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De Sousa SMC, McCormack A, Orsmond A, Shen A, Yates CJ, Clifton-Bligh R, Santoreneos S, King J, Feng J, Toubia J, Torpy DJ, Scott HS. Increased Prevalence of Germline Pathogenic CHEK2 Variants in Individuals With Pituitary Adenomas. J Clin Endocrinol Metab 2024; 109:2720-2728. [PMID: 38651569 PMCID: PMC11479685 DOI: 10.1210/clinem/dgae268] [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: 11/22/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
CONTEXT CHEK2 is a cell cycle checkpoint regulator gene with a long-established role as a clinically relevant, moderate risk breast cancer predisposition gene, with greater risk ascribed to truncating variants than missense variants. OBJECTIVE To assess the rate and pathogenicity of CHEK2 variants amongst individuals with pituitary adenomas (PAs). METHODS We assessed 165 individuals with PAs for CHEK2 variants. The study population comprised a primary cohort of 29 individuals who underwent germline and tumor whole-exome sequencing, and a second, independent cohort of 136 individuals who had a targeted next-generation sequencing panel performed on both germline and tumor DNA (n = 52) or germline DNA alone (n = 84). RESULTS We identified rare, coding, nonsynonymous germline CHEK2 variants amongst 3 of 29 (10.3%) patients in our primary cohort, and in 5 of 165 (3.0%) patients overall, with affected patients having a range of PA types (prolactinoma, thyrotropinoma, somatotropinoma, and nonfunctioning PA). No somatic variants were identified. Two variants were definitive null variants (c.1100delC, c.444 + 1G > A), classified as pathogenic. Two variants were missense variants (p.Asn186His, p.Thr476Met), classified as likely pathogenic. Even when considering the null variants only, the rate of CHEK2 variants was higher in our cohort compared to national control data (1.8% vs 0.5%; P = .049). CONCLUSION This is the first study to suggest a role for the breast cancer predisposition gene, CHEK2, in pituitary tumorigenesis, with pathogenic/likely pathogenic variants found in 3% of patients with PAs. As PAs are relatively common and typically lack classic autosomal dominant family histories, risk alleles-such as these variants found in CHEK2-might be a significant contributor to PA risk in the general population.
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Affiliation(s)
- Sunita M C De Sousa
- Endocrine & Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- South Australian Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Ann McCormack
- Department of Endocrinology, St Vincent's Hospital, Sydney, NSW 2000, Australia
- Hormones and Cancer Group, Garvan Institute of Medical Research, Sydney, NSW 2000, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2000, Australia
| | - Andreas Orsmond
- Hormones and Cancer Group, Garvan Institute of Medical Research, Sydney, NSW 2000, Australia
| | - Angeline Shen
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC 3000, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Christopher J Yates
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC 3000, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Roderick Clifton-Bligh
- Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, Sydney, NSW 2000, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia
- Department of Endocrinology, Royal North Shore Hospital, Sydney, NSW 2000, Australia
| | - Stephen Santoreneos
- Department of Neurosurgery, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - James King
- Department of Surgery, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Jinghua Feng
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, SA 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | - John Toubia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, SA 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | - David J Torpy
- Endocrine & Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Hamish S Scott
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, SA 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
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Akamandisa MP, Boddicker NJ, Yadav S, Hu C, Hart SN, Ambrosone C, Anton-Culver H, Auer PL, Bodelon C, Burnside ES, Chen F, Eliassen HA, Goldgar DE, Haiman C, Hodge JM, Huang H, John EM, Karam R, Lacey JV, Lindstroem S, Martinez E, Na J, Neuhausen SL, O'Brien KM, Olson JE, Pal T, Palmer JR, Patel AV, Pesaran T, Polley EC, Richardson ME, Ruddy K, Sandler DP, Teras LR, Trentham-Dietz A, Vachon CM, Weinberg C, Winham SJ, Yao S, Zirpoli G, Kraft P, Weitzel JN, Domchek SM, Couch FJ, Nathanson KL. Association of Gene Variant Type and Location with Breast Cancer Risk in the General Population. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.10.11.24315237. [PMID: 39417132 PMCID: PMC11482981 DOI: 10.1101/2024.10.11.24315237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Importance Pathogenic variants (PVs) in ATM, BRCA1, BRCA2, CHEK2 , and PALB2 are associated with increased breast cancer risk. However, it is unknown whether breast cancer risk differs by PV type or location in carriers ascertained from the general population. Objective To evaluate breast cancer risks associated with PV type and location in ATM, BRCA1, BRCA2, CHEK2 , and PALB2 . Design Age adjusted case-control association analysis for all participants, subsets of PV carriers, and women with no breast cancer family history in population-based and clinical testing cohorts. Setting Twelve US population-based studies within the Cancer Risk Estimates Related to Susceptibility (CARRIERS) Consortium, and breast cancer cases from the UK-Biobank and an Ambry Genetics clinical testing cohort. Participants 32,247 women with and 32,544 age-matched women without a breast cancer diagnosis from CARRIERS; 237 and 1351 women with BRCA2 PVs and breast cancer from the UKBB and Ambry Genetics, respectively. Exposures PVs in ATM, BRCA1, BRCA2, CHEK2, and PALB2. Main Outcomes and Measures PVs were grouped by type and location within genes and assessed for risks of breast cancer (odds ratios (OR), 95% confidence intervals (CI), and p-values) using logistic regression. Mean ages at diagnosis were compared using linear regression. Results Compared to women carrying BRCA2 exon 11 protein truncating variants (PTVs) in the CARRIERS population-based study, women with BRCA2 ex13-27 PTVs (OR=2.7, 95%CI 1.1-7.9) and ex1-10 PTVs (OR=1.6, 95%CI 0.8-3.5) had higher breast cancer risks, lower rates of ER-negative breast cancer (ex13-27 OR=0.5, 95%CI 0.2-0.9; ex1-10 OR=0.5, 95%CI 0.1-1.0), and earlier age of breast cancer diagnosis (ex13-27 5.5 years, p<0.001; ex1-10 2.4 years, p=0.17). These associations with ER-negative breast cancer and age replicated in a high-risk clinical cohort and the population-based UK Biobank cohort. No differences in risk or age at diagnosis by gene region were observed for PTVs in other predisposition genes. Conclusions and Relevance Population-based and clinical high-risk cohorts establish that PTVs in exon 11 of BRCA2 are associated with reduced risk of breast cancer, later age at diagnosis, and greater risk of ER-negative disease. These differential risks may improve individualized risk prediction and clinical management for women carrying BRCA2 PTVs. Key Points Question: Does ATM , BRCA1 , BRCA2 , CHEK2 and PALB2 pathogenic variant type and location influence breast cancer risk in population-based studies? Findings: Breast cancer risk and estrogen receptor status differ based on the type and location of pathogenic variants in BRCA2 . Women carrying protein truncating variants in exon 11 have a lower breast cancer risk in the population-based cohorts, older age at diagnosis and higher rates of estrogen receptor negative breast cancer than women with exon 1-10 or exon 13-27 truncation variants in population-based and clinical testing cohorts. Meaning: Incorporating pathogenic variant type and location in cancer risk models may improve individualized risk prediction.
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Phillips KA, Kotsopoulos J, Domchek SM, Terry MB, Chamberlain JA, Bassett JK, Aeilts AM, Andrulis IL, Buys SS, Cui W, Daly MB, Eisen AF, Foulkes WD, Friedlander ML, Gronwald J, Hopper JL, John EM, Karlan BY, Kim RH, Kurian AW, Lubinski J, Metcalfe K, Nathanson KL, Singer CF, Southey MC, Symecko H, Tung N, Narod SA, Milne RL. Hormonal Contraception and Breast Cancer Risk for Carriers of Germline Mutations in BRCA1 and BRCA2. J Clin Oncol 2024:JCO2400176. [PMID: 39356978 DOI: 10.1200/jco.24.00176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/10/2024] [Accepted: 08/06/2024] [Indexed: 10/04/2024] Open
Abstract
PURPOSE It is uncertain whether, and to what extent, hormonal contraceptives increase breast cancer (BC) risk for germline BRCA1 or BRCA2 mutation carriers. METHODS Using pooled observational data from four prospective cohort studies, associations between hormonal contraceptive use and BC risk for unaffected female BRCA1 and BRCA2 mutation carriers were assessed using Cox regression. RESULTS Of 3,882 BRCA1 and 1,509 BRCA2 mutation carriers, 53% and 71%, respectively, had ever used hormonal contraceptives for at least 1 year (median cumulative duration of use, 4.8 and 5.7 years, respectively). Overall, 488 BRCA1 and 191 BRCA2 mutation carriers developed BC during median follow-up of 5.9 and 5.6 years, respectively. Although for BRCA1 mutation carriers, neither current nor past use of hormonal contraceptives for at least 1 year was statistically significantly associated with BC risk (hazard ratio [HR], 1.40 [95% CI, 0.94 to 2.08], P = .10 for current use; 1.16 [0.80 to 1.69], P = .4, 1.40 [0.99 to 1.97], P = .05, and 1.27 [0.98 to 1.63], P = .07 for past use 1-5, 6-10, and >10 years before, respectively), ever use was associated with increased risk (HR, 1.29 [95% CI, 1.04 to 1.60], P = .02). Furthermore, BC risk increased with longer cumulative duration of use, with an estimated proportional increase in risk of 3% (1%-5%, P = .002) for each additional year of use. For BRCA2 mutation carriers, there was no evidence that current or ever use was associated with increased BC risk (HR, 0.70 [95% CI, 0.33 to 1.47], P = .3 and 1.07 [0.73 to 1.57], P = .7, respectively). CONCLUSION Hormonal contraceptives were associated with increased BC risk for BRCA1 mutation carriers, especially if used for longer durations. Decisions about their use in women with BRCA1 mutations should carefully weigh the risks and benefits for each individual.
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Affiliation(s)
- Kelly-Anne Phillips
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Joanne Kotsopoulos
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Susan M Domchek
- Basser Center for BRCA, University of Pennsylvania, Philadelphia, PA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
| | - James A Chamberlain
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Julie K Bassett
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Amber M Aeilts
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Saundra S Buys
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Wanda Cui
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA
| | - Andrea F Eisen
- Odette Cancer Centre, Sunnybrook Health Sciences, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Michael L Friedlander
- Department of Medical Oncology, Prince of Wales and Royal Hospital for Women, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Jacek Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Beth Y Karlan
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA
| | - Raymond H Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network and Sinai Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Allison W Kurian
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Jan Lubinski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Kelly Metcalfe
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada
- Bloomberg School of Nursing, University of Toronto, Toronto, ON, Canada
| | - Katherine L Nathanson
- Basser Center for BRCA, University of Pennsylvania, Philadelphia, PA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Christian F Singer
- Department of Obstetrics and Gynecology and Center for Breast Health, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Heather Symecko
- Basser Center for BRCA, University of Pennsylvania, Philadelphia, PA
| | - Nadine Tung
- Beth Israel Deaconess Medical Center, Boston, MA
| | - Steven A Narod
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
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Donoso FS, Carver T, Ficorella L, Fennell N, Antoniou AC, Easton DF, Tischkowitz M, Walter FM, Usher-Smith JA, Archer S. Improving the communication of multifactorial cancer risk assessment results for different audiences: a co-design process. J Community Genet 2024:10.1007/s12687-024-00729-4. [PMID: 39320563 DOI: 10.1007/s12687-024-00729-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/21/2024] [Indexed: 09/26/2024] Open
Abstract
BACKGROUND Multifactorial cancer risk prediction tools, such as CanRisk, are increasingly being incorporated into routine healthcare. Understanding risk information and communicating risk is challenging and healthcare professionals rely substantially on the outputs of risk prediction tools to communicate results. This work aimed to produce a new CanRisk report so users can directly access key information and communicate risk estimates effectively. METHODS Over a 13-month period, we led an 8-step co-design process with patients, the public, and healthcare professionals. Steps comprised 1) think aloud testing of the original CanRisk report; 2) structured feedback on the original report; 3) literature review; 4) development of a new report prototype; 5) first round of structured feedback; 6) updating the new report prototype; 7) second round of structured feedback; and 8) finalising and publishing the new CanRisk report. RESULTS We received 56 sets of feedback from 34 stakeholders. Overall, the original CanRisk report was not suitable for patients and the public. Building on the feedback, the new report has an overview of the information presented: section one summarises key information for individuals; sections two and three present information for healthcare professionals in different settings. New features also include explanatory text, definitions, graphs, keys and tables to support the interpretation of the information. DISCUSSION This co-design experience shows the value of collaboration for the successful communication of complex health information. As a result, the new CanRisk report has the potential to better support shared decision-making processes about cancer risk management across clinical settings.
