed include the Gail model (Gail), BC family history (FH, binary), BC polygenic risk score (PRS), and presence of loss-of-function (LoF) variants in BC predisposition genes. Youden J-index was used to select optimal thresholds for defining high-risk. RESULTS In total, 147,399 were considered at high risk for developing BC within the next 2 years by at least 1 of the 4 risk prediction tools examined (Gail2-year > 0.5%: 47%, PRS2-yea r > 0.7%: 30%, FH: 6%, and LoF: 1%); 92,851 (38%) were flagged by only 1 risk predictor. The overlap between individuals flagged as high-risk because of genetic (PRS) and Gail model risk factors was 30%. The best-performing combinatorial model comprises a union of high-risk women identified by PRS, FH, and, LoF (AUC2-year [95% CI]: 62.2 [60.8 to 63.6]). Assigning individual weights to each risk prediction tool increased discriminatory ability. CONCLUSION Risk-based BC screening may require a multipronged approach that includes PRS, predisposition genes, FH, and other recognized risk factors.
Collapse
Affiliation(s)
- Peh Joo Ho
- Laboratory of Women's Health and Genetics, Genome Institute of Singapore, A∗STAR Research Entities, Singapore; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Elaine H Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Mikael Hartman
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Department of Surgery, University Surgical Cluster, National University Hospital, Singapore, Singapore
| | - Fuh Yong Wong
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Jingmei Li
- Laboratory of Women's Health and Genetics, Genome Institute of Singapore, A∗STAR Research Entities, Singapore; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| |
Collapse
|
112
|
Herzog C, Jones A, Evans I, Zikan M, Cibula D, Harbeck N, Colombo N, Rådestad AF, Gemzell-Danielsson K, Pashayan N, Widschwendter M. DNA methylation at quantitative trait loci (mQTLs) varies with cell type and nonheritable factors and may improve breast cancer risk assessment. NPJ Precis Oncol 2023; 7:99. [PMID: 37758816 PMCID: PMC10533818 DOI: 10.1038/s41698-023-00452-2] [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: 03/27/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
To individualise breast cancer (BC) prevention, markers to follow a person's changing environment and health extending beyond static genetic risk scores are required. Here, we analysed cervical and breast DNA methylation (n = 1848) and single nucleotide polymorphisms (n = 1442) and demonstrate that a linear combination of methylation levels at 104 BC-associated methylation quantitative trait loci (mQTL) CpGs, termed the WID™-qtBC index, can identify women with breast cancer in hormone-sensitive tissues (AUC = 0.71 [95% CI: 0.65-0.77] in cervical samples). Women in the highest combined risk group (high polygenic risk score and WID™-qtBC) had a 9.6-fold increased risk for BC [95% CI: 4.7-21] compared to the low-risk group and tended to present at more advanced stages. Importantly, the WID™-qtBC is influenced by non-genetic BC risk factors, including age and body mass index, and can be modified by a preventive pharmacological intervention, indicating an interaction between genome and environment recorded at the level of the epigenome. Our findings indicate that methylation levels at mQTLs in relevant surrogate tissues could enable integration of heritable and non-heritable factors for improved disease risk stratification.
Collapse
Affiliation(s)
- Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Milser Str. 10, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, WC1E 6AU, London, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, WC1E 6AU, London, UK
| | - Michal Zikan
- Department of Gynecology and Obstetrics, Charles University in Prague, First Faculty of Medicine and Hospital Na Bulovce, Prague, Czech Republic
| | - David Cibula
- Gynaecologic Oncology Center, Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University in Prague, General University Hospital in Prague, Prague, Czech Republic
| | - Nadia Harbeck
- Breast Center, Department of Obstetrics and Gynecology and CCC Munich, LMU University Hospital, Munich, Germany
| | - Nicoletta Colombo
- Istituto Europeo di Oncologia, Milan, Italy
- University of Milano-Bicocca, Milan, Italy
| | | | | | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Milser Str. 10, 6060, Hall in Tirol, Austria.
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, WC1E 6AU, London, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
113
|
Im C, Sharafeldin N, Yuan Y, Wang Z, Sapkota Y, Lu Z, Spector LG, Howell RM, Arnold MA, Hudson MM, Ness KK, Robison LL, Bhatia S, Armstrong GT, Neglia JP, Yasui Y, Turcotte LM. Polygenic Risk and Chemotherapy-Related Subsequent Malignancies in Childhood Cancer Survivors: A Childhood Cancer Survivor Study and St Jude Lifetime Cohort Study Report. J Clin Oncol 2023; 41:4381-4393. [PMID: 37459583 PMCID: PMC10522108 DOI: 10.1200/jco.23.00428] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 05/18/2023] [Indexed: 08/07/2023] Open
Abstract
PURPOSE Chemotherapeutic exposures are associated with subsequent malignant neoplasm (SMN) risk. The role of genetic susceptibility in chemotherapy-related SMNs should be defined as use of radiation therapy (RT) decreases. PATIENTS AND METHODS SMNs among long-term childhood cancer survivors of European (EUR; N = 9,895) and African (AFR; N = 718) genetic ancestry from the Childhood Cancer Survivor Study and St Jude Lifetime Cohort Study were evaluated. An externally validated 179-variant polygenic risk score (PRS) associated with pleiotropic adult cancer risk from the UK Biobank Study (N > 400,000) was computed for each survivor. SMN cumulative incidence comparing top and bottom PRS quintiles was estimated, along with hazard ratios (HRs) from proportional hazards models. RESULTS A total of 1,594 survivors developed SMNs, with basal cell carcinomas (n = 822), breast cancers (n = 235), and thyroid cancers (n = 221) being the most frequent. Although SMN risk associations with the PRS were extremely modest in RT-exposed EUR survivors (HR, 1.22; P = .048; n = 4,630), the increase in 30-year SMN cumulative incidence and HRs comparing top and bottom PRS quintiles was statistically significant among nonirradiated EUR survivors (n = 4,322) treated with alkylating agents (17% v 6%; HR, 2.46; P < .01), anthracyclines (20% v 8%; HR, 2.86; P < .001), epipodophyllotoxins (23% v 1%; HR, 12.20; P < .001), or platinums (46% v 7%; HR, 8.58; P < .01). This PRS also significantly modified epipodophyllotoxin-related SMN risk among nonirradiated AFR survivors (n = 414; P < .01). Improvements in prediction attributable to the PRS were greatest for epipodophyllotoxin-exposed (AUC, 0.71 v 0.63) and platinum-exposed (AUC,0.68 v 0.58) survivors. CONCLUSION A pleiotropic cancer PRS has strong potential for improving SMN clinical risk stratification among nonirradiated survivors treated with specific chemotherapies. A polygenic risk screening approach may be a valuable complement to an early screening strategy on the basis of treatments and rare cancer-susceptibility mutations.
Collapse
Affiliation(s)
- Cindy Im
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Noha Sharafeldin
- Hematology Oncology Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Yan Yuan
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN
| | - Yadav Sapkota
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
| | - Zhanni Lu
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Logan G. Spector
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Rebecca M. Howell
- Department of Radiation Physics, University of Texas at MD Anderson Cancer Center, Houston, TX
| | - Michael A. Arnold
- Department of Pathology and Laboratory Medicine, University of Colorado and Children's Hospital Colorado, Anschutz Medical Campus, Aurora, CO
| | - Melissa M. Hudson
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Kirsten K. Ness
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
| | - Leslie L. Robison
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Gregory T. Armstrong
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Joseph P. Neglia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Yutaka Yasui
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
| | | |
Collapse
|
114
|
Strandberg R, Czene K, Hall P, Humphreys K. Novel predictions of invasive breast cancer risk in mammography screening cohorts. Stat Med 2023; 42:3816-3837. [PMID: 37337390 DOI: 10.1002/sim.9834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/23/2023] [Accepted: 06/04/2023] [Indexed: 06/21/2023]
Abstract
Mammography screening programs are aimed at reducing mortality due to breast cancer by detecting tumors at an early stage. There is currently interest in moving away from the age-based screening programs, and toward personalized screening based on individual risk factors. To accomplish this, risk prediction models for breast cancer are needed to determine who should be screened, and when. We develop a novel approach using a (random effects) continuous growth model, which we apply to a large population-based, Swedish screening cohort. Unlike existing breast cancer prediction models, this approach explicitly incorporates each woman's individual screening visits in the prediction. It jointly models invasive breast cancer tumor onset, tumor growth rate, symptomatic detection rate, and screening sensitivity. In addition to predicting the overall risk of invasive breast cancer, this model can make separate predictions regarding specific tumor sizes, and the mode of detection (eg, detected at screening, or through symptoms between screenings). It can also predict how these risks change depending on whether or not a woman will attend her next screening. In our study, we predict, given a future diagnosis, that the probability of having a tumor less than (as opposed to greater than) 10-mm diameter, at detection, will be, on average, 2.6 times higher if a woman in the cohort attends their next screening. This indicates that the model can be used to evaluate the short-term benefit of screening attendance, at an individual level.
Collapse
Affiliation(s)
- Rickard Strandberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Swedish eScience Research Centre (SeRC), Karolinska Institutet, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Swedish eScience Research Centre (SeRC), Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
115
|
Wang QL, Zhang Y, Zeng E, Grassmann F, He W, Czene K. Risk of estrogen receptor-specific breast cancer by family history of estrogen receptor subtypes and other cancers. J Natl Cancer Inst 2023; 115:1020-1028. [PMID: 37243749 PMCID: PMC10483332 DOI: 10.1093/jnci/djad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/02/2023] [Accepted: 05/25/2023] [Indexed: 05/29/2023] Open
Abstract
BACKGROUND The extent to which the risk of estrogen receptor (ER)-specific breast cancer is associated with ER status of breast cancer and other cancers among first-degree relatives is unclear. METHODS This population-based cohort included 464 707 cancer-free women in Stockholm, Sweden, during 1978-2019. For ER-negative and ER-positive breast cancers, we estimated hazard ratios (HRs) associated with ER status of female first-degree relatives with breast cancer and of other cancers in all first-degree relatives. Associations between ER-negative and ER-positive status by family cancer history were estimated using logistic regression in a case-only design. RESULTS Women with familial ER-positive breast cancer had 1.87 times (95% confidence interval [CI] = 1.77 to 1.97) higher risk of ER-positive subtype, whereas the corresponding hazard ratio for ER-negative was 2.54 (95% CI = 2.08 to 3.10) when having familial ER-negative breast cancer. The risk increased with an increasing number of female first-degree relatives having concordant subtypes and younger age at diagnosis (Ptrend <.001 for both). Nonbreast cancers among first-degree relatives were associated with both ER-positive (HR = 1.14, 95% CI = 1.10 to 1.17) and ER-negative (HR = 1.08, 95% CI = 1.01 to 1.16) breast cancers. Compared with women with ER-positive breast cancer, women with ER-negative breast cancer were more likely to have family history of liver (odds ratio [OR] = 1.33, 95% CI = 1.05 to 1.67), ovary (OR = 1.28, 95% CI = 1.01 to 1.61), and testicle cancer (OR = 1.79, 95% CI = 1.01 to 3.16) but less likely to have family history of endometrial cancer (OR = 0.77, 95% CI = 0.60 to 1.00) and leukemia (OR = 0.72, 95% CI = 0.56 to 0.91). CONCLUSIONS Risk of ER-specific breast cancer differs according to ER status of female first-degree relatives with breast cancer and some other cancers of first-degree relatives. This family history information should be considered in the individual risk prediction for ER subtypes.
Collapse
Affiliation(s)
- Qiao-Li Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Yuqi Zhang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Erwei Zeng
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Wei He
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, China
- Department of Nutrition and Food Hygiene, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
116
|
Timbres J, Kohut K, Caneppele M, Troy M, Schmidt MK, Roylance R, Sawyer E. DCIS and LCIS: Are the Risk Factors for Developing In Situ Breast Cancer Different? Cancers (Basel) 2023; 15:4397. [PMID: 37686673 PMCID: PMC10486708 DOI: 10.3390/cancers15174397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/09/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Ductal carcinoma in situ (DCIS) is widely accepted as a precursor of invasive ductal carcinoma (IDC). Lobular carcinoma in situ (LCIS) is considered a risk factor for invasive lobular carcinoma (ILC), and it is unclear whether LCIS is also a precursor. Therefore, it would be expected that similar risk factors predispose to both DCIS and IDC, but not necessarily LCIS and ILC. This study examined associations with risk factors using data from 3075 DCIS cases, 338 LCIS cases, and 1584 controls aged 35-60, recruited from the UK-based GLACIER and ICICLE case-control studies between 2007 and 2012. Analysis showed that breastfeeding in parous women was protective against DCIS and LCIS, which is consistent with research on invasive breast cancer (IBC). Additionally, long-term use of HRT in post-menopausal women increased the risk of DCIS and LCIS, with a stronger association in LCIS, similar to the association with ILC. Contrary to findings with IBC, parity and the number of births were not protective against DCIS or LCIS, while oral contraceptives showed an unexpected protective effect. These findings suggest both similarities and differences in risk factors for DCIS and LCIS compared to IBC and that there may be justification for increased breast surveillance in post-menopausal women taking long-term HRT.
Collapse
Affiliation(s)
- Jasmine Timbres
- Breast Cancer Genetics, King’s College London, London SE1 9RT, UK
| | - Kelly Kohut
- St George’s University Hospitals NHS Foundation Trust, Blackshaw Rd, London SW17 0QT, UK
| | | | - Maria Troy
- Guy’s and St Thomas’ NHS Foundation Trust, Great Maze Pond, London SE1 9RT, UK
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands
| | - Rebecca Roylance
- University College London Hospitals NHS Foundation Trust, 235 Euston Rd., London NW1 2BU, UK
| | - Elinor Sawyer
- Breast Cancer Genetics, King’s College London, London SE1 9RT, UK
| |
Collapse
|
117
|
Abstract
Since the publication of the first genome-wide association study for cancer in 2007, thousands of common alleles that are associated with the risk of cancer have been identified. The relative risk associated with individual variants is small and of limited clinical significance. However, the combined effect of multiple risk variants as captured by polygenic scores (PGSs) may be much greater and therefore provide risk discrimination that is clinically useful. We review the considerable research efforts over the past 15 years for developing statistical methods for PGSs and their application in large-scale genome-wide association studies to develop PGSs for various cancers. We review the predictive performance of these PGSs and the multiple challenges currently limiting the clinical application of PGSs. Despite this, PGSs are beginning to be incorporated into clinical multifactorial risk prediction models to stratify risk in both clinical trials and clinical implementation studies.
Collapse
Affiliation(s)
- Xin Yang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Siddhartha Kar
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul D P Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| |
Collapse
|
118
|
Kusters CDJ, Paul KC, Romero T, Sinsheimer JS, Ritz BR. Among men, androgens are associated with a decrease in Alzheimer's disease risk. Alzheimers Dement 2023; 19:3826-3834. [PMID: 36938850 PMCID: PMC10509321 DOI: 10.1002/alz.13013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 03/21/2023]
Abstract
INTRODUCTION Increased levels of sex hormones have been hypothesized to decrease Alzheimer's disease (AD) risk. We assessed the association between sex steroid hormones with AD using a Mendelian randomization (MR) approach. METHODS An inverse-variance weighting (IVW) MR analysis was performed using effect estimates from external genome-wide association study (GWAS) summary statistics. We included independent variants (linkage disequilibrium R2 < 0.001) and a p-value threshold of 5 × 10-8 . RESULTS An increase in androgens was associated with a decreased AD risk among men: testosterone (odds ratio [OR]: 0.53; 95% confidence interval [CI]: 0.32-0.88; p-value: 0.01; false discovery rate [FDR] p-value: 0.03); dehydroepiandrosterone sulfate (DHEAS; OR: 0.56; 95% CI: 0.38-0.85; p-value: 0.01; FDR p-value: 0.03); and androsterone sulfate (OR: 0.69; 95% CI: 0.46-1.02; p-value: 0.06; FDR p-value: 0.10). There was no association between sex steroid hormones and AD among women, although analysis for estradiol had limited statistical power. DISCUSSION A higher concentration of androgens was associated with a decreased risk of AD among men of European ancestry, suggesting that androgens among men might be neuroprotective and could potentially prevent or delay an AD diagnosis. HIGHLIGHTS Sex hormones are hypothesized to play a role in developing Alzheimer's disease (AD). The effect of sex hormones on AD was assessed using Mendelian randomization (MR) analysis. Among women, genetically determined effects of sex hormones were limited or null. Among men, a higher concentration of androgens decreased AD risk. This study suggests a causal relationship between androgens and AD among men.
Collapse
Affiliation(s)
- Cynthia D J Kusters
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, California, USA
| | - Kimberly C Paul
- Department of Neurology, David Geffen School of Medicine, Los Angeles, California, USA
| | - Tahmineh Romero
- Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Janet S Sinsheimer
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, California, USA
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, California, USA
- Department of Computational Medicine, David Geffen School of Medicine, Los Angeles, California, USA
| | - Beate R Ritz
- Department of Neurology, David Geffen School of Medicine, Los Angeles, California, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
- Department of Environmental Health, UCLA Fielding School of Public Health, Los Angeles, California, USA
| |
Collapse
|
119
|
Al-Jumaan M, Chu H, Alsulaiman A, Camp SY, Han S, Gillani R, Al Marzooq Y, Almulhim F, Vatte C, Al Nemer A, Almuhanna A, Van Allen EM, Al-Ali A, AlDubayan SH. Interplay of Mendelian and polygenic risk factors in Arab breast cancer patients. Genome Med 2023; 15:65. [PMID: 37658461 PMCID: PMC10474689 DOI: 10.1186/s13073-023-01220-4] [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: 05/04/2023] [Accepted: 08/09/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Breast cancer patients from the indigenous Arab population present much earlier than patients from Western countries and have traditionally been underrepresented in cancer genomics studies. The contribution of polygenic and Mendelian risk toward the earlier onset of breast cancer in the population remains elusive. METHODS We performed low-pass whole genome sequencing (lpWGS) and whole-exome sequencing (WES) from 220 female breast cancer patients unselected for positive family history from the indigenous Arab population. Using publicly available resources, we imputed population-specific variants and calculated breast cancer burden-sensitive polygenic risk scores (PRS). Variant pathogenicity was also evaluated on exome variants with high coverage. RESULTS Variants imputed from lpWGS showed high concordance with paired exome (median dosage correlation: 0.9459, Interquartile range: 0.9410-0.9490). After adjusting the PRS to the Arab population, we found significant associations between PRS performance in risk prediction and first-degree relative breast cancer history prediction (Spearman rho=0.43, p = 0.03), where breast cancer patients in the top PRS decile are 5.53 (95% CI 1.76-17.97, p = 0.003) times more likely also to have a first-degree relative diagnosed with breast cancer compared to those in the middle deciles. In addition, we found evidence for the genetic liability threshold model of breast cancer where among patients with a family history of breast cancer, pathogenic rare variant carriers had significantly lower PRS than non-carriers (p = 0.0205, Mann-Whitney U test) while for non-carriers every standard deviation increase in PRS corresponded to 4.52 years (95% CI 8.88-0.17, p = 0.042) earlier age of presentation. CONCLUSIONS Overall, our study provides a framework to assess polygenic risk in an understudied population using lpWGS and identifies common variant risk as a factor independent of pathogenic variant carrier status for earlier age of onset of breast cancer among indigenous Arab breast cancer patients.
Collapse
Affiliation(s)
- Mohammed Al-Jumaan
- College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Hoyin Chu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abdullah Alsulaiman
- College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Sabrina Y Camp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seunghun Han
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Riaz Gillani
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Yousef Al Marzooq
- College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Fatmah Almulhim
- College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Chittibabu Vatte
- College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Areej Al Nemer
- College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Afnan Almuhanna
- College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Amein Al-Ali
- College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Saud H AlDubayan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
| |
Collapse
|
120
|
Choi J, Ha TW, Choi HM, Lee HB, Shin HC, Chung W, Han W. Development of a Breast Cancer Risk Prediction Model Incorporating Polygenic Risk Scores and Nongenetic Risk Factors for Korean Women. Cancer Epidemiol Biomarkers Prev 2023; 32:1182-1189. [PMID: 37310812 PMCID: PMC10472098 DOI: 10.1158/1055-9965.epi-23-0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/19/2023] [Accepted: 06/09/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND To develop a breast cancer prediction model for Korean women using published polygenic risk scores (PRS) combined with nongenetic risk factors (NGRF). METHODS Thirteen PRS models generated from single or multiple combinations of the Asian and European PRSs were evaluated among 20,434 Korean women. The AUC and increase in OR per SD were compared for each PRS. The PRSs with the highest predictive power were combined with NGRFs; then, an integrated prediction model was established using the Individualized Coherent Absolute Risk Estimation (iCARE) tool. The absolute breast cancer risk was stratified for 18,142 women with available follow-up data. RESULTS PRS38_ASN+PRS190_EB, a combination of Asian and European PRSs, had the highest AUC (0.621) among PRSs, with an OR per SD increase of 1.45 (95% confidence interval: 1.31-1.61). Compared with the average risk group (35%-65%), women in the top 5% had a 2.5-fold higher risk of breast cancer. Incorporating NGRFs yielded a modest increase in the AUC of women ages >50 years. For PRS38_ASN+PRS190_EB+NGRF, the average absolute risk was 5.06%. The lifetime absolute risk at age 80 years for women in the top 5% was 9.93%, whereas that of women in the lowest 5% was 2.22%. Women at higher risks were more sensitive to NGRF incorporation. CONCLUSIONS Combined Asian and European PRSs were predictive of breast cancer in Korean women. Our findings support the use of these models for personalized screening and prevention of breast cancer. IMPACT Our study provides insights into genetic susceptibility and NGRFs for predicting breast cancer in Korean women.
Collapse
Affiliation(s)
- Jihye Choi
- Department of General Surgery, National Medical Center, Seoul, Republic of Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | | | - Han-Byoel Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
- DCGen, Co., Ltd., Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Hee-Chul Shin
- DCGen, Co., Ltd., Seoul, Republic of Korea
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | | | - Wonshik Han
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
- DCGen, Co., Ltd., Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
121
|
Lee SM, Shivakumar M, Xiao B, Jung SH, Nam Y, Yun JS, Choe EK, Jung YM, Oh S, Park JS, Jun JK, Kim D. Genome-wide polygenic risk scores for hypertensive disease during pregnancy can also predict the risk for long-term cardiovascular disease. Am J Obstet Gynecol 2023; 229:298.e1-298.e19. [PMID: 36933686 PMCID: PMC10504416 DOI: 10.1016/j.ajog.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Hypertensive disorders during pregnancy are associated with the risk of long-term cardiovascular disease after pregnancy, but it has not yet been determined whether genetic predisposition for hypertensive disorders during pregnancy can predict the risk for long-term cardiovascular disease. OBJECTIVE This study aimed to evaluate the risk for long-term atherosclerotic cardiovascular disease according to polygenic risk scores for hypertensive disorders during pregnancy. STUDY DESIGN Among UK Biobank participants, we included European-descent women (n=164,575) with at least 1 live birth. Participants were divided according to genetic risk categorized by polygenic risk scores for hypertensive disorders during pregnancy (low risk, score ≤25th percentile; medium risk, score 25th∼75th percentile; high risk, score >75th percentile), and were evaluated for incident atherosclerotic cardiovascular disease, defined as the new occurrence of one of the following: coronary artery disease, myocardial infarction, ischemic stroke, or peripheral artery disease. RESULTS Among the study population, 2427 (1.5%) had a history of hypertensive disorders during pregnancy, and 8942 (5.6%) developed incident atherosclerotic cardiovascular disease after enrollment. Women with high genetic risk for hypertensive disorders during pregnancy had a higher prevalence of hypertension at enrollment. After enrollment, women with high genetic risk for hypertensive disorders during pregnancy had an increased risk for incident atherosclerotic cardiovascular disease, including coronary artery disease, myocardial infarction, and peripheral artery disease, compared with those with low genetic risk, even after adjustment for history of hypertensive disorders during pregnancy. CONCLUSION High genetic risk for hypertensive disorders during pregnancy was associated with increased risk for atherosclerotic cardiovascular disease. This study provides evidence on the informative value of polygenic risk scores for hypertensive disorders during pregnancy in prediction of long-term cardiovascular outcomes later in life.