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Affiliation(s)
| | - Tim Carver
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Lorenzo Ficorella
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nichola Fennell
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Antonis C Antoniou
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Fiona M Walter
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Wolfson Institute of Population Health, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Juliet A Usher-Smith
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Stephanie Archer
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Psychology, University of Cambridge, Cambridge, UK
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Douglas AGL, Thompson AG, Turner MR, Talbot K. Personalised penetrance estimation for C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia. BMJ Neurol Open 2024; 6:e000792. [PMID: 39315390 PMCID: PMC11418571 DOI: 10.1136/bmjno-2024-000792] [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] [Accepted: 08/21/2024] [Indexed: 09/25/2024] Open
Abstract
Background C9orf72 hexanucleotide repeat expansions are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) in European populations. Variable disease penetrance between families presents a challenge for genetic counselling of at-risk relatives and reduces the predictive utility of testing asymptomatic relatives. We have developed a novel model for estimating penetrance in individual families affected by C9orf72 using available family history information, allowing the calculation of personalised risk estimates. Methods Published aggregated age-of-onset data for C9orf72-related ALS/FTD were used to generate age-related cumulative relative risks for at-risk relatives within pedigrees. Age-related relative risks are combined with a priori chance of individuals carrying an expansion based on known pedigree information. Penetrance is calculated as a number of affected individuals divided by the sum of cumulative age-related risks of relatives being affected by 80 years. Results This method allows family-specific penetrance to be estimated from family history and at-risk relatives' personalised age-related ALS/FTD risks to be calculated and illustrated graphically. Penetrance reduces as the number and age of at-risk unaffected relatives increases. Conclusions Family history remains the best indicator of penetrance in C9orf72 expansion carriers. Calculating family-specific penetrance can aid genetic counselling by allowing at-risk relatives a more accurate understanding of their individual risk.
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Affiliation(s)
- Andrew G L Douglas
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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Seung SJ, Mittmann N, Ante Z, Liu N, Blackmore KM, Richard ES, Wong A, Walker MJ, Earle CC, Simard J, Chiarelli AM. Evaluating Real World Health System Resource Utilization and Costs for a Risk-Based Breast Cancer Screening Approach in the Canadian PERSPECTIVE Integration and Implementation Project. Cancers (Basel) 2024; 16:3189. [PMID: 39335160 PMCID: PMC11430316 DOI: 10.3390/cancers16183189] [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: 07/22/2024] [Revised: 09/12/2024] [Accepted: 09/13/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND A prospective cohort study was undertaken within the PERSPECTIVE I&I project to evaluate healthcare resource utilization and costs associated with breast cancer risk assessment and screening and overall costs stratified by risk level, in Ontario, Canada. METHODS From July 2019 to December 2022, 1997 females aged 50 to 70 years consented to risk assessment and received their breast cancer risk level and personalized screening action plan in Ontario. The mean costs for risk-stratified screening-related activities included risk assessment, screening and diagnostic costs. The GETCOST macro from the Institute of Clinical Evaluative Sciences (ICES) assessed the mean overall healthcare system costs. RESULTS For the 1997 participants, 83.3%, 14.4% and 2.3% were estimated to be average, higher than average, and high risk, respectively (median age (IQR): 60 [56-64] years). Stratification into the three risk levels was determined using the validated multifactorial CanRisk prediction tool that includes family history information, a polygenic risk score (PRS), breast density and established lifestyle/hormonal risk factors. The mean number of genetic counseling visits, mammograms and MRIs per individual increased with risk level. High-risk participants incurred the highest overall mean risk-stratified screening-related costs in 2022 CAD (±SD) at CAD 905 (±269) followed by CAD 580 (±192) and CAD 521 (±163) for higher-than-average and average-risk participants, respectively. Among the breast screening-related costs, the greatest cost burden across all risk groups was the risk assessment cost, followed by total diagnostic and screening costs. The mean overall healthcare cost per participant (±SD) was the highest for the average risk participants with CAD 6311 (±19,641), followed by higher than average risk with CAD 5391 (±8325) and high risk with CAD 5169 (±7676). CONCLUSION Although high-risk participants incurred the highest risk-stratified screening-related costs, their costs for overall healthcare utilization costs were similar to other risk levels. Our study underscored the importance of integrating risk stratification as part of the screening pathway to support breast cancer detection at an earlier and more treatable stage, thereby reducing costs and the overall burden on the healthcare system.
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Affiliation(s)
- Soo-Jin Seung
- HOPE Research Centre, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
| | - Nicole Mittmann
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
- Department of Pharmacology & Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Zharmaine Ante
- ICES Central, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
| | - Ning Liu
- ICES Central, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
| | | | - Emilie S Richard
- HOPE Research Centre, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
| | - Anisia Wong
- HOPE Research Centre, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
| | - Meghan J Walker
- Ontario Health, 525 University Avenue, 5th Floor, Toronto, ON M5G 2L3, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Craig C Earle
- ICES Central, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
| | - Jacques Simard
- Research Center, University Hospital Center (CHU)-Laval University, Québec City, QC G1V 4G2, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada
| | - Anna M Chiarelli
- Ontario Health, 525 University Avenue, 5th Floor, Toronto, ON M5G 2L3, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A1, Canada
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Dubsky P, Jackisch C, Im SA, Hunt KK, Li CF, Unger S, Paluch-Shimon S. BRCA genetic testing and counseling in breast cancer: how do we meet our patients' needs? NPJ Breast Cancer 2024; 10:77. [PMID: 39237557 PMCID: PMC11377442 DOI: 10.1038/s41523-024-00686-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 08/19/2024] [Indexed: 09/07/2024] Open
Abstract
BRCA1 and BRCA2 are tumor suppressor genes that have been linked to inherited susceptibility of breast cancer. Germline BRCA1/2 pathogenic or likely pathogenic variants (gBRCAm) are clinically relevant for treatment selection in breast cancer because they confer sensitivity to poly(ADP-ribose) polymerase (PARP) inhibitors. BRCA1/2 mutation status may also impact decisions on other systemic therapies, risk-reducing measures, and choice of surgery. Consequently, demand for gBRCAm testing has increased. Several barriers to genetic testing exist, including limited access to testing facilities, trained counselors, and psychosocial support, as well as the financial burden of testing. Here, we describe current implications of gBRCAm testing for patients with breast cancer, summarize current approaches to gBRCAm testing, provide potential solutions to support wider adoption of mainstreaming testing practices, and consider future directions of testing.
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Affiliation(s)
- Peter Dubsky
- Breast and Tumor Center, Hirslanden Klinik St. Anna, Lucerne, Switzerland.
- University of Lucerne, Faculty of Health Sciences and Medicine, Lucerne, Switzerland.
| | - Christian Jackisch
- Department of Obstetrics and Gynecology, Breast and Gynecologic Cancer Center, Sana Klinikum Offenbach, Offenbach, Germany
| | - Seock-Ah Im
- Seoul National University Hospital, Cancer Research Institute, Seoul National University College of Medicine, Seoul National University, Seoul, Republic of Korea
| | | | - Chien-Feng Li
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | | | - Shani Paluch-Shimon
- Hadassah University Hospital & Faculty of Medicine, Hebrew University, Jerusalem, Israel
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Carley H, Kulkarni A. Reproductive decision-making in cancer susceptibility syndromes. Best Pract Res Clin Obstet Gynaecol 2024; 96:102527. [PMID: 38987108 DOI: 10.1016/j.bpobgyn.2024.102527] [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: 05/02/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
Cancer susceptibility syndromes confer an increased lifetime risk of cancer and occur due to germline likely-pathogenic or pathogenic variants in a cancer susceptibility gene. Clinical Genetics services advise patients of ways to manage their future cancer risks, often prefaced with uncertainties due to poor understandings of individualised risk. For individuals/couples whose future offspring are at risk of a cancer susceptibility syndrome, different options are available depending on their preferences and circumstances, including prenatal diagnosis and preimplantation genetic testing. This review provides an overview of the most common cancer susceptibility syndromes, available reproductive options and a genetic counselling framework recommended to support individuals/couples in their decision-making. We describe complexities of decision-making involving moderate penetrance and sex-specific variable penetrance genes and explore associated ethical issues arising in this complex area of medicine.
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Affiliation(s)
- Helena Carley
- Clinical Genetics, 7(th) Floor Borough Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK; Clinical Ethics, Law, & Society Group, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK.
| | - Anjana Kulkarni
- Clinical Genetics, 7(th) Floor Borough Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK; Guy's & St Thomas NHS Foundation Trust, UK.
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9
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Schreurs MAC, Schmidt MK, Hollestelle A, Schaapveld M, van Asperen CJ, Ausems MGEM, van de Beek I, Broekema MF, Margriet Collée J, van der Hout AH, van Kaam KJAF, Komdeur FL, Mensenkamp AR, Adank MA, Hooning MJ. Cancer risks for other sites in addition to breast in CHEK2 c.1100delC families. Genet Med 2024; 26:101171. [PMID: 38828701 DOI: 10.1016/j.gim.2024.101171] [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: 02/29/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024] Open
Abstract
PURPOSE Female CHEK2 c.1100delC heterozygotes are eligible for additional breast surveillance because of an increased breast cancer risk. Increased risks for other cancers have been reported. We studied whether CHEK2 c.1100delC is associated with an increased risk for other cancers within these families. METHODS Including 10,780 individuals from 609 families, we calculated standardized incidence rates (SIRs) and absolute excess risk (AER, per 10,000 person-years) by comparing first-reported cancer derived from the pedigrees with general Dutch population rates from 1970 onward. Attained-age analyses were performed for sites in which significant increased risks were found. Considering the study design, we primarily focused on cancer risk in women. RESULTS We found significant increased risks of colorectal cancer (CRC; SIR = 1.43, 95% CI = 1.14-1.76; AER = 1.43) and hematological cancers (SIR = 1.32; 95% CI = 1.02-1.67; AER = 0.87). CRC was significantly more frequent from age 45 onward. CONCLUSION A significantly increased risk of CRC, and hematological cancers in women was found, starting at a younger age than expected. Currently, colorectal surveillance starts at age 45 in high-risk individuals. Our results suggest that some CHEK2 c.1100delC families might benefit from this surveillance as well; however, further research is needed to determine who may profit from this additional colorectal surveillance.
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Affiliation(s)
- Maartje A C Schreurs
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marjanka K Schmidt
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Michael Schaapveld
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Margreet G E M Ausems
- Division of Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Irma van de Beek
- Department of Clinical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marjoleine F Broekema
- Department of Human Genetics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - J Margriet Collée
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Annemieke H van der Hout
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kim J A F van Kaam
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Fenne L Komdeur
- Department of Human Genetics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Muriel A Adank
- Department of Clinical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
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10
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Tsoulos N, Papadopoulou E, Agiannitopoulos K, Grigoriadis D, Tsaousis GN, Bouzarelou D, Gogas H, Troupis T, Venizelos V, Fountzilas E, Theochari M, Ziogas DC, Giassas S, Koumarianou A, Christopoulou A, Busby G, Nasioulas G, Markopoulos C. Polygenic Risk Score (PRS) Combined with NGS Panel Testing Increases Accuracy in Hereditary Breast Cancer Risk Estimation. Diagnostics (Basel) 2024; 14:1826. [PMID: 39202314 PMCID: PMC11353636 DOI: 10.3390/diagnostics14161826] [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: 06/11/2024] [Revised: 07/21/2024] [Accepted: 08/15/2024] [Indexed: 09/03/2024] Open
Abstract
Breast cancer (BC) is the most prominent tumor type among women, accounting for 32% of newly diagnosed cancer cases. BC risk factors include inherited germline pathogenic gene variants and family history of disease. However, the etiology of the disease remains occult in most cases. Therefore, in the absence of high-risk factors, a polygenic basis has been suggested to contribute to susceptibility. This information is utilized to calculate the Polygenic Risk Score (PRS) which is indicative of BC risk. This study aimed to evaluate retrospectively the clinical usefulness of PRS integration in BC risk calculation, utilizing a group of patients who have already been diagnosed with BC. The study comprised 105 breast cancer patients with hereditary genetic analysis results obtained by NGS. The selection included all testing results: high-risk gene-positive, intermediate/low-risk gene-positive, and negative. PRS results were obtained from an external laboratory (Allelica). PRS-based BC risk was computed both with and without considering additional risk factors, including gene status and family history. A significantly different PRS percentile distribution consistent with higher BC risk was observed in our cohort compared to the general population. Higher PRS-based BC risks were detected in younger patients and in those with FH of cancers. Among patients with a pathogenic germline variant detected, reduced PRS values were observed, while the BC risk was mainly determined by a monogenic etiology. Upon comprehensive analysis encompassing FH, gene status, and PRS, it was determined that 41.90% (44/105) of the patients demonstrated an elevated susceptibility for BC. Moreover, 63.63% of the patients with FH of BC and without an inherited pathogenic genetic variant detected showed increased BC risk by incorporating the PRS result. Our results indicate a major utility of PRS calculation in women with FH in the absence of a monogenic etiology detected by NGS. By combining high-risk strategies, such as inherited disease analysis, with low-risk screening strategies, such as FH and PRS, breast cancer risk stratification can be improved. This would facilitate the development of more effective preventive measures and optimize the allocation of healthcare resources.
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Affiliation(s)
- Nikolaos Tsoulos
- Genekor Medical S.A., 15344 Athens, Greece; (N.T.); (E.P.); (D.G.); (G.N.T.); (D.B.); (G.N.)
| | - Eirini Papadopoulou
- Genekor Medical S.A., 15344 Athens, Greece; (N.T.); (E.P.); (D.G.); (G.N.T.); (D.B.); (G.N.)
| | | | - Dimitrios Grigoriadis
- Genekor Medical S.A., 15344 Athens, Greece; (N.T.); (E.P.); (D.G.); (G.N.T.); (D.B.); (G.N.)
| | - Georgios N. Tsaousis
- Genekor Medical S.A., 15344 Athens, Greece; (N.T.); (E.P.); (D.G.); (G.N.T.); (D.B.); (G.N.)
| | - Dimitra Bouzarelou
- Genekor Medical S.A., 15344 Athens, Greece; (N.T.); (E.P.); (D.G.); (G.N.T.); (D.B.); (G.N.)
| | - Helen Gogas
- First Department of Internal Medicine, Laikon General Hospital, School of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece; (H.G.); (D.C.Z.)
| | - Theodore Troupis
- School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.T.); (C.M.)
| | | | - Elena Fountzilas
- Second Department of Medical Oncology, Euromedica General Clinic, 54645 Thessaloniki, Greece;
| | - Maria Theochari
- Oncology Unit, “Hippokrateion” General Hospital of Athens, 11527 Athens, Greece;
| | - Dimitrios C. Ziogas
- First Department of Internal Medicine, Laikon General Hospital, School of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece; (H.G.); (D.C.Z.)
| | - Stylianos Giassas
- Second Oncology Clinic IASO, General Maternity and Gynecology Clinic, 15123 Athens, Greece;
| | - Anna Koumarianou
- Hematology Oncology Unit, 4th Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, Attikon University Hospital, 12462 Athens, Greece;
| | | | - George Busby
- Allelica Inc., 447 Broadway, New York, NY 10013, USA;
| | - George Nasioulas
- Genekor Medical S.A., 15344 Athens, Greece; (N.T.); (E.P.); (D.G.); (G.N.T.); (D.B.); (G.N.)
| | - Christos Markopoulos
- School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.T.); (C.M.)
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11
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Kwong A, Ho CYS, Au CH, Tey SK, Ma ESK. Germline RAD51C and RAD51D Mutations in High-Risk Chinese Breast and/or Ovarian Cancer Patients and Families. J Pers Med 2024; 14:866. [PMID: 39202057 PMCID: PMC11355318 DOI: 10.3390/jpm14080866] [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: 07/09/2024] [Revised: 08/05/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
BACKGROUND RAD51C and RAD51D are crucial in homologous recombination (HR) DNA repair. The prevalence of the RAD51C and RAD51D mutations in breast cancer varies across ethnic groups. Associations of RAD51C and RAD51D germline pathogenic variants (GPVs) with breast and ovarian cancer predisposition have been recently reported and are of interest. METHODS We performed multi-gene panel sequencing to study the prevalence of RAD51C and RAD51D germline mutations among 3728 patients with hereditary breast and/or ovarian cancer (HBOC). RESULTS We identified 18 pathogenic RAD51C and RAD51D mutation carriers, with a mutation frequency of 0.13% (5/3728) and 0.35% (13/3728), respectively. The most common recurrent mutation was RAD51D c.270_271dupTA; p.(Lys91Ilefs*13), with a mutation frequency of 0.30% (11/3728), which was also commonly identified in Asians. Only four out of six cases (66.7%) of this common mutation tested positive for homologous recombination deficiency (HRD). CONCLUSIONS Taking the family studies in our registry and tumor molecular pathology together, we concluded that this relatively common RAD51D variant showed incomplete penetrance in our local Chinese community. Personalized genetic counseling emphasizing family history for families with this variant, as suggested at the UK Cancer Genetics Group (UKCGG) Consensus meeting, would also be appropriate in Chinese families.
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Affiliation(s)
- Ava Kwong
- Division of Breast Surgery, Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Cancer Genetics Centre, Breast Surgery Centre, Surgery Centre, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Cecilia Yuen Sze Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Sze Keong Tey
- Division of Breast Surgery, Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
| | - Edmond Shiu Kwan Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
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12
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McInerny S, Mascarenhas L, Yanes T, Petelin L, Chenevix-Trench G, Southey MC, Young MA, James PA. Using polygenic risk modification to improve breast cancer prevention: study protocol for the PRiMo multicentre randomised controlled trial. BMJ Open 2024; 14:e087874. [PMID: 39107016 PMCID: PMC11308879 DOI: 10.1136/bmjopen-2024-087874] [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: 04/21/2024] [Accepted: 07/16/2024] [Indexed: 08/09/2024] Open
Abstract
INTRODUCTION Established personal and familial risk factors contribute collectively to a woman's risk of breast or ovarian cancer. Existing clinical services offer genetic testing for pathogenic variants in high-risk genes to investigate these risks but recent information on the role of common genomic variants, in the form of a Polygenic Risk Score (PRS), has provided the potential to further personalise breast and ovarian cancer risk assessment. Data from cohort studies support the potential of an integrated risk assessment to improve targeted risk management but experience of this approach in clinical practice is limited. METHODS AND ANALYSIS The polygenic risk modification trial is an Australian multicentre prospective randomised controlled trial of integrated risk assessment including personal and family risk factors with inclusion of breast and ovarian PRS vs standard care. The study will enrol women, unaffected by cancer, undergoing predictive testing at a familial cancer clinic for a pathogenic variant in a known breast cancer (BC) or ovarian cancer (OC) predisposition gene (BRCA1, BRCA2, PALB2, CHEK2, ATM, RAD51C, RAD51D). Array-based genotyping will be used to generate breast cancer (313 SNP) and ovarian cancer (36 SNP) PRS. A suite of materials has been developed for the trial including an online portal for patient consent and questionnaires, and a clinician education programme to train healthcare providers in the use of integrated risk assessment. Long-term follow-up will evaluate differences in the assessed risk and management advice, patient risk management intentions and adherence, patient-reported experience and outcomes, and the health service implications of personalised risk assessment. ETHICS AND DISSEMINATION This study has been approved by the Human Research Ethics Committee of Peter MacCallum Cancer Centre and at all participating centres. Study findings will be disseminated via peer-reviewed publications and conference presentations, and directly to participants. TRIAL REGISTRATION NUMBER ACTRN12621000009819.
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Affiliation(s)
- Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Parkville Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Lyon Mascarenhas
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Parkville Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Tatiane Yanes
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Lara Petelin
- The Daffodil Centre, joint venture with Cancer Council NSW, The University of Sydney, Sydney, New South Wales, Australia
- The University of Melbourne School of Population and Global Health, Melbourne, Victoria, Australia
| | - Georgia Chenevix-Trench
- Cancer Genetics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Melissa C Southey
- Precision Medicine, Monash University School of Clinical Sciences at Monash Health, Clayton, Victoria, Australia
- Cancer Council Victoria Cancer Epidemiology Division, Melbourne, Victoria, Australia
| | - Mary-Anne Young
- Clinical Translation and Engagement Platform, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Parkville Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
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13
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Wallis M, Bodek SD, Munro J, Rafehi H, Bennett MF, Ye Z, Schneider A, Gardiner F, Valente G, Murdoch E, Uebergang E, Hunter J, Stutterd C, Huq A, Salmon L, Scheffer I, Eratne D, Meyn S, Fong CY, John T, Mullen S, White SM, Brown NJ, McGillivray G, Chen J, Richmond C, Hughes A, Krzesinski E, Fennell A, Chambers B, Santoreneos R, Le Fevre A, Hildebrand MS, Bahlo M, Christodoulou J, Delatycki M, Berkovic SF. Experience of the first adult-focussed undiagnosed disease program in Australia (AHA-UDP): solving rare and puzzling genetic disorders is ageless. Orphanet J Rare Dis 2024; 19:288. [PMID: 39095811 PMCID: PMC11297648 DOI: 10.1186/s13023-024-03297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Significant recent efforts have facilitated increased access to clinical genetics assessment and genomic sequencing for children with rare diseases in many centres, but there remains a service gap for adults. The Austin Health Adult Undiagnosed Disease Program (AHA-UDP) was designed to complement existing UDP programs that focus on paediatric rare diseases and address an area of unmet diagnostic need for adults with undiagnosed rare conditions in Victoria, Australia. It was conducted at a large Victorian hospital to demonstrate the benefits of bringing genomic techniques currently used predominantly in a research setting into hospital clinical practice, and identify the benefits of enrolling adults with undiagnosed rare diseases into a UDP program. The main objectives were to identify the causal mutation for a variety of diseases of individuals and families enrolled, and to discover novel disease genes. METHODS Unsolved patients in whom standard genomic diagnostic techniques such as targeted gene panel, exome-wide next generation sequencing, and/or chromosomal microarray, had already been performed were recruited. Genome sequencing and enhanced genomic analysis from the research setting were applied to aid novel gene discovery. RESULTS In total, 16/50 (32%) families/cases were solved. One or more candidate variants of uncertain significance were detected in 18/50 (36%) families. No candidate variants were identified in 16/50 (32%) families. Two novel disease genes (TOP3B, PRKACB) and two novel genotype-phenotype correlations (NARS, and KMT2C genes) were identified. Three out of eight patients with suspected mosaic tuberous sclerosis complex had their diagnosis confirmed which provided reproductive options for two patients. The utility of confirming diagnoses for patients with mosaic conditions (using high read depth sequencing and ddPCR) was not specifically envisaged at the onset of the project, but the flexibility to offer recruitment and analyses on an as-needed basis proved to be a strength of the AHA-UDP. CONCLUSION AHA-UDP demonstrates the utility of a UDP approach applying genome sequencing approaches in diagnosing adults with rare diseases who have had uninformative conventional genetic analysis, informing clinical management, recurrence risk, and recommendations for relatives.
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Affiliation(s)
- Mathew Wallis
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Simon D Bodek
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia.
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia.
| | - Jacob Munro
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Haloom Rafehi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Mark F Bennett
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Zimeng Ye
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Amy Schneider
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Fiona Gardiner
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Giulia Valente
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Emma Murdoch
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Eloise Uebergang
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
| | - Jacquie Hunter
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Chloe Stutterd
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Aamira Huq
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Genetic Medicine Service, The Royal Melbourne Hospital, Melbourne, Australia
| | - Lucinda Salmon
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Genetics Service, Royal Prince Alfred Hospital, Melbourne, Australia
| | - Ingrid Scheffer
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
- Department of Paediatrics, Austin Health, Melbourne, Australia
| | - Dhamidhu Eratne
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
- Neuropsychiatry, The Royal Melbourne Hospital, Melbourne, Australia
| | - Stephen Meyn
- Centre for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Chun Y Fong
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Tom John
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Saul Mullen
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Susan M White
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - George McGillivray
- Victorian Clinical Genetics Service, Melbourne, Australia
- Genetics Service, Mercy Hospital for Women, Melbourne, Australia
| | - Jesse Chen
- Neurology Service, Austin Health, Melbourne, Australia
| | - Chris Richmond
- Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Andrew Hughes
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
| | | | - Andrew Fennell
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Monash Health Genetics Clinic, Melbourne, Australia
| | - Brian Chambers
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
| | - Renee Santoreneos
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
| | - Anna Le Fevre
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Martin Delatycki
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Samuel F Berkovic
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
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14
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Baumann A, Ruckert C, Meier C, Hutschenreiter T, Remy R, Schnur B, Döbel M, Fankep RCN, Skowronek D, Kutz O, Arnold N, Katzke AL, Forster M, Kobiela AL, Thiedig K, Zimmer A, Ritter J, Weber BHF, Honisch E, Hackmann K, Schmidt G, Sturm M, Ernst C. Limitations in next-generation sequencing-based genotyping of breast cancer polygenic risk score loci. Eur J Hum Genet 2024; 32:987-997. [PMID: 38907004 PMCID: PMC11291653 DOI: 10.1038/s41431-024-01647-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/17/2024] [Accepted: 06/10/2024] [Indexed: 06/23/2024] Open
Abstract
Considering polygenic risk scores (PRSs) in individual risk prediction is increasingly implemented in genetic testing for hereditary breast cancer (BC) based on next-generation sequencing (NGS). To calculate individual BC risks, the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) with the inclusion of the BCAC 313 or the BRIDGES 306 BC PRS is commonly used. The PRS calculation depends on accurately reproducing the variant allele frequencies (AFs) and, consequently, the distribution of PRS values anticipated by the algorithm. Here, the 324 loci of the BCAC 313 and the BRIDGES 306 BC PRS were examined in population-specific database gnomAD and in real-world data sets of five centers of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC), to determine whether these expected AFs can be reproduced by NGS-based genotyping. Four PRS loci were non-existent in gnomAD v3.1.2 non-Finnish Europeans, further 24 loci showed noticeably deviating AFs. In real-world data, between 11 and 23 loci were reported with noticeably deviating AFs, and were shown to have effects on final risk prediction. Deviations depended on the sequencing approach, variant caller and calling mode (forced versus unforced) employed. Therefore, this study demonstrates the necessity to apply quality assurance not only in terms of sequencing coverage but also observed AFs in a sufficiently large cohort, when implementing PRSs in a routine diagnostic setting. Furthermore, future PRS design should be guided by the technical reproducibility of expected AFs across commonly used genotyping methods, especially NGS, in addition to the observed effect sizes.