Collapse
Affiliation(s)
- Seung Mi Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Korea
| | - Manu Shivakumar
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Brenda Xiao
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sang-Hyuk Jung
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Yonghyun Nam
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jae-Seung Yun
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Department of Internal Medicine, Catholic University of Korea School of Medicine, Seoul, Korea
| | - Eun Kyung Choe
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Department of Surgery, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea
| | - Young Mi Jung
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Sohee Oh
- Department of Biostatistics, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Joong Shin Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Kwan Jun
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.
| |
Collapse
|
122
|
Clift AK, Collins GS, Lord S, Petrou S, Dodwell D, Brady M, Hippisley-Cox J. Predicting 10-year breast cancer mortality risk in the general female population in England: a model development and validation study. Lancet Digit Health 2023; 5:e571-e581. [PMID: 37625895 DOI: 10.1016/s2589-7500(23)00113-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/06/2023] [Accepted: 06/12/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Identifying female individuals at highest risk of developing life-threatening breast cancers could inform novel stratified early detection and prevention strategies to reduce breast cancer mortality, rather than only considering cancer incidence. We aimed to develop a prognostic model that accurately predicts the 10-year risk of breast cancer mortality in female individuals without breast cancer at baseline. METHODS In this model development and validation study, we used an open cohort study from the QResearch primary care database, which was linked to secondary care and national cancer and mortality registers in England, UK. The data extracted were from female individuals aged 20-90 years without previous breast cancer or ductal carcinoma in situ who entered the cohort between Jan 1, 2000, and Dec 31, 2020. The primary outcome was breast cancer-related death, which was assessed in the full dataset. Cox proportional hazards, competing risks regression, XGBoost, and neural network modelling approaches were used to predict the risk of breast cancer death within 10 years using routinely collected health-care data. Death due to causes other than breast cancer was the competing risk. Internal-external validation was used to evaluate prognostic model performance (using Harrell's C, calibration slope, and calibration in the large), performance heterogeneity, and transportability. Internal-external validation involved dataset partitioning by time period and geographical region. Decision curve analysis was used to assess clinical utility. FINDINGS We identified data for 11 626 969 female individuals, with 70 095 574 person-years of follow-up. There were 142 712 (1·2%) diagnoses of breast cancer, 24 043 (0·2%) breast cancer-related deaths, and 696 106 (6·0%) deaths from other causes. Meta-analysis pooled estimates of Harrell's C were highest for the competing risks model (0·932, 95% CI 0·917-0·946). The competing risks model was well calibrated overall (slope 1·011, 95% CI 0·978-1·044), and across different ethnic groups. Decision curve analysis suggested favourable clinical utility across all age groups. The XGBoost and neural network models had variable performance across age and ethnic groups. INTERPRETATION A model that predicts the combined risk of developing and then dying from breast cancer at the population level could inform stratified screening or chemoprevention strategies. Further evaluation of the competing risks model should comprise effect and health economic assessment of model-informed strategies. FUNDING Cancer Research UK.
Collapse
Affiliation(s)
- Ash Kieran Clift
- Cancer Research UK Oxford Centre, University of Oxford, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK.
| | - Gary S Collins
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK
| | - Simon Lord
- Department of Oncology, University of Oxford, UK
| | - Stavros Petrou
- Nuffield Department of Primary Care Health Sciences, University of Oxford, UK
| | - David Dodwell
- Nuffield Department of Population Health, University of Oxford, UK
| | | | - Julia Hippisley-Cox
- Nuffield Department of Primary Care Health Sciences, University of Oxford, UK
| |
Collapse
|
123
|
Roberts E, van Veen EM, Byers H, Barnett-Griness O, Gronich N, Lejbkowicz F, Pinchev M, Smith MJ, Howell A, Newman WG, Woodward ER, Harkness EF, Brentnall AR, Cuzick J, Rennert G, Howell SJ, Evans DG. Breast cancer polygenic risk scores derived in White European populations are not calibrated for women of Ashkenazi Jewish descent. Genet Med 2023; 25:100846. [PMID: 37061873 DOI: 10.1016/j.gim.2023.100846] [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: 06/27/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/17/2023] Open
Abstract
PURPOSE Polygenic risk scores (PRSs) are a major component of accurate breast cancer (BC) risk prediction but require ethnicity-specific calibration. Ashkenazi Jewish (AJ) population is assumed to be of White European (WE) origin in some commercially available PRSs despite differing effect allele frequencies (EAFs). We conducted a case-control study of WE and AJ women from the Predicting Risk of Cancer at Screening Study. The Breast Cancer in Northern Israel Study provided a separate AJ population-based case-control validation series. METHODS All women underwent Illumina OncoArray single-nucleotide variation (SNV; formerly single-nucleotide polymorphism [SNP]) analysis. Two PRSs were assessed, SNV142 and SNV78. A total of 221 of 2243 WE women (discovery: cases = 111; controls = 110; validation: cases = 651; controls = 1772) and 221 AJ women (cases = 121; controls = 110) were included from the UK study; the Israeli series consisted of 2045 AJ women (cases = 1331; controls = 714). EAFs were obtained from the Genome Aggregation Database. RESULTS In the UK study, the mean SNV142 PRS demonstrated good calibration and discrimination in WE population, with mean PRS of 1.33 (95% CI 1.18-1.48) in cases and 1.01 (95% CI 0.89-1.13) in controls. In AJ women from Manchester, the mean PRS of 1.54 (1.38-1.70) in cases and 1.20 (1.08-1.32) in controls demonstrated good discrimination but overestimation of BC relative risk. After adjusting for EAFs for the AJ population, mean risk was corrected (mean SNV142 PRS cases = 1.30 [95% CI 1.16-1.44] and controls = 1.02 [95% CI 0.92-1.12]). This was recapitulated in the larger Israeli data set with good discrimination (area under the curve = 0.632 [95% CI 0.607-0.657] for SNV142). CONCLUSION AJ women should not be given BC relative risk predictions based on PRSs calibrated to EAFs from the WE population. PRSs need to be recalibrated using AJ-derived EAFs. A simple recalibration using the mean PRS adjustment ratio likely performs well.
Collapse
Affiliation(s)
- Eleanor Roberts
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Elke M van Veen
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Helen Byers
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Ofra Barnett-Griness
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Naomi Gronich
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Flavio Lejbkowicz
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Mila Pinchev
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Miriam J Smith
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Anthony Howell
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom; Nightingale/Prevent Breast Cancer Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The Christie Hospital, Manchester, United Kingdom
| | - William G Newman
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Elaine F Harkness
- Nightingale/Prevent Breast Cancer Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Informatics, Imaging & Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Adam R Brentnall
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Population Health, Charterhouse Square, London, United Kingdom
| | - Jack Cuzick
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Population Health, Charterhouse Square, London, United Kingdom
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Sacha J Howell
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom; Nightingale/Prevent Breast Cancer Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The Christie Hospital, Manchester, United Kingdom
| | - D Gareth Evans
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom; Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom; Nightingale/Prevent Breast Cancer Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The Christie Hospital, Manchester, United Kingdom.
| |
Collapse
|
124
|
Akdeniz BC, Mattingsdal M, Dominguez-Valentin M, Frei O, Shadrin A, Puustusmaa M, Saar R, Sõber S, Møller P, Andreassen OA, Padrik P, Hovig E. A Breast Cancer Polygenic Risk Score Is Feasible for Risk Stratification in the Norwegian Population. Cancers (Basel) 2023; 15:4124. [PMID: 37627152 PMCID: PMC10452897 DOI: 10.3390/cancers15164124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Statistical associations of numerous single nucleotide polymorphisms with breast cancer (BC) have been identified in genome-wide association studies (GWAS). Recent evidence suggests that a Polygenic Risk Score (PRS) can be a useful risk stratification instrument for a BC screening strategy, and a PRS test has been developed for clinical use. The performance of the PRS is yet unknown in the Norwegian population. AIM To evaluate the performance of PRS models for BC in a Norwegian dataset. METHODS We investigated a sample of 1053 BC cases and 7094 controls from different regions of Norway. PRS values were calculated using four PRS models, and their performance was evaluated by the area under the curve (AUC) and the odds ratio (OR). The effect of the PRS on the age of onset of BC was determined by a Cox regression model, and the lifetime absolute risk of developing BC was calculated using the iCare tool. RESULTS The best performing PRS model included 3820 SNPs, which yielded an AUC = 0.625 and an OR = 1.567 per one standard deviation increase. The PRS values of the samples correlate with an increased risk of BC, with a hazard ratio of 1.494 per one standard deviation increase (95% confidence interval of 1.406-1.588). The individuals in the highest decile of the PRS have at least twice the risk of developing BC compared to the individuals with a median PRS. The results in this study with Norwegian samples are coherent with the findings in the study conducted using Estonian and UK Biobank samples. CONCLUSION The previously validated PRS models have a similar observed accuracy in the Norwegian data as in the UK and Estonian populations. A PRS provides a meaningful association with the age of onset of BC and lifetime risk. Therefore, as suggested in Estonia, a PRS may also be integrated into the screening strategy for BC in Norway.
Collapse
Affiliation(s)
- Bayram Cevdet Akdeniz
- Center for Bioinformatics, Department of Informatics, University of Oslo, 0313 Oslo, Norway (E.H.)
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital, University of Oslo, 4956 Oslo, Norway (O.A.A.)
| | - Morten Mattingsdal
- Center for Bioinformatics, Department of Informatics, University of Oslo, 0313 Oslo, Norway (E.H.)
- Department of Medical Research, Vestre Viken Hospital Trust, Bærum Hospital, 1346 Gjettum, Norway
| | - Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway (P.M.)
| | - Oleksandr Frei
- Center for Bioinformatics, Department of Informatics, University of Oslo, 0313 Oslo, Norway (E.H.)
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital, University of Oslo, 4956 Oslo, Norway (O.A.A.)
| | - Alexey Shadrin
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital, University of Oslo, 4956 Oslo, Norway (O.A.A.)
| | | | - Regina Saar
- OÜ Antegenes, 50603 Tartu, Estonia; (M.P.); (R.S.)
| | - Siim Sõber
- OÜ Antegenes, 50603 Tartu, Estonia; (M.P.); (R.S.)
| | - Pål Møller
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway (P.M.)
| | - Ole A. Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital, University of Oslo, 4956 Oslo, Norway (O.A.A.)
| | | | - Eivind Hovig
- Center for Bioinformatics, Department of Informatics, University of Oslo, 0313 Oslo, Norway (E.H.)
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway (P.M.)
| |
Collapse
|
125
|
Nguyen AA, McCarthy AM, Kontos D. Combining Molecular and Radiomic Features for Risk Assessment in Breast Cancer. Annu Rev Biomed Data Sci 2023; 6:299-311. [PMID: 37159874 DOI: 10.1146/annurev-biodatasci-020722-092748] [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] [Indexed: 05/11/2023]
Abstract
Breast cancer risk is highly variable within the population and current research is leading the shift toward personalized medicine. By accurately assessing an individual woman's risk, we can reduce the risk of over/undertreatment by preventing unnecessary procedures or by elevating screening procedures. Breast density measured from conventional mammography has been established as one of the most dominant risk factors for breast cancer; however, it is currently limited by its ability to characterize more complex breast parenchymal patterns that have been shown to provide additional information to strengthen cancer risk models. Molecular factors ranging from high penetrance, or high likelihood that a mutation will show signs and symptoms of the disease, to combinations of gene mutations with low penetrance have shown promise for augmenting risk assessment. Although imaging biomarkers and molecular biomarkers have both individually demonstrated improved performance in risk assessment, few studies have evaluated them together. This review aims to highlight the current state of the art in breast cancer risk assessment using imaging and genetic biomarkers.
Collapse
Affiliation(s)
- Alex A Nguyen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anne Marie McCarthy
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Despina Kontos
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| |
Collapse
|
126
|
Stiller S, Drukewitz S, Lehmann K, Hentschel J, Strehlow V. Clinical Impact of Polygenic Risk Score for Breast Cancer Risk Prediction in 382 Individuals with Hereditary Breast and Ovarian Cancer Syndrome. Cancers (Basel) 2023; 15:3938. [PMID: 37568754 PMCID: PMC10417109 DOI: 10.3390/cancers15153938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Single nucleotide polymorphisms are currently not considered in breast cancer (BC) risk predictions used in daily practice of genetic counselling and clinical management of familial BC in Germany. This study aimed to assess the clinical value of incorporating a 313-variant-based polygenic risk score (PRS) into BC risk calculations in a cohort of German women with suspected hereditary breast and ovarian cancer syndrome (HBOC). Data from 382 individuals seeking counselling for HBOC were analysed. Risk calculations were performed using the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm with and without the inclusion of the PRS. Changes in risk predictions and their impact on clinical management were evaluated. The PRS led to changes in risk stratification based on 10-year risk calculations in 13.6% of individuals. Furthermore, the inclusion of the PRS in BC risk predictions resulted in clinically significant changes in 12.0% of cases, impacting the prevention recommendations established by the German Consortium for Hereditary Breast and Ovarian Cancer. These findings support the implementation of the PRS in genetic counselling for personalized BC risk assessment.