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Affiliation(s)
- Alexandra Baumann
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany
- ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Christian Ruckert
- Department of Medical Genetics, University Hospital Münster, Münster, Germany
| | - Christoph Meier
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Tim Hutschenreiter
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany
- ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Robert Remy
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Benedikt Schnur
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Marvin Döbel
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Rudel Christian Nkouamedjo Fankep
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Dariush Skowronek
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Oliver Kutz
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany
- ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany
| | - Norbert Arnold
- Department of Gynecology and Obstetrics, Institute of Clinical Chemistry Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Anna-Lena Katzke
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Michael Forster
- Department of Gynecology and Obstetrics, Institute of Clinical Chemistry Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Anna-Lena Kobiela
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Katharina Thiedig
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Andreas Zimmer
- Institute for Human Genetics, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Ritter
- Department of Human Genetics, Labor Berlin - Charité Vivantes GmbH, Berlin, Germany
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Ellen Honisch
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Karl Hackmann
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany
- ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Gunnar Schmidt
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany.
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15
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Ficorella L, Yang X, Easton DF, Antoniou AC. BOADICEA model: updates to the BRCA2 breast cancer risks for ages 60 years and older. BJC REPORTS 2024; 2:53. [PMID: 39072245 PMCID: PMC11269170 DOI: 10.1038/s44276-024-00079-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/26/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024]
Abstract
Breast cancer risks in older BRCA2 pathogenic variant carriers are understudied. Recent studies show a marked decline in the relative risk at older ages. We used data from two large studies to update the breast cancer risks in the BOADICEA model for BRCA2 carriers 60 years and older.
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Affiliation(s)
- Lorenzo Ficorella
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Xin Yang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - 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
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
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16
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Garmendia D, Weidner A, Venton L, Pal T. Comparing Cancer Risk Management between Females with Truncating CHEK2 1100delC versus Missense CHEK2 I157T Variants. Genes (Basel) 2024; 15:881. [PMID: 39062660 PMCID: PMC11276105 DOI: 10.3390/genes15070881] [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: 05/09/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Breast cancer (BC) risks imparted by CHEK2 c.1100delC ("1100delC") germline pathogenic/likely pathogenic variant (GPV) are 20-30%, compared to CHEK2 c.470T>C ("I157T") GPV with <20%, leading to different breast screening recommendations through MRI. We compared cancer risk management (CRM) across these two GPVs. Study participants were adult females with an 1100delC or I157T GPV drawn from the Inherited Cancer Registry (ICARE) across the United States. Cancer history, clinical characteristics, and CRM were compared using chi-squared tests, t-tests, and logistic regression. Of 150 CHEK2 carriers, 40.7% had BC, with a mean age of 50. Comparing 1100delC and I157T GPVs, there were no differences in rates of (1) breast MRI among those with (65.2% versus 55.6% of 23 and 9; p = 0.612) and without (44.0% versus 44.8% of 50 and 29; p = 0.943) BC; (2) risk-reducing mastectomy among those with (50% versus 38.9% of 46 and 15; p = 0.501) and without (13.8% versus 6.5% of 58 and 31; p = 0.296) BC; and (3) risk-reducing salpingo-oophorectomy among those with (24.2% versus 22.2% of 45 and 18; p = 0.852) and without (17.5% versus 16.7% of 57 and 30; p = 0.918) BC. The results suggest over-screening with breast MRI among CHEK2 I157T GPV carriers and possible overuse of risk-reducing surgeries among CHEK2 carriers.
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Affiliation(s)
- Diego Garmendia
- Vanderbilt University Medical Center, 1500 21st Ave. So., Suite 2810, Nashville, TN 37212, USA; (D.G.); (A.W.); (L.V.)
| | - Anne Weidner
- Vanderbilt University Medical Center, 1500 21st Ave. So., Suite 2810, Nashville, TN 37212, USA; (D.G.); (A.W.); (L.V.)
| | - Lindsay Venton
- Vanderbilt University Medical Center, 1500 21st Ave. So., Suite 2810, Nashville, TN 37212, USA; (D.G.); (A.W.); (L.V.)
| | - Tuya Pal
- Vanderbilt University Medical Center, 1500 21st Ave. So., Suite 2810, Nashville, TN 37212, USA; (D.G.); (A.W.); (L.V.)
- Vanderbilt-Ingram Cancer Center, 2220 Pierce Ave, Nashville, TN 37232, USA
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17
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Forer L, Taliun D, LeFaive J, Smith AV, Boughton A, Coassin S, Lamina C, Kronenberg F, Fuchsberger C, Schönherr S. Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers. Nucleic Acids Res 2024; 52:W70-W77. [PMID: 38709879 PMCID: PMC11223871 DOI: 10.1093/nar/gkae331] [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: 02/21/2024] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Polygenic scores (PGS) enable the prediction of genetic predisposition for a wide range of traits and diseases by calculating the weighted sum of allele dosages for genetic variants associated with the trait or disease in question. Present approaches for calculating PGS from genotypes are often inefficient and labor-intensive, limiting transferability into clinical applications. Here, we present 'Imputation Server PGS', an extension of the Michigan Imputation Server designed to automate a standardized calculation of polygenic scores based on imputed genotypes. This extends the widely used Michigan Imputation Server with new functionality, bringing the simplicity and efficiency of modern imputation to the PGS field. The service currently supports over 4489 published polygenic scores from publicly available repositories and provides extensive quality control, including ancestry estimation to report population stratification. An interactive report empowers users to screen and compare thousands of scores in a fast and intuitive way. Imputation Server PGS provides a user-friendly web service, facilitating the application of polygenic scores to a wide range of genetic studies and is freely available at https://imputationserver.sph.umich.edu.
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Affiliation(s)
- Lukas Forer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniel Taliun
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montreal, Québec, Canada
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
| | - Jonathon LeFaive
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Albert V Smith
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew P Boughton
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stefan Coassin
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudia Lamina
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian Fuchsberger
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
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18
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Youngs A, Forman A, Elms M, Kohut K, Hlaing MT, Short J, Hanson H, Snape K. Digital innovation for cancer risk assessment allows large-scale service redevelopment of regional cancer genetics service delivery. Fam Cancer 2024:10.1007/s10689-024-00407-x. [PMID: 38954285 DOI: 10.1007/s10689-024-00407-x] [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: 01/22/2024] [Accepted: 06/01/2024] [Indexed: 07/04/2024]
Abstract
Family-history assessment can identify individuals above population-risk for cancer to enable targeted Screening, Prevention and Early Detection (SPED). The online patient-facing cancer Family History Questionnaire Service (cFHQS) is a digitalised, resource efficient tool for family history data capture to facilitate this. The capturing of digital data from cFHQS allows for data interrogation of patients referred to Clinical Genetics for the purposes of service improvement. Digital data from 4,044 cFHQS respondents over a three-year period was collected and interrogated with respect to the number and type of familial tumour diagnoses to enable service improvement and streamlining of referral pathways. 81% of colorectal and 71% of breast screening assessments were population- or moderate-risk. Most patients who completed cFHQS reported more than one diagnosis of cancer/tumour/polyps in their family. 2.5% of family history assessment patients had a second indication that required assessment that would have been missed if single tumour type assessment was undertaken. Implementation of an innovative, digital family history data collection pathway has allowed large scale interrogation of referral patterns and assessment outcomes to enable service development. The high volume of inappropriate referrals to Clinical Genetics for population and moderate risk patients highlighted the need for dedicated secondary care pathway provision for these patients. The use of cFHQS streamlined family history assessment allows for redistribution of resources to improve equity and access to genetic cancer risk assessment.
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Affiliation(s)
- Alice Youngs
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, SW17 0QT, London, England
| | - Andrea Forman
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, SW17 0QT, London, England
| | - Marisa Elms
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, SW17 0QT, London, England
| | - Kelly Kohut
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, SW17 0QT, London, England
| | - Min Theik Hlaing
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, SW17 0QT, London, England
| | - John Short
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, SW17 0QT, London, England
| | - Helen Hanson
- Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, EX1 2ED, Exeter, England
| | - Katie Snape
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, SW17 0QT, London, England.
- St George's University, London, UK.
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19
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Balasubramanian JB, Choudhury PP, Mukhopadhyay S, Ahearn T, Chatterjee N, García-Closas M, Almeida JS. Wasm-iCARE: a portable and privacy-preserving web module to build, validate, and apply absolute risk models. JAMIA Open 2024; 7:ooae055. [PMID: 38938691 PMCID: PMC11208928 DOI: 10.1093/jamiaopen/ooae055] [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: 09/20/2023] [Revised: 04/24/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
Objectives Absolute risk models estimate an individual's future disease risk over a specified time interval. Applications utilizing server-side risk tooling, the R-based iCARE (R-iCARE), to build, validate, and apply absolute risk models, face limitations in portability and privacy due to their need for circulating user data in remote servers for operation. We overcome this by porting iCARE to the web platform. Materials and Methods We refactored R-iCARE into a Python package (Py-iCARE) and then compiled it to WebAssembly (Wasm-iCARE)-a portable web module, which operates within the privacy of the user's device. Results We showcase the portability and privacy of Wasm-iCARE through 2 applications: for researchers to statistically validate risk models and to deliver them to end-users. Both applications run entirely on the client side, requiring no downloads or installations, and keep user data on-device during risk calculation. Conclusions Wasm-iCARE fosters accessible and privacy-preserving risk tools, accelerating their validation and delivery.
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Affiliation(s)
- Jeya Balaji Balasubramanian
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
| | - Parichoy Pal Choudhury
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
- Surveillance & Health Equity Science, American Cancer Society, Atlanta, GA 30303, United States
| | - Srijon Mukhopadhyay
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
| | - Thomas Ahearn
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
| | - Nilanjan Chatterjee
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Montserrat García-Closas
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
- The Cancer Epidemiology and Prevention Research Unit, The Institute of Cancer Research, London, SM2 5NG, United Kingdom
| | - Jonas S Almeida
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
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20
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Gootzen TA, Steenbeek MP, van Bommel M, IntHout J, Kets CM, Hermens R, de Hullu JA. Risk-reducing salpingectomy with delayed oophorectomy to prevent ovarian cancer in women with an increased inherited risk: insights into an alternative strategy. Fam Cancer 2024:10.1007/s10689-024-00412-0. [PMID: 38907139 DOI: 10.1007/s10689-024-00412-0] [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: 03/14/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
Epithelial ovarian cancer (EOC) is the most lethal type of gynaecological cancer, due to lack of effective screening possibilities and because the disease tends to metastasize before onset of symptoms. Women with an increased inherited risk for EOC are advised to undergo a risk-reducing salpingo-oophorectomy (RRSO), which decreases their EOC risk by 96% when performed within guideline ages. However, it also induces premature menopause, which has harmful consequences. There is compelling evidence that the majority of EOCs originate in the fallopian tube. Therefore, a risk-reducing salpingectomy with delayed oophorectomy (RRS with DO) has gained interest as an alternative strategy. Previous studies have shown that this alternative strategy has a positive effect on menopause-related quality of life and sexual health when compared to the standard RRSO. It is hypothesized that the alternative strategy is non-inferior to the standard RRSO with respect to oncological safety (EOC incidence). Three prospective studies are currently including patients to compare the safety and/or quality of life of the two distinct strategies. In this article we discuss the background, opportunities, and challenges of the current and alternative strategy.