Collapse
Affiliation(s)
- Sarah Stiller
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Stephan Drukewitz
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Partner Site Dresden, 01307 Dresden, Germany
| | - Kathleen Lehmann
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| |
Collapse
|
127
|
He H, Shen Q, He MM, Qiu W, Wang H, Zhang S, Qin S, Lu Z, Zhu Y, Tian J, Chang J, Wang K, Zhang X, Miao X, Song M, Zhong R. In Utero and Childhood/Adolescence Exposure to Tobacco Smoke, Genetic Risk, and Cancer Incidence in Adulthood: A Prospective Cohort Study. Mayo Clin Proc 2023; 98:1164-1176. [PMID: 37422733 DOI: 10.1016/j.mayocp.2023.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 03/11/2023] [Accepted: 03/28/2023] [Indexed: 07/10/2023]
Abstract
OBJECTIVE To evaluate the association of early-life tobacco smoke exposure, especially interacting with cancer genetic variants, with adult cancer. PARTICIPANTS AND METHODS We examined the associations of in utero tobacco smoke exposure, age of smoking initiation, and their interaction with genetic risk levels with cancer incidence in 393,081 participants from the UK Biobank. Information on tobacco exposure was obtained by self-reported questionnaires. A cancer polygenic risk score was constructed by weighting and integrating 702 genome-wide association studies-identified risk variants. Cox proportional hazards regression models were used to calculate hazard ratios (HRs) for overall cancer and organ-specific cancer incidence. RESULTS During 11.8 years of follow-up, 23,450 (5.97%) and 23,413 (6.03%) incident cancers were included in the analyses of in utero exposure and age of smoking initiation, respectively. The HR (95% CI) for incident cancer in participants with in utero exposure to tobacco smoke was 1.04 (1.01-1.07) for overall cancer, 1.59 (1.44-1.75) for respiratory cancer, and 1.09 (1.03-1.17) for gastrointestinal cancer. The relative risk of incident cancer increased with earlier smoking initiation (Ptrend<.001), with the HR (95% CI) of 1.44 (1.36-1.51) for overall cancer, 13.28 (11.39-15.48) for respiratory cancer, and 1.72 (1.54-1.91) for gastrointestinal cancer in smokers with initiation in childhood compared with never smokers. Importantly, a positive additive interaction between age of smoking initiation and genetic risk was observed for overall cancer (Padditive=.04) and respiratory cancer (Padditive=.003) incidence. CONCLUSION In utero exposure and earlier smoking initiation are associated with overall and organ-specific cancer, and age of smoking initiation interaction with genetic risk is associated with respiratory cancer.
Collapse
Affiliation(s)
- Heng He
- Department of Epidemiology and Biostatistics, Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Qian Shen
- Department of Epidemiology and Biostatistics, Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ming-Ming He
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Weihong Qiu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Haoxue Wang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shanshan Zhang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shifan Qin
- Department of Epidemiology and Biostatistics, Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Wang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Xuehong Zhang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Mingyang Song
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA; Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
128
|
Henkel J, Laner A, Locher M, Wohlfrom T, Neitzel B, Becker K, Neuhann T, Abicht A, Steinke-Lange V, Holinski-Feder E. Diagnostic yield and clinical relevance of expanded germline genetic testing for nearly 7000 suspected HBOC patients. Eur J Hum Genet 2023; 31:925-930. [PMID: 37188824 PMCID: PMC10400578 DOI: 10.1038/s41431-023-01380-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/18/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Here we report the results of a retrospective germline analysis of 6941 individuals fulfilling the criteria necessary for genetic testing of hereditary breast- and ovarian cancer (HBOC) according to the German S3 or AGO Guidelines. Genetic testing was performed by next-generation sequencing using 123 cancer-associated genes based on the Illumina TruSight® Cancer Sequencing Panel. In 1431 of 6941 cases (20.6%) at least one variant was reported (ACMG/AMP classes 3-5). Of those 56.3% (n = 806) were class 4 or 5 and 43.7% (n = 625) were a class 3 (VUS). We defined a 14 gene HBOC core gene panel and compared this to a national and different internationally recommended gene panels (German Hereditary Breast and Ovarian Cancer Consortium HBOC Consortium, ClinGen expert Panel, Genomics England PanelsApp) in regard of diagnostic yield, revealing a diagnostic range of pathogenic variants (class 4/5) from 7.8 to 11.6% depending on the panel evaluated. With the 14 HBOC core gene panel having a diagnostic yield of pathogenic variants (class 4/5) of 10.8%. Additionally, 66 (1%) pathogenic variants (ACMG/AMP class 4 or 5) were found in genes outside the 14 HBOC core gene set (secondary findings) that would have been missed with the restriction to the analysis of HBOC genes. Furthermore, we evaluated a workflow for a periodic re-evaluation of variants of uncertain clinical significance (VUS) for the improvement of clinical validity of germline genetic testing.
Collapse
Affiliation(s)
- Jan Henkel
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
| | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
| | | | | | | | | | | | - Angela Abicht
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, München, Germany
| | - Verena Steinke-Lange
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität, München, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, München, Germany.
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität, München, Germany.
| |
Collapse
|
129
|
Chiorino G, Petracci E, Sehovic E, Gregnanin I, Camussi E, Mello-Grand M, Ostano P, Riggi E, Vergini V, Russo A, Berrino E, Ortale A, Garena F, Venesio T, Gallo F, Favettini E, Frigerio A, Matullo G, Segnan N, Giordano L. Plasma microRNA ratios associated with breast cancer detection in a nested case-control study from a mammography screening cohort. Sci Rep 2023; 13:12040. [PMID: 37491482 PMCID: PMC10368693 DOI: 10.1038/s41598-023-38886-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/17/2023] [Indexed: 07/27/2023] Open
Abstract
Mammographic breast cancer screening is effective in reducing breast cancer mortality. Nevertheless, several limitations are known. Therefore, developing an alternative or complementary non-invasive tool capable of increasing the accuracy of the screening process is highly desirable. The objective of this study was to identify circulating microRNA (miRs) ratios associated with BC in women attending mammography screening. A nested case-control study was conducted within the ANDROMEDA cohort (women of age 46-67 attending BC screening). Pre-diagnostic plasma samples, information on life-styles and common BC risk factors were collected. Small-RNA sequencing was carried out on plasma samples from 65 cases and 66 controls. miR ratios associated with BC were selected by two-sample Wilcoxon test and lasso logistic regression. Subsequent assessment by RT-qPCR of the miRs contained in the selected miR ratios was carried out as a platform validation. To identify the most promising biomarkers, penalised logistic regression was further applied to candidate miR ratios alone, or in combination with non-molecular factors. Small-RNA sequencing yielded 20 candidate miR ratios associated with BC, which were further assessed by RT-qPCR. In the resulting model, penalised logistic regression selected seven miR ratios (miR-199a-3p_let-7a-5p, miR-26b-5p_miR-142-5p, let-7b-5p_miR-19b-3p, miR-101-3p_miR-19b-3p, miR-93-5p_miR-19b-3p, let-7a-5p_miR-22-3p and miR-21-5p_miR-23a-3p), together with body mass index (BMI), menopausal status (MS), the interaction term BMI * MS, life-style score and breast density. The ROC AUC of the model was 0.79 with a sensitivity and specificity of 71.9% and 76.6%, respectively. We identified biomarkers potentially useful for BC screening measured through a widespread and low-cost technique. This is the first study reporting circulating miRs for BC detection in a screening setting. Validation in a wider sample is warranted.Trial registration: The Andromeda prospective cohort study protocol was retrospectively registered on 27-11-2015 (NCT02618538).
Collapse
Affiliation(s)
- Giovanna Chiorino
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Elisabetta Petracci
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Emir Sehovic
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy.
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
| | - Ilaria Gregnanin
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Elisa Camussi
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Maurizia Mello-Grand
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Paola Ostano
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Emilia Riggi
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Viviana Vergini
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Alessia Russo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy
- Pathology Unit, Candiolo Cancer Institute, FPO IRCCS, Candiolo, Italy
| | - Andrea Ortale
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Francesca Garena
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO IRCCS, Candiolo, Italy
| | - Federica Gallo
- Epidemiology Unit, Staff Health Direction, Local Health Authority 1 of Cuneo, Cuneo, Italy
| | | | - Alfonso Frigerio
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Nereo Segnan
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy.
| | - Livia Giordano
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| |
Collapse
|
130
|
Raben TG, Lello L, Widen E, Hsu SDH. Biobank-scale methods and projections for sparse polygenic prediction from machine learning. Sci Rep 2023; 13:11662. [PMID: 37468507 PMCID: PMC10356957 DOI: 10.1038/s41598-023-37580-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023] Open
Abstract
In this paper we characterize the performance of linear models trained via widely-used sparse machine learning algorithms. We build polygenic scores and examine performance as a function of training set size, genetic ancestral background, and training method. We show that predictor performance is most strongly dependent on size of training data, with smaller gains from algorithmic improvements. We find that LASSO generally performs as well as the best methods, judged by a variety of metrics. We also investigate performance characteristics of predictors trained on one genetic ancestry group when applied to another. Using LASSO, we develop a novel method for projecting AUC and correlation as a function of data size (i.e., for new biobanks) and characterize the asymptotic limit of performance. Additionally, for LASSO (compressed sensing) we show that performance metrics and predictor sparsity are in agreement with theoretical predictions from the Donoho-Tanner phase transition. Specifically, a future predictor trained in the Taiwan Precision Medicine Initiative for asthma can achieve an AUC of [Formula: see text] and for height a correlation of [Formula: see text] for a Taiwanese population. This is above the measured values of [Formula: see text] and [Formula: see text], respectively, for UK Biobank trained predictors applied to a European population.
Collapse
Affiliation(s)
- Timothy G Raben
- Department of Physics and Astronomy, Michigan State University, Michigan, USA.
| | - Louis Lello
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Erik Widen
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Stephen D H Hsu
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| |
Collapse
|
131
|
Sigurdsson AI, Louloudis I, Banasik K, Westergaard D, Winther O, Lund O, Ostrowski S, Erikstrup C, Pedersen O, Nyegaard M, Brunak S, Vilhjálmsson B, Rasmussen S. Deep integrative models for large-scale human genomics. Nucleic Acids Res 2023; 51:e67. [PMID: 37224538 PMCID: PMC10325897 DOI: 10.1093/nar/gkad373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/18/2023] [Accepted: 04/28/2023] [Indexed: 05/26/2023] Open
Abstract
Polygenic risk scores (PRSs) are expected to play a critical role in precision medicine. Currently, PRS predictors are generally based on linear models using summary statistics, and more recently individual-level data. However, these predictors mainly capture additive relationships and are limited in data modalities they can use. We developed a deep learning framework (EIR) for PRS prediction which includes a model, genome-local-net (GLN), specifically designed for large-scale genomics data. The framework supports multi-task learning, automatic integration of other clinical and biochemical data, and model explainability. When applied to individual-level data from the UK Biobank, the GLN model demonstrated a competitive performance compared to established neural network architectures, particularly for certain traits, showcasing its potential in modeling complex genetic relationships. Furthermore, the GLN model outperformed linear PRS methods for Type 1 Diabetes, likely due to modeling non-additive genetic effects and epistasis. This was supported by our identification of widespread non-additive genetic effects and epistasis in the context of T1D. Finally, we constructed PRS models that integrated genotype, blood, urine, and anthropometric data and found that this improved performance for 93% of the 290 diseases and disorders considered. EIR is available at https://github.com/arnor-sigurdsson/EIR.