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Affiliation(s)
- T A Gootzen
- Department of Gynaecology and Obstetrics, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, GA, 6525, The Netherlands.
| | - M P Steenbeek
- Department of Gynaecology and Obstetrics, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, GA, 6525, The Netherlands
| | - Mhd van Bommel
- Department of Gynaecology and Obstetrics, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, GA, 6525, The Netherlands
| | - J IntHout
- Department of IQ Health, Radboudumc, Kapittelweg 54, Nijmegen, EP, 6525, The Netherlands
| | - C M Kets
- Department of Genetics, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, GA, 6525, The Netherlands
| | - Rpmg Hermens
- Department of IQ Health, Radboudumc, Kapittelweg 54, Nijmegen, EP, 6525, The Netherlands
| | - J A de Hullu
- Department of Gynaecology and Obstetrics, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, GA, 6525, The Netherlands
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21
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Nguyen NH, Dodd-Eaton EB, Corredor JL, Woodman-Ross J, Green S, Gutierrez AM, Arun BK, Wang W. Validating Risk Prediction Models for Multiple Primaries and Competing Cancer Outcomes in Families With Li-Fraumeni Syndrome Using Clinically Ascertained Data. J Clin Oncol 2024; 42:2186-2195. [PMID: 38569124 PMCID: PMC11191065 DOI: 10.1200/jco.23.01926] [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: 09/04/2023] [Revised: 12/02/2023] [Accepted: 02/07/2024] [Indexed: 04/05/2024] Open
Abstract
PURPOSE There exists a barrier between developing and disseminating risk prediction models in clinical settings. We hypothesize that this barrier may be lifted by demonstrating the utility of these models using incomplete data that are collected in real clinical sessions, as compared with the commonly used research cohorts that are meticulously collected. MATERIALS AND METHODS Genetic counselors (GCs) collect family history when patients (ie, probands) come to MD Anderson Cancer Center for risk assessment of Li-Fraumeni syndrome, a genetic disorder characterized by deleterious germline mutations in the TP53 gene. Our clinical counseling-based (CCB) cohort consists of 3,297 individuals across 124 families (522 cases of single primary cancer and 125 cases of multiple primary cancers). We applied our software suite LFSPRO to make risk predictions and assessed performance in discrimination using AUC and in calibration using observed/expected (O/E) ratio. RESULTS For prediction of deleterious TP53 mutations, we achieved an AUC of 0.78 (95% CI, 0.71 to 0.85) and an O/E ratio of 1.66 (95% CI, 1.53 to 1.80). Using the LFSPRO.MPC model to predict the onset of the second cancer, we obtained an AUC of 0.70 (95% CI, 0.58 to 0.82). Using the LFSPRO.CS model to predict the onset of different cancer types as the first primary, we achieved AUCs between 0.70 and 0.83 for sarcoma, breast cancer, or other cancers combined. CONCLUSION We describe a study that fills in the critical gap in knowledge for the utility of risk prediction models. Using a CCB cohort, our previously validated models have demonstrated good performance and outperformed the standard clinical criteria. Our study suggests that better risk counseling may be achieved by GCs using these already-developed mathematical models.
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Affiliation(s)
- Nam H. Nguyen
- The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computation Biology, Houston, TX
- Rice University, Department of Statistics, Houston, TX
| | - Elissa B. Dodd-Eaton
- The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computation Biology, Houston, TX
| | - Jessica L. Corredor
- The University of Texas MD Anderson Cancer Center, Department of Clinical Cancer Genetics, Houston, TX
| | - Jacynda Woodman-Ross
- The University of Texas MD Anderson Cancer Center, Department of Clinical Cancer Genetics, Houston, TX
| | - Sierra Green
- The University of Texas MD Anderson Cancer Center, Department of Clinical Cancer Genetics, Houston, TX
| | - Angelica M. Gutierrez
- The University of Texas MD Anderson Cancer Center, Department of Breast Medical Oncology, Houston, TX
| | - Banu K. Arun
- The University of Texas MD Anderson Cancer Center, Department of Clinical Cancer Genetics, Houston, TX
- The University of Texas MD Anderson Cancer Center, Department of Breast Medical Oncology, Houston, TX
| | - Wenyi Wang
- The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computation Biology, Houston, TX
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22
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Al-Shinnag M, Cheong PL, Goodwin A, Trent R, Yu B. Germline potential should not be overlooked for cancer variants identified in tumour-only somatic mutation testing. Pathology 2024; 56:468-472. [PMID: 38627125 DOI: 10.1016/j.pathol.2024.03.001] [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: 11/09/2023] [Revised: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 05/13/2024]
Abstract
DNA sequencing of tumour tissue has become the standard care for many solid cancers because of the option to detect somatic variants that have significant therapeutic, diagnostic and prognostic implications. Variants found within the tumour may be either somatic or germline in origin. Somatic cancer gene panels are developed to detect acquired (somatic) variants that are relevant for therapeutic or molecular characterisation of the tumour, expanding gene panels now include genes which may also inform patient management such as cancer predisposition syndromes (CPS) genes. Identifying germline cancer predisposition variants can alter cancer management, the risk of developing new primary cancers and risk for cancer in at-risk family members. This paper discusses the clinical, technical and ethical challenges related to identifying and reporting potential germline pathogenic variants that are detected on tumour sequencing. It also highlights the existence of the eviQ national guidelines for CPS with advice on germline confirmation of somatic findings to pathology laboratories in Australia.
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Affiliation(s)
- Mohammad Al-Shinnag
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown NSW, Australia; Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Camperdown, NSW, Australia; New South Wales Health Pathology (East), NSW, Australia; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
| | - Pak Leng Cheong
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown NSW, Australia; Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Camperdown, NSW, Australia; New South Wales Health Pathology (East), NSW, Australia; Central Clinical School, Faculty of Medicine and Health, the University of Sydney, NSW, Australia
| | - Annabel Goodwin
- Central Clinical School, Faculty of Medicine and Health, the University of Sydney, NSW, Australia; Department of Cancer Genetics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Medical Oncology, Concord Repatriation General Hospital, Concord, NSW, Australia
| | - Ronald Trent
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown NSW, Australia; Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Camperdown, NSW, Australia; New South Wales Health Pathology (East), NSW, Australia; Central Clinical School, Faculty of Medicine and Health, the University of Sydney, NSW, Australia
| | - Bing Yu
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown NSW, Australia; Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Camperdown, NSW, Australia; New South Wales Health Pathology (East), NSW, Australia; Central Clinical School, Faculty of Medicine and Health, the University of Sydney, NSW, Australia.
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23
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Tsoulaki O, Tischkowitz M, Antoniou AC, Musgrave H, Rea G, Gandhi A, Cox K, Irvine T, Holcombe S, Eccles D, Turnbull C, Cutress R, Archer S, Hanson H. Joint ABS-UKCGG-CanGene-CanVar consensus regarding the use of CanRisk in clinical practice. Br J Cancer 2024; 130:2027-2036. [PMID: 38834743 PMCID: PMC11183136 DOI: 10.1038/s41416-024-02733-4] [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: 03/06/2024] [Revised: 04/26/2024] [Accepted: 05/21/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND The CanRisk tool, which operationalises the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) is used by Clinical Geneticists, Genetic Counsellors, Breast Oncologists, Surgeons and Family History Nurses for breast cancer risk assessments both nationally and internationally. There are currently no guidelines with respect to the day-to-day clinical application of CanRisk and differing inputs to the model can result in different recommendations for practice. METHODS To address this gap, the UK Cancer Genetics Group in collaboration with the Association of Breast Surgery and the CanGene-CanVar programme held a workshop on 16th of May 2023, with the aim of establishing best practice guidelines. RESULTS Using a pre-workshop survey followed by structured discussion and in-meeting polling, we achieved consensus for UK best practice in use of CanRisk in making recommendations for breast cancer surveillance, eligibility for genetic testing and the input of available information to undertake an individualised risk assessment. CONCLUSIONS Whilst consensus recommendations were achieved, the meeting highlighted some of the barriers limiting the use of CanRisk in clinical practice and identified areas that require further work and collaboration with relevant national bodies and policy makers to incorporate wider use of CanRisk into routine breast cancer risk assessments.
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Affiliation(s)
- Olga Tsoulaki
- St George's University of London, London, UK
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, 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
| | - Hannah Musgrave
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Gillian Rea
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Ashu Gandhi
- Manchester University Hospitals; Manchester Breast Centre, Division of Cancer Sciences, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Karina Cox
- Maidstone and Tunbridge Wells NHS Trust, Maidstone, UK
| | | | | | - Diana Eccles
- Department of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Clare Turnbull
- Translational Genetics Team, Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Ramsey Cutress
- University of Southampton and University Hospital Southampton, Somers Research Building, Tremona Road, Southampton, UK
| | - Stephanie Archer
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Helen Hanson
- Translational Genetics Team, Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK.
- Faculty of Health and Life Sciences, University of Exeter Medical School, Exeter, UK.
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24
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Evans DG, Green K, Burghel GJ, Forde C, Lalloo F, Schlecht H, Woodward ER. Cascade screening in HBOC and Lynch syndrome: guidelines and procedures in a UK centre. Fam Cancer 2024; 23:187-195. [PMID: 38478259 PMCID: PMC11153258 DOI: 10.1007/s10689-024-00360-9] [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: 10/18/2023] [Accepted: 01/25/2024] [Indexed: 06/06/2024]
Abstract
In the 33 years since the first diagnostic cancer predisposition gene (CPG) tests in the Manchester Centre for Genomic Medicine, there has been substantial changes in the identification of index cases and cascade testing for at-risk family members. National guidelines in England and Wales are usually determined from the National Institute of healthcare Evidence and these have impacted on the thresholds for testing BRCA1/2 in Hereditary Breast Ovarian Cancer (HBOC) and in determining that all cases of colorectal and endometrial cancer should undergo screening for Lynch syndrome. Gaps for testing other CPGs relevant to HBOC have been filled by the UK Cancer Genetics Group and CanGene-CanVar project (web ref. https://www.cangene-canvaruk.org/ ). We present time trends (1990-2020) of identification of index cases with germline CPG variants and numbers of subsequent cascade tests, for BRCA1, BRCA2, and the Lynch genes (MLH1, MSH2, MSH6 and PMS2). For BRCA1/2 there was a definite increase in the proportion of index cases with ovarian cancer only and pre-symptomatic index tests both doubling from 16 to 32% and 3.2 to > 8% respectively. A mean of 1.73-1.74 additional family tests were generated for each BRCA1/2 index case within 2 years. Overall close to one positive cascade test was generated per index case resulting in > 1000 risk reducing surgery operations. In Lynch syndrome slightly more cascade tests were performed in the first two years potentially reflecting the increased actionability in males with 42.2% of pre-symptomatic tests in males compared to 25.8% in BRCA1/2 (p < 0.0001).
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Affiliation(s)
- D Gareth Evans
- Manchester Centre for Genomic Medicine and North-West Genomics Hub, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK.
- Division of Evolution Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, M13 9PL, UK.
| | - Kate Green
- Manchester Centre for Genomic Medicine and North-West Genomics Hub, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine and North-West Genomics Hub, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Claire Forde
- Manchester Centre for Genomic Medicine and North-West Genomics Hub, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine and North-West Genomics Hub, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine and North-West Genomics Hub, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine and North-West Genomics Hub, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
- Division of Evolution Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, M13 9PL, UK
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25
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Walker MJ, Blackmore KM, Chang A, Lambert-Côté L, Turgeon A, Antoniou AC, Bell KA, Broeders MJM, Brooks JD, Carver T, Chiquette J, Després P, Easton DF, Eisen A, Eloy L, Evans DG, Fienberg S, Joly Y, Kim RH, Kim SJ, Knoppers BM, Lofters AK, Nabi H, Paquette JS, Pashayan N, Sheppard AJ, Stockley TL, Dorval M, Simard J, Chiarelli AM. Implementing Multifactorial Risk Assessment with Polygenic Risk Scores for Personalized Breast Cancer Screening in the Population Setting: Challenges and Opportunities. Cancers (Basel) 2024; 16:2116. [PMID: 38893236 PMCID: PMC11171515 DOI: 10.3390/cancers16112116] [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: 04/12/2024] [Revised: 05/11/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
Risk-stratified breast screening has been proposed as a strategy to overcome the limitations of age-based screening. A prospective cohort study was undertaken within the PERSPECTIVE I&I project, which will generate the first Canadian evidence on multifactorial breast cancer risk assessment in the population setting to inform the implementation of risk-stratified screening. Recruited females aged 40-69 unaffected by breast cancer, with a previous mammogram, underwent multifactorial breast cancer risk assessment. The adoption of multifactorial risk assessment, the effectiveness of methods for collecting risk factor information and the costs of risk assessment were examined. Associations between participant characteristics and study sites, as well as data collection methods, were assessed using logistic regression; all p-values are two-sided. Of the 4246 participants recruited, 88.4% completed a risk assessment, with 79.8%, 15.7% and 4.4% estimated at average, higher than average and high risk, respectively. The total per-participant cost for risk assessment was CAD 315. Participants who chose to provide risk factor information on paper/telephone (27.2%) vs. online were more likely to be older (p = 0.021), not born in Canada (p = 0.043), visible minorities (p = 0.01) and have a lower attained education (p < 0.0001) and perceived fair/poor health (p < 0.001). The 34.4% of participants requiring risk factor verification for missing/unusual values were more likely to be visible minorities (p = 0.009) and have a lower attained education (p ≤ 0.006). This study demonstrates the feasibility of risk assessment for risk-stratified screening at the population level. Implementation should incorporate an equity lens to ensure cancer-screening disparities are not widened.