Collapse
Affiliation(s)
- Arnór I Sigurdsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ioannis Louloudis
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ole Winther
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
| | - Ole Lund
- Danish National Genome Center, Ørestads Boulevard 5, 2300 Copenhagen S, Denmark
- DTU Health Tech, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, 8000 Aarhus C, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Ole Birger Vesterager Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Clinical Immunology, Zealand University Hospital, 4600 Køge, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, DK- 9260 Gistrup, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Bjarni J Vilhjálmsson
- National Centre for Register-Based Research (NCRR), Aarhus University, 8000 Aarhus C, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), 8210 Aarhus V, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, 8000 Aarhus C, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
132
|
Yajnik CS, Wagh R, Kunte P, Asplund O, Ahlqvist E, Bhat D, Shukla SR, Prasad RB. Polygenic scores of diabetes-related traits in subgroups of type 2 diabetes in India: a cohort study. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 14:100182. [PMID: 37492423 PMCID: PMC10363502 DOI: 10.1016/j.lansea.2023.100182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/08/2022] [Accepted: 03/09/2023] [Indexed: 07/27/2023]
Abstract
Background A machine-learning approach identified five subgroups of diabetes in Europeans which included severe autoimmune diabetes (SAID), severe insulin-deficient diabetes (SIDD), severe insulin-resistant diabetes (SIRD), mild obesity-related diabetes (MOD) and mild age-related diabetes (MARD) with partially distinct genetic aetiologies. We previously validated four of the non-autoimmune subgroups in people with young-onset type 2 diabetes (T2D) from the Indian WellGen study. Here, we aimed to apply European-derived centroids and genetic risk scores (GRSs) to the unselected (for age) WellGen to test their applicability and investigate the genetic aetiology of the Indian T2D subgroups. Methods We applied European derived centroids and GRSs to T2D participants of Indian ancestry (WellGen, n = 2217, 821 genotyped) and compared them with normal glucose tolerant controls (Pune Maternal Nutrition Study, n = 461). Findings SIDD was the predominant subgroup followed by MOD, whereas SIRD and MARD were less frequent. Weighted-GRS for T2D, obesity and lipid-related traits associated with T2D. We replicated some of the previous associations of GRS for T2D, insulin secretion, and BMI with SIDD and MOD. Unique to Indian subgroups was the association of GRS for (a) proinsulin with MOD and MARD, (b) liver-lipids with SIDD, SIRD and MOD, and (c) opposite effect of beta-cell GRS with SIDD and MARD, obesity GRS with MARD compared to Europeans. Genetic variants of fucosyltransferases were associated with T2D and MOD in Indians but not Europeans. Interpretation The similarities emphasise the applicability of some of the European-derived GRSs to T2D and its subgroups in India while the differences highlight the need for large-scale studies to identify aetiologies in diverse ancestries. The data provide robust evidence for genetically distinct aetiologies for the T2D subgroups and at least partly mirror those seen in Europeans. Funding Vetenskapsrådet, Diabetes Wellness, and Hjärt-Lungfonden (Sweden), DST (India), Wellcome Trust, Crafoord Foundation and Albert Påhlsson Foundation.
Collapse
Affiliation(s)
- Chittaranjan S. Yajnik
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
| | - Rucha Wagh
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed) University, Pune, 411021, India
| | - Pooja Kunte
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown Campus, Sydney, 2560, NSW, Australia
| | - Olof Asplund
- Department of Clinical Sciences, Diabetes and Endocrinology, CRC, Lund University, Malmö SE-205 02, Sweden
| | - Emma Ahlqvist
- Department of Clinical Sciences, Diabetes and Endocrinology, CRC, Lund University, Malmö SE-205 02, Sweden
| | - Dattatrey Bhat
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
| | - Sharvari R. Shukla
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
- Symbiosis Statistical Institute, Symbiosis International University, Pune, 411005, India
| | - Rashmi B. Prasad
- Department of Clinical Sciences, Diabetes and Endocrinology, CRC, Lund University, Malmö SE-205 02, Sweden
- Institute for Molecular Medicine Finland FIMM, Helsinki University, 00290, Helsinki, Finland
| |
Collapse
|
133
|
Casauria S, Lewis S, Lynch F, Saffery R. Australian parental perceptions of genomic newborn screening for non-communicable diseases. Front Genet 2023; 14:1209762. [PMID: 37434950 PMCID: PMC10330815 DOI: 10.3389/fgene.2023.1209762] [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: 04/21/2023] [Accepted: 06/15/2023] [Indexed: 07/13/2023] Open
Abstract
Background: Newborn bloodspot screening (NBS) programs have improved neonatal healthcare since the 1960s. Genomic sequencing now offers potential to generate polygenic risk score (PRS) that could be incorporated into NBS programs, shifting the focus from treatment to prevention of future noncommunicable disease (NCD). However, Australian parents' knowledge and attitudes regarding PRS for NBS is currently unknown. Methods: Parents with at least one Australian-born child under 18 years were invited via social media platforms to complete an online questionnaire aimed at examining parents' knowledge of NCDs, PRS, and precision medicine, their opinions on receiving PRS for their child, and considerations of early-intervention strategies to prevent the onset of disease. Results: Of 126 participants, 90.5% had heard the term "non-communicable disease or chronic condition," but only 31.8% and 34.4% were aware of the terms "polygenic risk score" and "precision medicine" respectively. A large proportion of participants said they would consider screening their newborn to receive a PRS for allergies (77.9%), asthma (81.0%), cancer (64.8%), cardiovascular disease (65.7%), mental illness (56.7%), obesity (49.5%), and type 2 diabetes (66.7%). Additionally, participants would primarily consider diet and exercise as interventions for specific NCDs. Discussion: The results from this study will inform future policy for genomic NBS, including expected rate of uptake and interventions that parents would consider employing to prevent the onset of disease.
Collapse
Affiliation(s)
- Sarah Casauria
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - Sharon Lewis
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Fiona Lynch
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Richard Saffery
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
134
|
Andersen LVB, Larsen MJ, Davies H, Degasperi A, Nielsen HR, Jensen LA, Kroeldrup L, Gerdes AM, Lænkholm AV, Kruse TA, Nik-Zainal S, Thomassen M. Non-BRCA1/BRCA2 high-risk familial breast cancers are not associated with a high prevalence of BRCAness. Breast Cancer Res 2023; 25:69. [PMID: 37316882 DOI: 10.1186/s13058-023-01655-y] [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: 08/09/2022] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Familial breast cancer is in most cases unexplained due to the lack of identifiable pathogenic variants in the BRCA1 and BRCA2 genes. The somatic mutational landscape and in particular the extent of BRCA-like tumour features (BRCAness) in these familial breast cancers where germline BRCA1 or BRCA2 mutations have not been identified is to a large extent unknown. METHODS We performed whole-genome sequencing on matched tumour and normal samples from high-risk non-BRCA1/BRCA2 breast cancer families to understand the germline and somatic mutational landscape and mutational signatures. We measured BRCAness using HRDetect. As a comparator, we also analysed samples from BRCA1 and BRCA2 germline mutation carriers. RESULTS We noted for non-BRCA1/BRCA2 tumours, only a small proportion displayed high HRDetect scores and were characterized by concomitant promoter hypermethylation or in one case a RAD51D splice variant previously reported as having unknown significance to potentially explain their BRCAness. Another small proportion showed no features of BRCAness but had mutationally active tumours. The remaining tumours lacked features of BRCAness and were mutationally quiescent. CONCLUSIONS A limited fraction of high-risk familial non-BRCA1/BRCA2 breast cancer patients is expected to benefit from treatment strategies against homologue repair deficient cancer cells.
Collapse
Affiliation(s)
- Lars V B Andersen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Helen Davies
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Andrea Degasperi
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | | | - Louise A Jensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lone Kroeldrup
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anne-Vibeke Lænkholm
- Department of Surgical Pathology, Zealand University Hospital, 4000, Roskilde, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Serena Nik-Zainal
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- European Sperm Bank, Copenhagen, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| |
Collapse
|
135
|
Prom-Wormley EC, Wells JL, Landes L, Edmondson AN, Sankoh M, Jamieson B, Delk KJ, Surya S, Bhati S, Clifford J. A scoping review of smoking cessation pharmacogenetic studies to advance future research across racial, ethnic, and ancestral populations. Front Genet 2023; 14:1103966. [PMID: 37359362 PMCID: PMC10285878 DOI: 10.3389/fgene.2023.1103966] [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: 11/21/2022] [Accepted: 04/25/2023] [Indexed: 06/28/2023] Open
Abstract
Abstinence rates among smokers attempting to quit remain low despite the wide availability and accessibility of pharmacological smoking cessation treatments. In addition, the prevalence of cessation attempts and abstinence differs by individual-level social factors such as race and ethnicity. Clinical treatment of nicotine dependence also continues to be challenged by individual-level variability in effectiveness to promote abstinence. The use of tailored smoking cessation strategies that incorporate information on individual-level social and genetic factors hold promise, although additional pharmacogenomic knowledge is still needed. In particular, genetic variants associated with pharmacological responses to smoking cessation treatment have generally been conducted in populations with participants that self-identify as White race or who are determined to be of European genetic ancestry. These results may not adequately capture the variability across all smokers as a result of understudied differences in allele frequencies across genetic ancestry populations. This suggests that much of the current pharmacogenetic study results for smoking cessation may not apply to all populations. Therefore, clinical application of pharmacogenetic results may exacerbate health inequities by racial and ethnic groups. This scoping review examines the extent to which racial, ethnic, and ancestral groups that experience differences in smoking rates and smoking cessation are represented in the existing body of published pharmacogenetic studies of smoking cessation. We will summarize results by race, ethnicity, and ancestry across pharmacological treatments and study designs. We will also explore current opportunities and challenges in conducting pharmacogenomic research on smoking cessation that encourages greater participant diversity, including practical barriers to clinical utilization of pharmacological smoking cessation treatment and clinical implementation of pharmacogenetic knowledge.
Collapse
Affiliation(s)
- Elizabeth C. Prom-Wormley
- Division of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, Richmond, VA, United States
| | - Jonathan L. Wells
- Division of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, Richmond, VA, United States
| | - Lori Landes
- Department of Family Medicine and Population Health, Virginia Commonwealth University, Richmond, VA, United States
| | - Amy N. Edmondson
- Division of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, Richmond, VA, United States
| | - Mariam Sankoh
- Department of Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA, United States
| | - Brendan Jamieson
- Division of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, Richmond, VA, United States
| | - Kayla J. Delk
- Division of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, Richmond, VA, United States
| | - Sanya Surya
- Division of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, Richmond, VA, United States
| | - Shambhavi Bhati
- Division of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, Richmond, VA, United States
| | - James Clifford
- Department of Public Health, Brody School of Medicine, East Carolina University, Greenville, United States
| |
Collapse
|
136
|
Liu X, Morelli D, Littlejohns TJ, Clifton DA, Clifton L. Combining machine learning with Cox models to identify predictors for incident post-menopausal breast cancer in the UK Biobank. Sci Rep 2023; 13:9221. [PMID: 37286615 DOI: 10.1038/s41598-023-36214-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023] Open
Abstract
We aimed to identify potential novel predictors for breast cancer among post-menopausal women, with pre-specified interest in the role of polygenic risk scores (PRS) for risk prediction. We utilised an analysis pipeline where machine learning was used for feature selection, prior to risk prediction by classical statistical models. An "extreme gradient boosting" (XGBoost) machine with Shapley feature-importance measures were used for feature selection among [Formula: see text] 1.7 k features in 104,313 post-menopausal women from the UK Biobank. We constructed and compared the "augmented" Cox model (incorporating the two PRS, known and novel predictors) with a "baseline" Cox model (incorporating the two PRS and known predictors) for risk prediction. Both of the two PRS were significant in the augmented Cox model ([Formula: see text]). XGBoost identified 10 novel features, among which five showed significant associations with post-menopausal breast cancer: plasma urea (HR = 0.95, 95% CI 0.92-0.98, [Formula: see text]), plasma phosphate (HR = 0.68, 95% CI 0.53-0.88, [Formula: see text]), basal metabolic rate (HR = 1.17, 95% CI 1.11-1.24, [Formula: see text]), red blood cell count (HR = 1.21, 95% CI 1.08-1.35, [Formula: see text]), and creatinine in urine (HR = 1.05, 95% CI 1.01-1.09, [Formula: see text]). Risk discrimination was maintained in the augmented Cox model, yielding C-index 0.673 vs 0.667 (baseline Cox model) with the training data and 0.665 vs 0.664 with the test data. We identified blood/urine biomarkers as potential novel predictors for post-menopausal breast cancer. Our findings provide new insights to breast cancer risk. Future research should validate novel predictors, investigate using multiple PRS and more precise anthropometry measures for better breast cancer risk prediction.
Collapse
Affiliation(s)
- Xiaonan Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, UK.