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Affiliation(s)
- Meghan J. Walker
- Ontario Health (Cancer Care Ontario), Toronto, ON M5G 2L3, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A1, Canada
| | | | - Amy Chang
- Ontario Health (Cancer Care Ontario), Toronto, ON M5G 2L3, Canada
| | | | - Annie Turgeon
- CHU de Québec-Université Laval Research Center, Queébec City, QC G1V 4G2, Canada
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kathleen A. Bell
- Ontario Health (Cancer Care Ontario), Toronto, ON M5G 2L3, Canada
| | - Mireille J. M. Broeders
- Department for Health Evidence, Radboud University Medical Center, 6525EP Nijmegen, The Netherlands
| | - Jennifer D. Brooks
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Tim Carver
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jocelyne Chiquette
- CHU de Québec-Université Laval Research Center, Queébec City, QC G1V 4G2, Canada
- Department of Family Medicine and Emergency Medicine, Faculty of Medicine, Université Laval, Québec City, QC G1V 0A6, Canada;
| | - Philippe Després
- Department of Physics, Engineering Physics and Optics, Faculty of Science and Engineering, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge CB1 8RN, UK
| | - Andrea Eisen
- Ontario Health (Cancer Care Ontario), Toronto, ON M5G 2L3, Canada
- Sunnybrook Health Science Center, Toronto, ON M4N 3M5, Canada
| | - Laurence Eloy
- Québec Cancer Program, Ministère de la Santé et des Services Sociaux, Quebec City, QC G1S 2M1, Canada
| | - D. Gareth Evans
- Division of Evolution Infection and Genomic Sciences, The University of Manchester, Manchester M13 9PL, UK
| | | | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montreal, QC H3A 0G1, Canada
| | - Raymond H. Kim
- Ontario Health (Cancer Care Ontario), Toronto, ON M5G 2L3, Canada
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Shana J. Kim
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Bartha M. Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, QC H3A 0G1, Canada
| | - Aisha K. Lofters
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A1, Canada
- Women’s College Research Institute, Toronto, ON M5G 1N8, Canada
| | - Hermann Nabi
- CHU de Québec-Université Laval Research Center, Queébec City, QC G1V 4G2, Canada
- Department of Social and Preventive Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Université Laval Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Jean-Sébastien Paquette
- Department of Family Medicine and Emergency Medicine, Faculty of Medicine, Université Laval, Québec City, QC G1V 0A6, Canada;
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Applied Health Research, Institute of Epidemiology and Healthcare, University College London, London WC1E 6BT, UK
| | - Amanda J. Sheppard
- Ontario Health (Cancer Care Ontario), Toronto, ON M5G 2L3, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Tracy L. Stockley
- Division of Clinical Laboratory Genetics, University Health Network, Toronto, ON M5G 2C4, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michel Dorval
- CHU de Québec-Université Laval Research Center, Queébec City, QC G1V 4G2, Canada
- Université Laval Cancer Research Center, Quebec City, QC G1R 3S3, Canada
- Faculty of Pharmacy, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Jacques Simard
- CHU de Québec-Université Laval Research Center, Queébec City, QC G1V 4G2, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada
| | - Anna M. Chiarelli
- Ontario Health (Cancer Care Ontario), Toronto, ON M5G 2L3, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A1, Canada
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26
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Yang DW, Miller JA, Xue WQ, Tang M, Lei L, Zheng Y, Diao H, Wang TM, Liao Y, Wu YX, Zheng XH, Zhou T, Li XZ, Zhang PF, Chen XY, Yu X, Li F, Ji M, Sun Y, He YQ, Jia WH. Polygenic risk-stratified screening for nasopharyngeal carcinoma in high-risk endemic areas of China: a cost-effectiveness study. Front Public Health 2024; 12:1375533. [PMID: 38756891 PMCID: PMC11097958 DOI: 10.3389/fpubh.2024.1375533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Background Nasopharyngeal carcinoma (NPC) has an extremely high incidence rate in Southern China, resulting in a severe disease burden for the local population. Current EBV serologic screening is limited by false positives, and there is opportunity to integrate polygenic risk scores for personalized screening which may enhance cost-effectiveness and resource utilization. Methods A Markov model was developed based on epidemiological and genetic data specific to endemic areas of China, and further compared polygenic risk-stratified screening [subjects with a 10-year absolute risk (AR) greater than a threshold risk underwent EBV serological screening] to age-based screening (EBV serological screening for all subjects). For each initial screening age (30-34, 35-39, 40-44, 45-49, 50-54, 55-59, 60-64, and 65-69 years), a modeled cohort of 100,000 participants was screened until age 69, and then followed until age 79. Results Among subjects aged 30 to 54 years, polygenic risk-stratified screening strategies were more cost-effective than age-based screening strategies, and almost comprised the cost-effectiveness efficiency frontier. For men, screening strategies with a 1-year frequency and a 10-year absolute risk (AR) threshold of 0.7% or higher were cost-effective, with an incremental cost-effectiveness ratio (ICER) below the willingness to pay (¥203,810, twice the local per capita GDP). Specifically, the strategies with a 10-year AR threshold of 0.7% or 0.8% are the most cost-effective strategies, with an ICER ranging from ¥159,752 to ¥201,738 compared to lower-cost non-dominated strategies on the cost-effectiveness frontiers. The optimal strategies have a higher probability (29.4-35.8%) of being cost-effective compared to other strategies on the frontier. Additionally, they reduce the need for nasopharyngoscopies by 5.1-27.7% compared to optimal age-based strategies. Likewise, for women aged 30-54 years, the optimal strategy with a 0.3% threshold showed similar results. Among subjects aged 55 to 69 years, age-based screening strategies were more cost-effective for men, while no screening may be preferred for women. Conclusion Our economic evaluation found that the polygenic risk-stratified screening could improve the cost-effectiveness among individuals aged 30-54, providing valuable guidance for NPC prevention and control policies in endemic areas of China.
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Affiliation(s)
- Da-Wei Yang
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jacob A. Miller
- Department of Radiation Oncology, Cleveland Clinic, Cleveland, OH, United States
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | | | - Lin Lei
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Yuming Zheng
- Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
| | - Hua Diao
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xue-Yin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xia Yu
- Cancer Research Institute of Zhongshan City, Zhongshan Hospital of Sun Yat-sen University, Zhongshan, China
| | - Fugui Li
- Cancer Research Institute of Zhongshan City, Zhongshan Hospital of Sun Yat-sen University, Zhongshan, China
| | - Mingfang Ji
- Cancer Research Institute of Zhongshan City, Zhongshan Hospital of Sun Yat-sen University, Zhongshan, China
| | - Ying Sun
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei-Hua Jia
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
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27
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Rahman I, Barwell J. Genomic medicine for the 21 st century. Ann R Coll Surg Engl 2024; 106:295-299. [PMID: 38555870 PMCID: PMC10981982 DOI: 10.1308/rcsann.2024.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024] Open
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28
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Schwarzerova J, Hurta M, Barton V, Lexa M, Walther D, Provaznik V, Weckwerth W. A perspective on genetic and polygenic risk scores-advances and limitations and overview of associated tools. Brief Bioinform 2024; 25:bbae240. [PMID: 38770718 PMCID: PMC11106636 DOI: 10.1093/bib/bbae240] [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: 10/03/2023] [Revised: 04/14/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Polygenetic Risk Scores are used to evaluate an individual's vulnerability to developing specific diseases or conditions based on their genetic composition, by taking into account numerous genetic variations. This article provides an overview of the concept of Polygenic Risk Scores (PRS). We elucidate the historical advancements of PRS, their advantages and shortcomings in comparison with other predictive methods, and discuss their conceptual limitations in light of the complexity of biological systems. Furthermore, we provide a survey of published tools for computing PRS and associated resources. The various tools and software packages are categorized based on their technical utility for users or prospective developers. Understanding the array of available tools and their limitations is crucial for accurately assessing and predicting disease risks, facilitating early interventions, and guiding personalized healthcare decisions. Additionally, we also identify potential new avenues for future bioinformatic analyzes and advancements related to PRS.
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Affiliation(s)
- Jana Schwarzerova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 10, Brno 61600, Czechia
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna 1010, Austria
| | - Martin Hurta
- Department of Computer Systems, Faculty of Information Technology, Brno University of Technology, Brno 612 00, Czechia
| | - Vojtech Barton
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 10, Brno 61600, Czechia
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno 62500, Czech Republic
| | - Matej Lexa
- Faculty of Informatics, Masaryk University, Botanicka 68a, Brno 60200, Czech Republic
| | - Dirk Walther
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Valentine Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 10, Brno 61600, Czechia
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna 1010, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna 1010, Austria
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29
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Irelli A, Patruno LV, Chiatamone Ranieri S, Di Giacomo D, Malatesta S, Alesse E, Tessitore A, Cannita K. Role of Breast Cancer Risk Estimation Models to Identify Women Eligible for Genetic Testing and Risk-Reducing Surgery. Biomedicines 2024; 12:714. [PMID: 38672070 PMCID: PMC11048717 DOI: 10.3390/biomedicines12040714] [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: 02/27/2024] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Hereditary breast and ovarian cancer (HBOC) syndrome is responsible for approximately 10% of breast cancers (BCs). The HBOC gene panel includes both high-risk genes, i.e., a four times higher risk of BC (BRCA1, BRCA2, PALB2, CDH1, PTEN, STK11 and TP53), and moderate-risk genes, i.e., a two to four times higher risk of BC (BARD1, CHEK2, RAD51C, RAD51D and ATM). Pathogenic germline variants (PGVs) in HBOC genes confer an absolute risk of BC that changes according to the gene considered. We illustrate and compare different BC risk estimation models, also describing their limitations. These models allow us to identify women eligible for genetic testing and possibly to offer surgical strategies for primary prevention, i.e., risk-reducing mastectomies and salpingo-oophorectomies.
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Affiliation(s)
- Azzurra Irelli
- Medical Oncology Unit, Department of Oncology, “Giuseppe Mazzini” Hospital, AUSL 04 Teramo, 64100 Teramo, Italy; (L.V.P.); (K.C.)
| | - Leonardo Valerio Patruno
- Medical Oncology Unit, Department of Oncology, “Giuseppe Mazzini” Hospital, AUSL 04 Teramo, 64100 Teramo, Italy; (L.V.P.); (K.C.)
| | - Sofia Chiatamone Ranieri
- Pathology Unit, Department of Services, AUSL 04 Teramo, 64100 Teramo, Italy; (S.C.R.); (D.D.G.); (S.M.)
| | - Daniela Di Giacomo
- Pathology Unit, Department of Services, AUSL 04 Teramo, 64100 Teramo, Italy; (S.C.R.); (D.D.G.); (S.M.)
| | - Sara Malatesta
- Pathology Unit, Department of Services, AUSL 04 Teramo, 64100 Teramo, Italy; (S.C.R.); (D.D.G.); (S.M.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (E.A.); (A.T.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (E.A.); (A.T.)
| | - Katia Cannita
- Medical Oncology Unit, Department of Oncology, “Giuseppe Mazzini” Hospital, AUSL 04 Teramo, 64100 Teramo, Italy; (L.V.P.); (K.C.)
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30
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Woodward ER, Lalloo F, Forde C, Pugh S, Burghel GJ, Schlecht H, Harkness EF, Howell A, Howell SJ, Gandhi A, Evans DG. Germline testing of BRCA1, BRCA2, PALB2 and CHEK2 c.1100delC in 1514 triple negative familial and isolated breast cancers from a single centre, with extended testing of ATM, RAD51C and RAD51D in over 400. J Med Genet 2024; 61:385-391. [PMID: 38123987 DOI: 10.1136/jmg-2023-109671] [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: 10/03/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The identification of germline pathogenic gene variants (PGVs) in triple negative breast cancer (TNBC) is important to inform further primary cancer risk reduction and TNBC treatment strategies. We therefore investigated the contribution of breast cancer associated PGVs to familial and isolated invasive TNBC. METHODS Outcomes of germline BRCA1, BRCA2 and CHEK2_c.1100delC testing were recorded in 1514 women (743-isolated, 771-familial), and for PALB2 in 846 women (541-isolated, 305-familial), with TNBC and smaller numbers for additional genes. Breast cancer free controls were identified from Predicting Risk Of Cancer At Screening and BRIDGES (Breast cancer RIsk after Diagnostic GEne Sequencing) studies. RESULTS BRCA1_PGVs were detected in 52 isolated (7.0%) and 195 (25.3%) familial cases (isolated-OR=58.9, 95% CI: 16.6 to 247.0), BRCA2_PGVs in 21 (2.8%) isolated and 67 (8.7%) familial cases (isolated-OR=5.0, 95% CI: 2.3 to 11.2), PALB2_PGVs in 9 (1.7%) isolated and 12 (3.9%) familial cases (isolated-OR=8.8, 95% CI: 2.5 to 30.4) and CHEK2_c.1100delC in 0 isolated and 3 (0.45%) familial cases (isolated-OR=0.0, 95% CI: 0.00 to 2.11). BRCA1_PGV detection rate was >10% for all familial TNBC age groups and significantly higher for younger diagnoses (familial: <50 years, n=165/538 (30.7%); ≥50 years, n=30/233 (12.9%); p<0.0001). Women with a G3_TNBC were more likely to have a BRCA1_PGV as compared with a BRCA2 or PALB2_PGV (p<0.0001). 0/743 isolated TNBC had the CHEK2_c.1100delC PGV and 0/305 any ATM_PGV, but 2/240 (0.83%) had a RAD51D_PGV. CONCLUSION PGVs in BRCA1 are associated with G3_TNBCs. Familial TNBCs and isolated TNBCs <30 years have a >10% likelihood of a PGV in BRCA1. BRCA1_PGVs are associated with younger age of familial TNBC. There was no evidence for any increased risk of TNBC with CHEK2 or ATM PGVs.