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK.
| | - Davide Morelli
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Thomas J Littlejohns
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - David A Clifton
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Lei Clifton
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| |
Collapse
|
137
|
Jee YH, Ho WK, Park S, Easton DF, Teo SH, Jung KJ, Kraft P. Polygenic risk scores for prediction of breast cancer in Korean women. Int J Epidemiol 2023; 52:796-805. [PMID: 36343017 PMCID: PMC10244045 DOI: 10.1093/ije/dyac206] [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: 11/21/2021] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Polygenic risk scores (PRSs) for breast cancer, developed using European and Asian genome-wide association studies (GWAS), have been shown to have good discrimination in Asian women. However, prospective calibration of absolute risk prediction models, based on a PRS or PRS combined with lifestyle, clinical and environmental factors, in Asian women is limited. METHODS We consider several PRSs trained using European and/or Asian GWAS. For each PRS, we evaluate the discrimination and calibration of three absolute risk models among 41 031 women from the Korean Cancer Prevention Study (KCPS)-II Biobank: (i) a model using incidence, mortality and risk factor distributions (reference inputs) among US women and European relative risks; (ii) a recalibrated model, using Korean reference but European relative risks; and (iii) a fully Korean-based model using Korean reference and relative risk estimates from KCPS. RESULTS All Asian and European PRS improved discrimination over lifestyle, clinical and environmental (Qx) factors in Korean women. US-based absolute risk models overestimated the risks for women aged ≥50 years, and this overestimation was larger for models that only included PRS (expected-to-observed ratio E/O = 1.2 for women <50, E/O = 2.7 for women ≥50). Recalibrated and Korean-based risk models had better calibration in the large, although the risk in the highest decile was consistently overestimated. Absolute risk projections suggest that risk-reducing lifestyle changes would lead to larger absolute risk reductions among women at higher PRS. CONCLUSIONS Absolute risk models incorporating PRS trained in European and Asian GWAS and population-appropriate average age-specific incidences may be useful for risk-stratified interventions in Korean women.
Collapse
Affiliation(s)
- Yon Ho Jee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Weang-Kee Ho
- School of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Sohee Park
- Department of Biostatistics, Yonsei University Graduate School of Public Health, Seoul, Republic of Korea
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Sime Darby Medical Centre, Subang Jaya, Selangor, Malaysia
| | - Keum Ji Jung
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
- Nuffield Department Population Health, University of Oxford, Oxford, UK
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| |
Collapse
|
138
|
De Roo AC, Chen Y, Du X, Handelman S, Byrnes M, Regenbogen SE, Speliotes EK, Maguire LH. Polygenic Risk Prediction in Diverticulitis. Ann Surg 2023; 277:e1262-e1268. [PMID: 35876359 PMCID: PMC10874245 DOI: 10.1097/sla.0000000000005623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To derive and validate a polygenic risk score (PRS) to predict the occurrence and severity of diverticulitis and to understand the potential for incorporation of a PRS in current decision-making. BACKGROUND PRS quantifies genetic variation into a continuous measure of risk. There is a need for improved risk stratification to guide surgical decision-making that could be fulfilled by PRS. It is unknown how surgeons might integrate PRS in decision-making. METHODS We derived a PRS with 44 single-nucleotide polymorphisms associated with diverticular disease in the UK Biobank and validated this score in the Michigan Genomics Initiative (MGI). We performed a discrete choice experiment of practicing colorectal surgeons. Surgeons rated the influence of clinical factors and a hypothetical polygenic risk prediction tool. RESULTS Among 2812 MGI participants with diverticular disease, 1964 were asymptomatic, 574 had mild disease, and 274 had severe disease. PRS was associated with occurrence and severity. Patients in the highest PRS decile were more likely to have diverticulitis [odds ratio (OR)=1.84; 95% confidence interval (CI), 1.42-2.38)] and more likely to have severe diverticulitis (OR=1.61; 95% CI, 1.04-2.51) than the bottom 50%. Among 213 surveyed surgeons, extreme disease-specific factors had the largest utility (3 episodes in the last year, +74.4; percutaneous drain, + 69.4). Factors with strongest influence against surgery included 1 lifetime episode (-63.3), outpatient management (-54.9), and patient preference (-39.6). PRS was predicted to have high utility (+71). CONCLUSIONS A PRS derived from a large national biobank was externally validated, and found to be associated with the incidence and severity of diverticulitis. Surgeons have clear guidance at clinical extremes, but demonstrate equipoise in intermediate scenarios. Surgeons are receptive to PRS, which may be most useful in marginal clinical situations. Given the current lack of accurate prognostication in recurrent diverticulitis, PRS may provide a novel approach for improving patient counseling and decision-making.
Collapse
Affiliation(s)
- Ana C De Roo
- Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Yanhua Chen
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, MI
| | - Xiaomeng Du
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, MI
| | | | - Mary Byrnes
- Department of Surgery, University of Michigan, Ann Arbor, MI
| | | | - Elizabeth K Speliotes
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI
| | | |
Collapse
|
139
|
Hartkopf AD, Fehm TN, Welslau M, Müller V, Schütz F, Fasching PA, Janni W, Witzel I, Thomssen C, Beierlein M, Belleville E, Untch M, Thill M, Tesch H, Ditsch N, Lux MP, Aktas B, Banys-Paluchowski M, Kolberg-Liedtke C, Wöckel A, Kolberg HC, Harbeck N, Stickeler E, Bartsch R, Schneeweiss A, Ettl J, Würstlein R, Krug D, Taran FA, Lüftner D. Update Breast Cancer 2023 Part 1 - Early Stage Breast Cancer. Geburtshilfe Frauenheilkd 2023; 83:653-663. [PMID: 37916183 PMCID: PMC10617391 DOI: 10.1055/a-2074-0551] [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: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 11/03/2023] Open
Abstract
With abemaciclib (monarchE study) and olaparib (OlympiA study) gaining approval in the adjuvant treatment setting, a significant change in the standard of care for patients with early stage breast cancer has been established for some time now. Accordingly, some diverse developments are slowly being transferred from the metastatic to the adjuvant treatment setting. Recently, there have also been positive reports of the NATALEE study. Other clinical studies are currently investigating substances that are already established in the metastatic setting. These include, for example, the DESTINY Breast05 study with trastuzumab deruxtecan and the SASCIA study with sacituzumab govitecan. In this review paper, we summarize and place in context the latest developments over the past months.
Collapse
Affiliation(s)
- Andreas D. Hartkopf
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Tanja N. Fehm
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Düsseldorf, Germany
| | | | - Volkmar Müller
- Department of Gynecology, Hamburg-Eppendorf University Medical Center, Hamburg, Germany
| | - Florian Schütz
- Gynäkologie und Geburtshilfe, Diakonissen-Stiftungs-Krankenhaus Speyer, Speyer, Germany
| | - Peter A. Fasching
- Erlangen University Hospital, Department of Gynecology and Obstetrics; Comprehensive Cancer Center Erlangen EMN, Friedrich-Alexander University Erlangen-Nuremberg,
Erlangen, Germany
| | - Wolfgang Janni
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Isabell Witzel
- Klinik für Gynäkologie, Universitätsspital Zürich, Zürich, Switzerland
| | - Christoph Thomssen
- Department of Gynaecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Milena Beierlein
- Erlangen University Hospital, Department of Gynecology and Obstetrics; Comprehensive Cancer Center Erlangen EMN, Friedrich-Alexander University Erlangen-Nuremberg,
Erlangen, Germany
| | | | - Michael Untch
- Clinic for Gynecology and Obstetrics, Breast Cancer Center, Gynecologic Oncology Center, Helios Klinikum Berlin Buch, Berlin, Germany
| | - Marc Thill
- Department of Gynecology and Gynecological Oncology, Agaplesion Markus Krankenhaus, Frankfurt am Main, Germany
| | - Hans Tesch
- Oncology Practice at Bethanien Hospital, Frankfurt am Main, Germany
| | - Nina Ditsch
- Department of Gynecology and Obstetrics, University Hospital Augsburg, Augsburg, Germany
| | - Michael P. Lux
- Klinik für Gynäkologie und Geburtshilfe, Frauenklinik St. Louise, Paderborn, St. Josefs-Krankenhaus, Salzkotten, St. Vincenz Krankenhaus GmbH, Paderborn, Germany
| | - Bahriye Aktas
- Department of Gynecology, University of Leipzig Medical Center, Leipzig, Germany
| | - Maggie Banys-Paluchowski
- Department of Gynecology and Obstetrics, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | | | - Achim Wöckel
- Department of Gynecology and Obstetrics, University Hospital Würzburg, Würzburg, Germany
| | | | - Nadia Harbeck
- Breast Center, Department of Gynecology and Obstetrics and CCC Munich LMU, LMU University Hospital, München, Germany
| | - Elmar Stickeler
- Department of Obstetrics and Gynecology, Center for Integrated Oncology (CIO Aachen, Bonn, Cologne, Düsseldorf), University Hospital of RWTH Aachen, Aachen, Germany
| | - Rupert Bartsch
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Johannes Ettl
- Klinik für Frauenheilkunde und Gynäkologie, Klinikum Kempten, Klinikverbund Allgäu, Kempten, Germany
| | - Rachel Würstlein
- Breast Center, Department of Gynecology and Obstetrics and CCC Munich LMU, LMU University Hospital, München, Germany
| | - David Krug
- Klinik für Strahlentherapie, Universitätsklinkum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Florin-Andrei Taran
- Department of Gynecology and Obstetrics, University Hospital Freiburg, Freiburg, Germany
| | - Diana Lüftner
- Medical University of Brandenburg Theodor-Fontane, Immanuel Hospital Märkische Schweiz, Buckow, Germany
| |
Collapse
|
140
|
Campa D, Gentiluomo M, Stein A, Aoki MN, Oliverius M, Vodičková L, Jamroziak K, Theodoropoulos G, Pasquali C, Greenhalf W, Arcidiacono PG, Uzunoglu F, Pezzilli R, Luchini C, Puzzono M, Loos M, Giaccherini M, Katzke V, Mambrini A, Kiudeliene E, Federico KE, Johansen J, Hussein T, Mohelnikova-Duchonova B, van Eijck CHJ, Brenner H, Farinella R, Pérez JS, Lovecek M, Büchler MW, Hlavac V, Izbicki JR, Hackert T, Chammas R, Zerbi A, Lawlor R, Felici A, Götz M, Capurso G, Ginocchi L, Gazouli M, Kupcinskas J, Cavestro GM, Vodicka P, Moz S, Neoptolemos JP, Kunovsky L, Bojesen SE, Carrara S, Gioffreda D, Morkunas E, Abian O, Bunduc S, Basso D, Boggi U, Wlodarczyk B, Szentesi A, Vanella G, Chen I, Bijlsma MF, Kiudelis V, Landi S, Schöttker B, Corradi C, Giese N, Kaaks R, Peduzzi G, Hegyi P, Morelli L, Furbetta N, Soucek P, Latiano A, Talar-Wojnarowska R, Lindgaard SC, Dijk F, Milanetto AC, Tavano F, Cervena K, Erőss B, Testoni SG, Verhagen-Oldenampsen JHE, Małecka-Wojciesko E, Costello E, Salvia R, Maiello E, Ermini S, Sperti C, Holleczek B, Perri F, Skieceviciene J, Archibugi L, Lucchesi M, Rizzato C, Canzian F. The PANcreatic Disease ReseArch (PANDoRA) consortium: Ten years' experience of association studies to understand the genetic architecture of pancreatic cancer. Crit Rev Oncol Hematol 2023; 186:104020. [PMID: 37164172 DOI: 10.1016/j.critrevonc.2023.104020] [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: 03/06/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/12/2023] Open
Abstract
Pancreatic cancer has an incidence that almost matches its mortality. Only a small number of risk factors and 33 susceptibility loci have been identified. so Moreover, the relative rarity of pancreatic cancer poses significant hurdles for research aimed at increasing our knowledge of the genetic mechanisms contributing to the disease. Additionally, the inability to adequately power research questions prevents small monocentric studies from being successful. Several consortia have been established to pursue a better understanding of the genetic architecture of pancreatic cancers. The Pancreatic disease research (PANDoRA) consortium is the largest in Europe. PANDoRA is spread across 12 European countries, Brazil and Japan, bringing together 29 basic and clinical research groups. In the last ten years, PANDoRA has contributed to the discovery of 25 susceptibility loci, a feat that will be instrumental in stratifying the population by risk and optimizing preventive strategies.