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Affiliation(s)
- Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- 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, UK
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Claire Forde
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Sarah Pugh
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Elaine F Harkness
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Anthony Howell
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
- Prevent Breast Cancer Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Sacha J Howell
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
- Prevent Breast Cancer Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Ashu Gandhi
- Prevent Breast Cancer Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- 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, UK
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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Hussain S, Ali M, Naseem U, Nezhadmoghadam F, Jatoi MA, Gulliver TA, Tamez-Peña JG. Breast cancer risk prediction using machine learning: a systematic review. Front Oncol 2024; 14:1343627. [PMID: 38571502 PMCID: PMC10987819 DOI: 10.3389/fonc.2024.1343627] [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: 11/23/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Background Breast cancer is the leading cause of cancer-related fatalities among women worldwide. Conventional screening and risk prediction models primarily rely on demographic and patient clinical history to devise policies and estimate likelihood. However, recent advancements in artificial intelligence (AI) techniques, particularly deep learning (DL), have shown promise in the development of personalized risk models. These models leverage individual patient information obtained from medical imaging and associated reports. In this systematic review, we thoroughly investigated the existing literature on the application of DL to digital mammography, radiomics, genomics, and clinical information for breast cancer risk assessment. We critically analyzed these studies and discussed their findings, highlighting the promising prospects of DL techniques for breast cancer risk prediction. Additionally, we explored ongoing research initiatives and potential future applications of AI-driven approaches to further improve breast cancer risk prediction, thereby facilitating more effective screening and personalized risk management strategies. Objective and methods This study presents a comprehensive overview of imaging and non-imaging features used in breast cancer risk prediction using traditional and AI models. The features reviewed in this study included imaging, radiomics, genomics, and clinical features. Furthermore, this survey systematically presented DL methods developed for breast cancer risk prediction, aiming to be useful for both beginners and advanced-level researchers. Results A total of 600 articles were identified, 20 of which met the set criteria and were selected. Parallel benchmarking of DL models, along with natural language processing (NLP) applied to imaging and non-imaging features, could allow clinicians and researchers to gain greater awareness as they consider the clinical deployment or development of new models. This review provides a comprehensive guide for understanding the current status of breast cancer risk assessment using AI. Conclusion This study offers investigators a different perspective on the use of AI for breast cancer risk prediction, incorporating numerous imaging and non-imaging features.
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Affiliation(s)
- Sadam Hussain
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
- Department of Electrical and Computer Engineering, University of Victoria, Victoria, BC, Canada
| | - Mansoor Ali
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Usman Naseem
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | | | - Munsif Ali Jatoi
- Department of Biomedical Engineering, Salim Habib University, Karachi, Pakistan
| | - T. Aaron Gulliver
- Department of Electrical and Computer Engineering, University of Victoria, Victoria, BC, Canada
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Riess O, Sturm M, Menden B, Liebmann A, Demidov G, Witt D, Casadei N, Admard J, Schütz L, Ossowski S, Taylor S, Schaffer S, Schroeder C, Dufke A, Haack T. Genomes in clinical care. NPJ Genom Med 2024; 9:20. [PMID: 38485733 PMCID: PMC10940576 DOI: 10.1038/s41525-024-00402-2] [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: 09/01/2023] [Accepted: 02/07/2024] [Indexed: 03/18/2024] Open
Abstract
In the era of precision medicine, genome sequencing (GS) has become more affordable and the importance of genomics and multi-omics in clinical care is increasingly being recognized. However, how to scale and effectively implement GS on an institutional level remains a challenge for many. Here, we present Genome First and Ge-Med, two clinical implementation studies focused on identifying the key pillars and processes that are required to make routine GS and predictive genomics a reality in the clinical setting. We describe our experience and lessons learned for a variety of topics including test logistics, patient care processes, data reporting, and infrastructure. Our model of providing clinical care and comprehensive genomic analysis from a single source may be used by other centers with a similar structure to facilitate the implementation of omics-based personalized health concepts in medicine.
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Affiliation(s)
- Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- NGS Competence Center Tübingen, University of Tübingen, Tübingen, Germany.
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany.
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Benita Menden
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Alexandra Liebmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Dennis Witt
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Leon Schütz
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | | | | | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany
| | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany
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Rodriguez J, Grassmann F, Xiao Q, Eriksson M, Mao X, Bajalica-Lagercrantz S, Hall P, Czene K. Investigation of Genetic Alterations Associated With Interval Breast Cancer. JAMA Oncol 2024; 10:372-379. [PMID: 38270937 PMCID: PMC10811589 DOI: 10.1001/jamaoncol.2023.6287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/16/2023] [Indexed: 01/26/2024]
Abstract
Importance Breast cancers (BCs) diagnosed between 2 screening examinations are called interval cancers (ICs), and they have worse clinicopathological characteristics and poorer prognosis than screen-detected cancers (SDCs). However, the association of rare germline genetic variants with IC have not been studied. Objective To evaluate whether rare germline deleterious protein-truncating variants (PTVs) can be applied to discriminate between IC and SDC while considering mammographic density. Design, Setting, and Participants This population-based genetic association study was based on women aged 40 to 76 years who were attending mammographic screening in Sweden. All women with a diagnosis of BC between January 2001 and January 2016 were included, together with age-matched controls. Patients with BC were followed up for survival until 2021. Statistical analysis was performed from September 2021 to December 2022. Exposure Germline PTVs in 34 BC susceptibility genes as analyzed by targeted sequencing. Main Outcomes and Measures Odds ratios (ORs) were used to compare IC with SDC using logistic regression. Hazard ratios were used to investigate BC-specific survival using Cox regression. Results All 4121 patients with BC (IC, n = 1229; SDC, n = 2892) were female, with a mean (SD) age of 55.5 (7.1) years. There were 5631 age-matched controls. The PTVs of the ATM, BRCA1, BRCA2, CHEK2, and PALB2 genes were more common in patients with IC compared with SDC (OR, 1.48; 95% CI, 1.06-2.05). This association was primarily influenced by BRCA1/2 and PALB2 variants. A family history of BC together with PTVs of any of these genes synergistically increased the probability of receiving a diagnosis of IC rather than SDC (OR, 3.95; 95% CI, 1.97-7.92). Furthermore, 10-year BC-specific survival revealed that if a patient received a diagnosis of an IC, carriers of PTVs in any of these 5 genes had significantly worse survival compared with patients not carrying any of them (hazard ratio, 2.04; 95% CI, 1.06-3.92). All of these associations were further pronounced in a subset of patients with IC who had a low mammographic density at prior screening examination. Conclusions and Relevance The results of this study may be helpful in future optimizations of screening programs that aim to lower mortality as well as the clinical treatment of patients with BC.
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Affiliation(s)
- Juan Rodriguez
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Health and Medical University, Potsdam, Germany
| | - Qingyang Xiao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Xinhe Mao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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Schwartz M, Ibadioune S, Chansavang A, Vacher S, Caputo SM, Delhomelle H, Wong J, Abidallah K, Moncoutier V, Becette V, Popova T, Suybeng V, De Pauw A, Stern MH, Colas C, Mouret-Fourme E, Stoppa-Lyonnet D, Golmard L, Bieche I, Masliah-Planchon J. Mosaic BRCA1 promoter methylation contribution in hereditary breast/ovarian cancer pedigrees. J Med Genet 2024; 61:284-288. [PMID: 37748860 DOI: 10.1136/jmg-2023-109325] [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] [Received: 04/07/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
PURPOSE Mosaic BRCA1 promoter methylation (BRCA1meth) increases the risk of early-onset breast cancer, triple-negative breast cancer and ovarian cancer. As mosaic BRCA1meth are believed to occur de novo, their role in family breast/ovarian cancer has not been assessed. PATIENTS Blood-derived DNA from 20 unrelated affected cases from families with aggregation of breast/ovarian cancer, but with no germline pathogenic variants in BRCA1/2, PALB2 or RAD51C/D, were screened by methylation-sensitive high-resolution melting. CpG analysis was performed by pyrosequencing on blood and buccal swab. Two probands carried a pathogenic variant in a moderate-penetrance gene (ATM and BARD1), and 8 of 18 others (44%) carried BRCA1meth (vs none of the 20 age-matched controls). Involvement of BRCA1 in tumourigenesis in methylated probands was demonstrated in most tested cases by detection of a loss of heterozygosity and a homologous recombination deficiency signature. Among the eight methylated probands, two had relatives with breast cancer with detectable BRCA1meth in blood, including one with high methylation levels in two non-tumour tissues. CONCLUSIONS The high prevalence of mosaic BRCA1meth in patients with breast/ovarian cancer with affected relatives, as well as this first description of a family aggregation of mosaic BRCA1meth, shows how this de novo event can contribute to hereditary breast/ovarian cancer pedigrees.
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Affiliation(s)
- Mathias Schwartz
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- UMR3244, Curie Institute, Paris, France
| | - Sabrina Ibadioune
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Albain Chansavang
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Sophie Vacher
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Sandrine M Caputo
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Hélène Delhomelle
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Jennifer Wong
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Khadija Abidallah
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Virginie Moncoutier
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Véronique Becette
- Paris Sciences & Lettres Research University, Paris, France
- Department of Pathology, Curie Institute, Saint-Cloud, France
| | - Tatiana Popova
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Voreak Suybeng
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Antoine De Pauw
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Marc-Henri Stern
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Chrystelle Colas
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Emmanuelle Mouret-Fourme
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Université de Paris Cité, Paris, France
| | - Lisa Golmard
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Ivan Bieche
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Université de Paris Cité, Paris, France
| | - Julien Masliah-Planchon
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
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Xiang R, Kelemen M, Xu Y, Harris LW, Parkinson H, Inouye M, Lambert SA. Recent advances in polygenic scores: translation, equitability, methods and FAIR tools. Genome Med 2024; 16:33. [PMID: 38373998 PMCID: PMC10875792 DOI: 10.1186/s13073-024-01304-9] [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: 06/09/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
Polygenic scores (PGS) can be used for risk stratification by quantifying individuals' genetic predisposition to disease, and many potentially clinically useful applications have been proposed. Here, we review the latest potential benefits of PGS in the clinic and challenges to implementation. PGS could augment risk stratification through combined use with traditional risk factors (demographics, disease-specific risk factors, family history, etc.), to support diagnostic pathways, to predict groups with therapeutic benefits, and to increase the efficiency of clinical trials. However, there exist challenges to maximizing the clinical utility of PGS, including FAIR (Findable, Accessible, Interoperable, and Reusable) use and standardized sharing of the genomic data needed to develop and recalculate PGS, the equitable performance of PGS across populations and ancestries, the generation of robust and reproducible PGS calculations, and the responsible communication and interpretation of results. We outline how these challenges may be overcome analytically and with more diverse data as well as highlight sustained community efforts to achieve equitable, impactful, and responsible use of PGS in healthcare.