Collapse
Affiliation(s)
- Daniele Campa
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy.
| | - Manuel Gentiluomo
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Angelika Stein
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, Brazil
| | - Martin Oliverius
- Department of Surgery, University Hospital Kralovske Vinohrady, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodičková
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Faculty of Medicine Charles University and General University Hospital in Prague, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen Charles University, Pilsen, Czech Republic
| | - Krzysztof Jamroziak
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - George Theodoropoulos
- First Department of Propaedeutic Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Claudio Pasquali
- Dept. of Surgery, Oncology and Gastroenterology, University of Padova Chirurgia Generale 3, Padova, Italy
| | - William Greenhalf
- Liverpool Experimental Cancer Medicine Centre, University of Liverpool, Liverpool, United Kingdom
| | - Paolo Giorgio Arcidiacono
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientic Institute, Milan, Italy
| | - Faik Uzunoglu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Marta Puzzono
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martin Loos
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Verena Katzke
- Division of Cancer Epidemiology C020, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea Mambrini
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Edita Kiudeliene
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | | | - Julia Johansen
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Tamás Hussein
- Institute of Pancreatic Diseases, Semmelweis University, Budapest, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary
| | | | - Casper H J van Eijck
- Department of Surgery, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Juan Sainz Pérez
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Complejo Hospitales Universitarios de Granada, Universidad de Granada, Granada, Spain; Department of Immunology, University of Granada, Granada, Spain
| | - Martin Lovecek
- Department of Surgery I, University Hospital Olomouc, Olomouc, Czech Republic
| | - Markus W Büchler
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Roger Chammas
- Center for Translational Research in Oncology (LIM24), Departamento de Radiologia e Oncologia, Instituto Do Câncer Do Estado de São Paulo (ICESP), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil
| | - Alessandro Zerbi
- Pancreatic Unit, IRCCS Humanitas Research Hospital, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Rita Lawlor
- ARC-Net Research Center, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
| | - Alessio Felici
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Mara Götz
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Capurso
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy; Digestive and Liver Disease Unit, Sant' Andrea Hospital, Rome, Italy
| | - Laura Ginocchi
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Maria Gazouli
- Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Juozas Kupcinskas
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Faculty of Medicine Charles University and General University Hospital in Prague, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen Charles University, Pilsen, Czech Republic
| | - Stefania Moz
- Azienda Ospedale-Università di Padova Medicina di Laboratorio, Padova, Italy
| | - John P Neoptolemos
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Lumir Kunovsky
- Department of Surgery, University Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic; Department of Gastroenterology and Digestive Endoscopy, Masaryk Memorial Cancer Institute, Brno, Czech Republic; 2nd Department of Internal Medicine - Gastroenterology and Geriatrics, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Stig E Bojesen
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Silvia Carrara
- Endoscopic Unit, Department of Gastroenterology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Domenica Gioffreda
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Egidijus Morkunas
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Olga Abian
- Instituto BIFI-Universidad de Zaragoza, Zaragoza, Spain
| | - Stefania Bunduc
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Carol Davila University of Medicine and Pharmacy, Bucharest, Romania; Center for Digestive Diseases and Liver Transplant, Fundeni Clinical Insitute, Bucharest, Romania
| | - Daniela Basso
- Dept. of Medicine, University of Padova Medicina di Laboratorio, Padova, Italy
| | - Ugo Boggi
- Division of General and Transplant Surgery, Pisa University Hospital, Pisa, Italy
| | - Barbara Wlodarczyk
- Dept of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Andrea Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Giuseppe Vanella
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy; Digestive and Liver Disease Unit, Sant' Andrea Hospital, Rome, Italy
| | - Inna Chen
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Maarten F Bijlsma
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Vytautas Kiudelis
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Stefano Landi
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chiara Corradi
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Nathalia Giese
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology C020, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Giulia Peduzzi
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Péter Hegyi
- Institute of Pancreatic Diseases, Semmelweis University, Budapest, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary; Translational Pancreatology Research Group, Interdisciplinary Centre of Excellence for Research Development and Innovation University of Szeged, Szeged, Hungary
| | - Luca Morelli
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Niccolò Furbetta
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Anna Latiano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | | | - Sidsel C Lindgaard
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Frederike Dijk
- Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, the Netherlands; Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
| | - Anna Caterina Milanetto
- Dept. of Surgery, Oncology and Gastroenterology, University of Padova Chirurgia Generale 3, Padova, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Faculty of Medicine Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Bálint Erőss
- Institute of Pancreatic Diseases, Semmelweis University, Budapest, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Sabrina G Testoni
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientic Institute, Milan, Italy
| | | | | | - Eithne Costello
- Liverpool Experimental Cancer Medicine Centre, University of Liverpool, Liverpool, United Kingdom
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Evaristo Maiello
- Department of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | | | - Cosimo Sperti
- Dept. of Surgery, Oncology and Gastroenterology, University of Padova Chirurgia Generale 1, Padova, Italy
| | - Bernd Holleczek
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Saarland Cancer Registry, Saarbrücken, Germany
| | - Francesco Perri
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Jurgita Skieceviciene
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Livia Archibugi
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy; Digestive and Liver Disease Unit, Sant' Andrea Hospital, Rome, Italy
| | - Maurizio Lucchesi
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Cosmeri Rizzato
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
141
|
Berga-Švītiņa E, Maksimenko J, Miklaševičs E, Fischer K, Vilne B, Mägi R. Polygenic Risk Score Predicts Modified Risk in BRCA1 Pathogenic Variant c.4035del and c.5266dup Carriers in Breast Cancer Patients. Cancers (Basel) 2023; 15:cancers15112957. [PMID: 37296919 DOI: 10.3390/cancers15112957] [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: 04/28/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
The aim of this study was to assess the power of the polygenic risk score (PRS) in estimating the overall genetic risk of women carrying germline BRCA1 pathogenic variants (PVs) c.4035del or c.5266dup to develop breast (BC) or ovarian cancer (OC) due to additional genetic variations. In this study, PRSs previously developed from two joint models using summary statistics of age-at-onset (BayesW model) and case-control data (BayesRR-RC model) from a genome-wide association analysis (GWAS) were applied to 406 germline BRCA1 PV (c.4035del or c.5266dup) carriers affected by BC or OC, compared with unaffected individuals. A binomial logistic regression model was used to assess the association of PRS with BC or OC development risk. We observed that the best-fitting BayesW PRS model effectively predicted the individual's BC risk (OR = 1.37; 95% CI = 1.03-1.81, p = 0.02905 with AUC = 0.759). However, none of the applied PRS models was a good predictor of OC risk. The best-fitted PRS model (BayesW) contributed to assessing the risk of developing BC for germline BRCA1 PV (c.4035del or c.5266dup) carriers and may facilitate more precise and timely patient stratification and decision-making to improve the current BC treatment or even prevention strategies.
Collapse
Affiliation(s)
- Egija Berga-Švītiņa
- Bioinformatics Lab, Rīga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia
- Institute of Oncology, Rīga Stradiņš University, Pilsoņu Street 13, Block 13, LV-1002 Riga, Latvia
| | - Jeļena Maksimenko
- Institute of Oncology, Rīga Stradiņš University, Pilsoņu Street 13, Block 13, LV-1002 Riga, Latvia
- Pauls Stradiņš Clinical University Hospital, Pilsoņu Street 13, LV-1002 Riga, Latvia
| | - Edvīns Miklaševičs
- Institute of Oncology, Rīga Stradiņš University, Pilsoņu Street 13, Block 13, LV-1002 Riga, Latvia
- Department of Biology and Microbiology, Rīga Stradiņš University, LV-1007 Riga, Latvia
| | - Krista Fischer
- Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Narva mnt 18, 51009 Tartu, Estonia
| | - Baiba Vilne
- Bioinformatics Lab, Rīga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia
| | - Reedik Mägi
- Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| |
Collapse
|
142
|
Luoh SW, Minnier J, Zhao H, Gao L. Predicting Breast Cancer Risk for Women Veterans of African Ancestry in the Million Veteran Program. Health Equity 2023; 7:303-306. [PMID: 37284538 PMCID: PMC10240329 DOI: 10.1089/heq.2023.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 06/08/2023] Open
Abstract
Breast cancer is a leading cause of cancer and, therefore, a major health threat for women in the United States and worldwide. We have seen over the years major advances in breast cancer prevention and care. Breast cancer screening with mammography leads to reduction in breast cancer mortality, and breast cancer prevention treatment with antiestrogens results in reduction in breast cancer incidence. More progress, however, is urgently needed for this common cancer that affects 1 in 11 American women in their lifetime. Not all women have the same breast cancer risk. A personalized approach is highly desirable as women with higher breast cancer risk may benefit from more intense breast cancer screening and/or prevention intervention while lower risk women may be spared with the cost, inconvenience, and emotional burden of these procedures. In addition to age, demographics, family history, lifestyle, and personal health, genetics is an important determinant of an individual's risk for breast cancer. Over the past 10 years, advances in cancer genomics identified multiple common genetic variants from population studies that collectively can contribute significantly to an individual's breast cancer risk. The effects of these genetic variants can be summarized as a "polygenic risk score" (PRS). We are among the first groups to prospectively evaluate the performance of these risk prediction instruments among women veterans of the Million Veteran Program (MVP). A 313-variant PRS (PRS313) predicted incident breast cancer for a prospective cohort of European (EUR) ancestry women veterans with an area under the receiver operating characteristic curve (AUC) of 0.622. The PRS313 performed less well for AFR ancestry however, with an AUC of 0.579. This is not surprising as most genome-wide association studies were conducted in people of European ancestry. This is an important area of health disparity and unmet need. The large population size and diversity of the MVP provide a unique and important opportunity to explore novel approaches to produce accurate and clinically useful genetic risk prediction instruments for minority populations.
Collapse
Affiliation(s)
- Shiuh-Wen Luoh
- VA Portland Health Care System, Portland, Oregon, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Jessica Minnier
- VA Portland Health Care System, Portland, Oregon, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
- OHSU-PSU School of Public Health, Portland, Oregon, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, VA Connecticut Health Care System, New Haven, Connecticut, USA
| | - Lina Gao
- VA Portland Health Care System, Portland, Oregon, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| |
Collapse
|
143
|
Zhai S, Guo B, Wu B, Mehrotra DV, Shen J. Integrating multiple traits for improving polygenic risk prediction in disease and pharmacogenomics GWAS. Brief Bioinform 2023:7169140. [PMID: 37200155 DOI: 10.1093/bib/bbad181] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/30/2023] [Accepted: 04/21/2023] [Indexed: 05/20/2023] Open
Abstract
Polygenic risk score (PRS) has been recently developed for predicting complex traits and drug responses. It remains unknown whether multi-trait PRS (mtPRS) methods, by integrating information from multiple genetically correlated traits, can improve prediction accuracy and power for PRS analysis compared with single-trait PRS (stPRS) methods. In this paper, we first review commonly used mtPRS methods and find that they do not directly model the underlying genetic correlations among traits, which has been shown to be useful in guiding multi-trait association analysis in the literature. To overcome this limitation, we propose a mtPRS-PCA method to combine PRSs from multiple traits with weights obtained from performing principal component analysis (PCA) on the genetic correlation matrix. To accommodate various genetic architectures covering different effect directions, signal sparseness and across-trait correlation structures, we further propose an omnibus mtPRS method (mtPRS-O) by combining P values from mtPRS-PCA, mtPRS-ML (mtPRS based on machine learning) and stPRSs using Cauchy Combination Test. Our extensive simulation studies show that mtPRS-PCA outperforms other mtPRS methods in both disease and pharmacogenomics (PGx) genome-wide association studies (GWAS) contexts when traits are similarly correlated, with dense signal effects and in similar effect directions, and mtPRS-O is consistently superior to most other methods due to its robustness under various genetic architectures. We further apply mtPRS-PCA, mtPRS-O and other methods to PGx GWAS data from a randomized clinical trial in the cardiovascular domain and demonstrate performance improvement of mtPRS-PCA in both prediction accuracy and patient stratification as well as the robustness of mtPRS-O in PRS association test.
Collapse
Affiliation(s)
- Song Zhai
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Bin Guo
- Data and Genome Science, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Baolin Wu
- Department of Epidemiology and Biostatistics, University of California Irvine, Irvine, CA 92697, USA
| | - Devan V Mehrotra
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., North Wales, PA 19454, USA
| | - Judong Shen
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., Rahway, NJ 07065, USA
| |
Collapse
|
144
|
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.
Collapse
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
| |
Collapse
|
145
|
Khan A, Shang N, Nestor JG, Weng C, Hripcsak G, Harris PC, Gharavi AG, Kiryluk K. Polygenic risk affects the penetrance of monogenic kidney disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.07.23289614. [PMID: 37214819 PMCID: PMC10197721 DOI: 10.1101/2023.05.07.23289614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Chronic kidney disease (CKD) is a genetically complex disease determined by an interplay of monogenic, polygenic, and environmental risks. Most forms of monogenic kidney diseases have incomplete penetrance and variable expressivity. It is presently unknown if some of the variability in penetrance can be attributed to polygenic factors. Methods Using the UK Biobank (N=469,835 participants) and the All of Us (N=98,622 participants) datasets, we examined two most common forms of monogenic kidney disorders, autosomal dominant polycystic kidney disease (ADPKD) caused by deleterious variants in the PKD1 or PKD2 genes, and COL4A-associated nephropathy (COL4A-AN caused by deleterious variants in COL4A3, COL4A4, or COL4A5 genes). We used the eMERGE-III electronic CKD phenotype to define cases (estimated glomerular filtration rate (eGFR) <60 mL/min/1.73m2 or kidney failure) and controls (eGFR >90 mL/min/1.73m2 in the absence of kidney disease diagnoses). The effects of the genome-wide polygenic score (GPS) for CKD were tested in monogenic variant carriers and non-carriers using logistic regression controlling for age, sex, diabetes, and genetic ancestry. Results As expected, the carriers of known pathogenic and rare predicted loss-of-function variants in PKD1 or PKD2 had a high risk of CKD (ORmeta=17.1, 95% CI: 11.1-26.4, P=1.8E-37). The GPS was comparably predictive of CKD in both ADPKD variant carriers (ORmeta=2.28 per SD, 95%CI: 1.55-3.37, P=2.6E-05) and non-carriers (ORmeta=1.72 per SD, 95% CI=1.69-1.76, P< E-300) independent of age, sex, diabetes, and genetic ancestry. Compared to the middle tertile of the GPS distribution for non-carriers, ADPKD variant carriers in the top tertile had a 54-fold increased risk of CKD, while ADPKD variant carriers in the bottom tertile had only a 3-fold increased risk of CKD. Similarly, the GPS was predictive of CKD in both COL4-AN variant carriers (ORmeta=1.78, 95% CI=1.22-2.58, P=2.38E-03) and non-carriers (ORmeta=1.70, 95%CI: 1.68-1.73 P Conclusions Variable penetrance of kidney disease in ADPKD and COL4-AN is partially explained by differences in polygenic risk profiles. Accounting for polygenic factors has the potential to improve risk stratification in monogenic kidney disease and may have implications for genetic counseling.
Collapse
Affiliation(s)
- Atlas Khan
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Ning Shang
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Jordan G. Nestor
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Peter C. Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Ali G. Gharavi
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Krzysztof Kiryluk
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| |
Collapse
|
146
|
Abu-El-Haija A, Reddi HV, Wand H, Rose NC, Mori M, Qian E, Murray MF. The clinical application of polygenic risk scores: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100803. [PMID: 36920474 DOI: 10.1016/j.gim.2023.100803] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 03/16/2023] Open
Affiliation(s)
- Aya Abu-El-Haija
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Honey V Reddi
- Department of Pathology & Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Hannah Wand
- Division of Cardiovascular Medicine, Department of Medicine, Stanford Medicine, Stanford, CA
| | - Nancy C Rose
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, School of Medicine, University of Utah Health, Salt Lake City, UT
| | - Mari Mori
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH; Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Emily Qian
- Department of Genetics, Yale University, New Haven, CT
| | | |
Collapse
|
147
|
Xiao X, Wu Q. Ethnic disparities in fracture risk assessment using polygenic scores. Osteoporos Int 2023; 34:943-953. [PMID: 36840773 PMCID: PMC11225529 DOI: 10.1007/s00198-023-06712-y] [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: 06/21/2022] [Accepted: 02/17/2023] [Indexed: 02/26/2023]
Abstract
Whether the PGS developed using data from European ancestry is predictive of fracture risk for minorities remains unclear. This study demonstrated that PGSs based on common BMD-related genetic variants discovered in the European ancestry cohort are predictive of fracture risk in people of Asian but not African ancestry. PURPOSE Large-scale genome-wide association studies (GWAS) on bone mineral density (BMD) have been conducted predominantly in European cohorts. Genetic models based on common variants associated with BMD have been evaluated using almost exclusively European data, which could potentially exacerbate health disparities due to different linkage disequilibrium among different ethnic groups. METHODS UK Biobank (UKB) is a large-scale population-based observational study starting in 2006 that recruited 502,617 individuals aged between 40 and 69 years with genotypic and phenotypic data available. Based on the summary statistics of two GWAS studies of femoral neck BMD and total body BMD, we derived four PGSs and assessed the association between each PGS and prevalent/incident fractures within each ethnic group separately using Multivariate logistic regressions and Cox proportional hazard models. All models were adjusted for age, sex, and the first four principal components. RESULTS We assessed four PGSs derived from European cohorts. Significant associations were observed between PGSs and fracture in European and Asian cohorts but not in the African cohort. Of all four PGSs, [Formula: see text] performed the best. A standard deviation decreases in [Formula: see text] were associated with an increased hazard ratio (HR) of 1.24 (1.22-1.27), 1.28 (0.83-1.99), and 1.34 (1.10-1.64) in European, African, and Asian ancestry, respectively. A low BMD-related PGS is associated with up to 2.35- and 4.31-fold increased fracture risk in European and Asian populations. CONCLUSIONS These results showed that PGSs based on common BMD-related genetic variants discovered in the European ancestry cohort are predictive of fracture risk in people of Asian but not African ancestry.
Collapse
Affiliation(s)
- Xiangxue Xiao
- Nevada Institute of Personalized Medicine, College of Science, University of Nevada, Las Vegas, NV, USA
- Department of Epidemiology and Biostatistics, School of Public Health, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Qing Wu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 320K Lincoln Tower, 1800 Cannon Dr., Columbus, OH, 43210, USA.
| |
Collapse
|
148
|
Richardson A, Darst B, Wojcik G, Wagle N, Haricharan S. Research Silos in Cancer Disparities: Obstacles to Improving Clinical Outcomes for Underserved Patient Populations. Clin Cancer Res 2023; 29:1194-1199. [PMID: 36638200 PMCID: PMC10073283 DOI: 10.1158/1078-0432.ccr-22-3182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/08/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Despite much vaunted progress in cancer therapeutics and diagnostics, outcomes for many groups of non-White patients with cancer remain worse than those for their White compatriots. One reason for this is the lack of inclusion and representation of non-White patients in clinical trials, preclinical datasets, and among researchers, a shortfall that is gaining wide recognition within the cancer research community and the lay public. Several reviews and editorials have commented on the negative impacts of the status quo on progress in cancer research toward medical breakthroughs that help all communities and not just White patients with cancer. In this perspective, we describe the existence of research silos focused either on the impact of socioeconomic factors proceeding from systemic racism on cancer outcomes, or on genetic ancestry as it affects the molecular biology of cancer developing in specific patient populations. While both these research areas are critical for progress toward precision medicine equity, breaking down these silos will help us gain an integrated understanding of how race and racism impact cancer development, progression, and patient outcomes. Bringing this comprehensive approach to cancer disparities research will undoubtedly improve our overall understanding of how stress and environmental factors affect the molecular biology of cancer, which will lead to the development of new diagnostics and therapeutics that are applicable across cancer patient demographics.
Collapse
Affiliation(s)
| | - Burcu Darst
- Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Genevieve Wojcik
- Dept of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Nikhil Wagle
- Dept of Medicine, Harvard Medical School, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
| | - Svasti Haricharan
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| |
Collapse
|
149
|
Lakeman IMM, Rodríguez-Girondo MDM, Lee A, Celosse N, Braspenning ME, van Engelen K, van de Beek I, van der Hout AH, Gómez García EB, Mensenkamp AR, Ausems MGEM, Hooning MJ, Adank MA, Hollestelle A, Schmidt MK, van Asperen CJ, Devilee P. Clinical applicability of the Polygenic Risk Score for breast cancer risk prediction in familial cases. J Med Genet 2023; 60:327-336. [PMID: 36137616 DOI: 10.1136/jmg-2022-108502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/19/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Common low-risk variants are presently not used to guide clinical management of familial breast cancer (BC). We explored the additive impact of a 313-variant-based Polygenic Risk Score (PRS313) relative to standard gene testing in non-BRCA1/2 Dutch BC families. METHODS We included 3918 BC cases from 3492 Dutch non-BRCA1/2 BC families and 3474 Dutch population controls. The association of the standardised PRS313 with BC was estimated using a logistic regression model, adjusted for pedigree-based family history. Family history of the controls was imputed for this analysis. SEs were corrected to account for relatedness of individuals. Using the BOADICEA (Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm) V.5 model, lifetime risks were retrospectively calculated with and without individual PRS313. For 2586 cases and 2584 controls, the carrier status of pathogenic variants (PVs) in ATM, CHEK2 and PALB2 was known. RESULTS The family history-adjusted PRS313 was significantly associated with BC (per SD OR=1.97, 95% CI 1.84 to 2.11). Including the PRS313 in BOADICEA family-based risk prediction would have changed screening recommendations in up to 27%, 36% and 34% of cases according to BC screening guidelines from the USA, UK and the Netherlands (National Comprehensive Cancer Network, National Institute for Health and Care Excellence, and Netherlands Comprehensive Cancer Organisation), respectively. For the population controls, without information on family history, this was up to 39%, 44% and 58%, respectively. Among carriers of PVs in known moderate BC susceptibility genes, the PRS313 had the largest impact for CHEK2 and ATM. CONCLUSIONS Our results support the application of the PRS313 in risk prediction for genetically uninformative BC families and families with a PV in moderate BC risk genes.
Collapse
Affiliation(s)
- Inge M M Lakeman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mar D M Rodríguez-Girondo
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrew Lee
- Public Health and Primary Care, University of Cambridge Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Nandi Celosse
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Merel E Braspenning
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Klaartje van Engelen
- Department of Human Genetics, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Irma van de Beek
- Department of Human Genetics, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Annemiek H van der Hout
- Department of Clinical Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Encarna B Gómez García
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, University Medical Center Nijmegen, Nijmegen, The Netherlands
| | - Margreet G E M Ausems
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Muriel A Adank
- Family Cancer Clinic, Antoni van Leeuwenhoek Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marjanka K Schmidt
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Division of Psychosocial Research and Epidemiology, Antoni van Leeuwenhoek Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
150
|
Xiao X, Wu Q. The clinical utility of the BMD-related comprehensive genome-wide polygenic score in identifying individuals with a high risk of osteoporotic fractures. Osteoporos Int 2023; 34:681-692. [PMID: 36622390 PMCID: PMC11225087 DOI: 10.1007/s00198-022-06654-x] [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: 03/26/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
The potential of bone mineral density (BMD)-related genome-wide polygenic score (PGS) in identifying individuals with a high risk of fractures remains unclear. This study suggests that an efficient PGS enables the identification of strata with up to a 1.5-fold difference in fracture incidence. Incorporating PGS into clinical diagnosis is anticipated to increase the population-level screening benefits. PURPOSE This study sought to construct genome-wide polygenic scores for femoral neck and total body BMD and to estimate their potential in identifying individuals with a high risk of osteoporotic fractures. METHODS Genome-wide polygenic scores were developed and validated for femoral neck and total body BMD. We externally tested the PGSs, both by themselves and in combination with available clinical risk factors, in 455,663 European ancestry individuals from the UK Biobank. The predictive accuracy of the developed genome-wide PGS was also compared with previously published restricted PGS employed in fracture risk assessment. RESULTS For each unit decrease in PGSs, the genome-wide PGSs were associated with up to 1.17-fold increased fracture risk. Out of four studied PGSs, [Formula: see text] (HR: 1.03; 95%CI 1.01-1.05, p = 0.001) had the weakest and the [Formula: see text] (HR: 1.17; 95%CI 1.15-1.19, p < 0.0001) had the strongest association with an incident fracture. In the reclassification analysis, compared to the FRAX base model, the models with [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] improved the reclassification of fracture by 1.2% (95% CI, 1.0 to 1.3%), 0.2% (95% CI, 0.1 to 0.3%), 1.4% (95% CI, 1.3 to 1.5%), and 2.2% (95% CI, 2.1 to 2.4%), respectively. CONCLUSIONS Our findings suggested that an efficient PGS estimate enables the identification of strata with up to a 1.7-fold difference in fracture incidence. Incorporating PGS information into clinical diagnosis is anticipated to increase the benefits of screening programs at the population level.
Collapse
Affiliation(s)
- Xiangxue Xiao
- Nevada Institute of Personalized Medicine, College of Science, University of Nevada, Las Vegas, NV, USA
- Department of Epidemiology and Biostatistics, School of Public Health, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Qing Wu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|