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Affiliation(s)
- Ruidong Xiang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Martin Kelemen
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Yu Xu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Laura W Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
| | - Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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36
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Yiangou K, Mavaddat N, Dennis J, Zanti M, Wang Q, Bolla MK, Abubakar M, Ahearn TU, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Augustinsson A, Baten A, Behrens S, Bermisheva M, de Gonzalez AB, Białkowska K, Boddicker N, Bodelon C, Bogdanova NV, Bojesen SE, Brantley KD, Brauch H, Brenner H, Camp NJ, Canzian F, Castelao JE, Cessna MH, Chang-Claude J, Chenevix-Trench G, Chung WK, Colonna SV, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Devilee P, Dörk T, Dunning AM, Eccles DM, Eliassen AH, Engel C, Eriksson M, Evans DG, Fasching PA, Fletcher O, Flyger H, Fritschi L, Gago-Dominguez M, Gentry-Maharaj A, González-Neira A, Guénel P, Hahnen E, Haiman CA, Hamann U, Hartikainen JM, Ho V, Hodge J, Hollestelle A, Honisch E, Hooning MJ, Hoppe R, Hopper JL, Howell S, Howell A, Jakovchevska S, Jakubowska A, Jernström H, Johnson N, Kaaks R, Khusnutdinova EK, Kitahara CM, Koutros S, Kristensen VN, Lacey JV, Lambrechts D, Lejbkowicz F, Lindblom A, Lush M, Mannermaa A, Mavroudis D, Menon U, Murphy RA, Nevanlinna H, Obi N, Offit K, Park-Simon TW, Patel AV, Peng C, Peterlongo P, Pita G, Plaseska-Karanfilska D, Pylkäs K, Radice P, Rashid MU, Rennert G, Roberts E, Rodriguez J, Romero A, Rosenberg EH, Saloustros E, Sandler DP, Sawyer EJ, Schmutzler RK, Scott CG, Shu XO, Southey MC, Stone J, Taylor JA, Teras LR, van de Beek I, Willett W, Winqvist R, Zheng W, Vachon CM, Schmidt MK, Hall P, MacInnis RJ, Milne RL, Pharoah PD, Simard J, Antoniou AC, Easton DF, Michailidou K. Differences in polygenic score distributions in European ancestry populations: implications for breast cancer risk prediction. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.12.24302043. [PMID: 38410445 PMCID: PMC10896416 DOI: 10.1101/2024.02.12.24302043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The 313-variant polygenic risk score (PRS313) provides a promising tool for breast cancer risk prediction. However, evaluation of the PRS313 across different European populations which could influence risk estimation has not been performed. Here, we explored the distribution of PRS313 across European populations using genotype data from 94,072 females without breast cancer, of European-ancestry from 21 countries participating in the Breast Cancer Association Consortium (BCAC) and 225,105 female participants from the UK Biobank. The mean PRS313 differed markedly across European countries, being highest in south-eastern Europe and lowest in north-western Europe. Using the overall European PRS313 distribution to categorise individuals leads to overestimation and underestimation of risk in some individuals from south-eastern and north-western countries, respectively. Adjustment for principal components explained most of the observed heterogeneity in mean PRS. Country-specific PRS distributions may be used to calibrate risk categories in individuals from different countries.
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Affiliation(s)
- Kristia Yiangou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus, 2371
| | - Nasim Mavaddat
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Maria Zanti
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus, 2371
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA, 20850
| | - Thomas U. Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA, 20850
| | - Irene L. Andrulis
- Fred A, Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA, 92617
| | - Natalia N. Antonenkova
- NN Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus, 223040
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Kristan J. Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen’s University, Kingston, ON, Canada, K7L 3N6
| | | | - Adinda Baten
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium, 3000
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
- St Petersburg State University, St, Petersburg, Russia, 199034
| | | | - Katarzyna Białkowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland, 71-252
| | - Nicholas Boddicker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA, 55905
| | - Clara Bodelon
- Department of Population Science, American Cancer Society, Atlanta, GA, USA, 30303
| | - Natalia V. Bogdanova
- NN Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus, 223040
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany, 30625
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany, 30625
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark, 2730
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark, 2730
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, 2200
| | - Kristen D. Brantley
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA, 02115
| | - Hiltrud Brauch
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, 70376
- iFIT-Cluster of Excellence, University of Tübingen, Tübingen, Germany, 72074
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany, 72074
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany, 69120
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Nicola J. Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA, 84112
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Jose E. Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS) Foundation, Complejo Hospitalario Universitario de Santiago, SERGAS, Vigo, Spain, 36312
| | - Melissa H. Cessna
- Department of Pathology, Intermountain Healthcare, Salt Lake City, UT, USA, 84143
- Intermountain Biorepository, Intermountain Healthcare, Salt Lake City, UT, USA, 84143
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, 20246
| | - Georgia Chenevix-Trench
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia, 4006
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA, 10032
| | - NBCS Collaborators
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway, 0379
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway, 0450
- Department of Research, Vestre Viken Hospital, Drammen, Norway, 3019
- Section for Breast- and Endocrine Surgery, Department of Cancer, Division of Surgery, Cancer and Transplantation Medicine, Oslo University Hospital-Ullevål, Oslo, Norway, 0450
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway, 0379
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway, 1478
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, 0379
- Department of Oncology, Division of Surgery, Cancer and Transplantation Medicine, Oslo University Hospital-Radiumhospitalet, Oslo, Norway, 0379
- National Advisory Unit on Late Effects after Cancer Treatment, Oslo University Hospital, Oslo, Norway, 0379
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway, 1478
- Oslo Breast Cancer Research Consortium, Oslo University Hospital, Oslo, Norway, 0379
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway, 0379
| | - Sarah V. Colonna
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA, 84112
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA, 55905
| | - Angela Cox
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK, S10 2TN
| | - Simon S. Cross
- Division of Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, UK, S10 2TN
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 171 65
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA, 19111
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands, 2333 ZA
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands, 2333 ZA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany, 30625
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Diana M. Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK, SO17 1BJ
| | - A. Heather Eliassen
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA, 02115
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA, 02115
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA, 02115
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany, 04107
- LIFE - Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany, 04103
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 171 65
| | - D. Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK, M13 9WL
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK, M13 9WL
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany, 91054
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK, SW7 3RP
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark, 2730
| | - Lin Fritschi
- School of Population Health, Curtin University, Perth, Western Australia, Australia, 6102
| | - Manuela Gago-Dominguez
- Cancer Genetics and Epidemiology Group, Genomic Medicine Group, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain, 15706
| | - Aleksandra Gentry-Maharaj
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK, WC1V 6LJ
- Department of Women’s Cancer, Elizabeth Garrett Anderson Institute for Women’s Health, University College London, London, UK
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain, 28029
- Spanish Network on Rare Diseases (CIBERER)
| | - Pascal Guénel
- Team ‘Exposome and Heredity’, CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France, 94805
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, 50937
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, 50937
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA, 90033
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Jaana M. Hartikainen
- Cancer RC, University of Eastern Finland, Kuopio, Finland, 70210
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland, 70210
| | - Vikki Ho
- Health Innovation and Evaluation Hub, Université de Montréal Hospital Research Centre (CRCHUM), Montréal, Québec, Canada
| | - James Hodge
- Department of Population Science, American Cancer Society, Atlanta, GA, USA, 30303
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands, 3015 GD
| | - Ellen Honisch
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany, 40225
| | - Maartje J. Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands, 3015 GD
| | - Reiner Hoppe
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, 70376
- University of Tübingen, Tübingen, Germany, 72074
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia, 3010
| | - Sacha Howell
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Nightingale/Prevent Breast Cancer Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Breast Centre, Manchester Cancer Research Centre, The Christie Hospital, Manchester, UK
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK, M13 9PL
| | - ABCTB Investigators
- Australian Breast Cancer Tissue Bank, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia, 2145
| | - kConFab Investigators
- Research Department, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia, 3000
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia, 3000
| | - Simona Jakovchevska
- Research Centre for Genetic Engineering and Biotechnology ‘Georgi D, Efremov’, MASA, Skopje, Republic of North Macedonia, 1000
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland, 71-252
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland, 171-252
| | - Helena Jernström
- Oncology, Clinical Sciences in Lund, Lund University, Lund, Sweden, 221 85
| | - Nichola Johnson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK, SW7 3RP
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
| | - Elza K. Khusnutdinova
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
- Department of Genetics and Fundamental Medicine, Ufa University of Science and Technology, Ufa, Russia, 450076
| | - Cari M. Kitahara
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA, 20892
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA, 20850
| | - Vessela N. Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway, 0450
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway, 0379
| | - James V. Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA, 91010
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA, 91010
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, 3000
- VIB Center for Cancer Biology, VIB, Leuven, Belgium, 3001
| | | | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden, 171 76
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden, 171 76
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Arto Mannermaa
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland, 70210
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland, 70210
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece, 711 10
| | - Usha Menon
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK, WC1V 6LJ
| | - Rachel A. Murphy
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada, V5Z 1L3
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland, 00290
| | - Nadia Obi
- Institute for Occupational and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, 20246
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, 20246
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10065
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10065
| | | | - Alpa V. Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA, 30303
| | - Cheng Peng
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA, 02115
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy, 20139
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain, 28029
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology ‘Georgi D, Efremov’, MASA, Skopje, Republic of North Macedonia, 1000
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland, 90220
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland, 90220
| | - Paolo Radice
- Unit of Predictice Medicine, Molecular Bases of Genetic Risk, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy, 20133
| | - Muhammad U. Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany, 69120
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan, 54000
| | - Gad Rennert
- Technion, Faculty of Medicine and Association for Promotion of Research in Precision Medicine, Haifa, Israel
| | - Eleanor Roberts
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Juan Rodriguez
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 171 65
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain, 28222
| | - Efraim H. Rosenberg
- Department of Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands, 1066 CX
| | | | - Dale P. Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA, 27709
| | - Elinor J. Sawyer
- School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy’s Campus, King’s College London, London, UK
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, 50937
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, 50937
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, 50931
| | - Christopher G. Scott
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA, 55905
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA, 37232
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia, 3168
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia, 3010
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia, 3004
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia, 3010
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia, Perth, Western Australia, Australia, 6000
| | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA, 27709
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA, 27709
| | - Lauren R. Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA, 30303
| | - Irma van de Beek
- Department of Clinical Genetics, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands, 1066 CX
| | - Walter Willett
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA, 02115
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA, 02115
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA, 02115
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland, 90220
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland, 90220
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA, 37232
| | - Celine M. Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA, 55905
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands, 1066 CX
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands, 1066 CX
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands, 2333 ZA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 171 65
- Department of Oncology, Södersjukhuset, Stockholm, Sweden, 118 83
| | - Robert J. MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia, 3010
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia, 3004
| | - Roger L. Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia, 3010
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia, 3168
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia, 3004
| | - Paul D.P. Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA, 90069
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec – Université Laval Research Center, Québec City, Québec, Canada, G1V 4G2
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK, CB1 8RN
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus, 2371
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, CB1 8RN
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Tüchler A, De Pauw A, Ernst C, Anota A, Lakeman IMM, Dick J, van der Stoep N, van Asperen CJ, Maringa M, Herold N, Blümcke B, Remy R, Westerhoff A, Stommel-Jenner DJ, Frouin E, Richters L, Golmard L, Kütting N, Colas C, Wappenschmidt B, Rhiem K, Devilee P, Stoppa-Lyonnet D, Schmutzler RK, Hahnen E. Clinical implications of incorporating genetic and non-genetic risk factors in CanRisk-based breast cancer risk prediction. Breast 2024; 73:103615. [PMID: 38061307 PMCID: PMC10749276 DOI: 10.1016/j.breast.2023.103615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/28/2023] Open
Abstract
BACKGROUND Breast cancer (BC) risk prediction models consider cancer family history (FH) and germline pathogenic variants (PVs) in risk genes. It remains elusive to what extent complementation with polygenic risk score (PRS) and non-genetic risk factor (NGRFs) data affects individual intensified breast surveillance (IBS) recommendations according to European guidelines. METHODS For 425 cancer-free women with cancer FH (mean age 40·6 years, range 21-74), recruited in France, Germany and the Netherlands, germline PV status, NGRFs, and a 306 variant-based PRS (PRS306) were assessed to calculate estimated lifetime risks (eLTR) and estimated 10-year risks (e10YR) using CanRisk. The proportions of women changing country-specific European risk categories for IBS recommendations, i.e. ≥20 % and ≥30 % eLTR, or ≥5 % e10YR were determined. FINDINGS Of the women with non-informative PV status, including PRS306 and NGRFs changed clinical recommendations for 31·0 %, (57/184, 20 % eLTR), 15·8 % (29/184, 30 % eLTR) and 22·4 % (41/183, 5 % e10YR), respectively whereas of the women tested negative for a PV observed in their family, clinical recommendations changed for 16·7 % (25/150), 1·3 % (2/150) and 9·5 % (14/147). No change was observed for 82 women with PVs in high-risk genes (BRCA1/2, PALB2). Combined consideration of eLTRs and e10YRs identified BRCA1/2 PV carriers benefitting from IBS <30 years, and women tested non-informative/negative for whom IBS may be postponed. INTERPRETATION For women who tested non-informative/negative, PRS and NGRFs have a considerable impact on IBS recommendations. Combined consideration of eLTRs and e10YRs allows personalizing IBS starting age. FUNDING Horizon 2020, German Cancer Aid, Federal Ministry of Education and Research, Köln Fortune.
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Affiliation(s)
- Anja Tüchler
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Antoine De Pauw
- Institut Curie, Department of Genetics, Paris, France; Université PSL, Paris, France
| | - Corinna Ernst
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Amélie Anota
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France; Human and Social Sciences Department, Centre Léon Bérard, Lyon, France; French National Platform Quality of Life and Cancer, Centre Léon Bérard, Lyon, France
| | - Inge M M Lakeman
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Julia Dick
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Nienke van der Stoep
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Monika Maringa
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Natalie Herold
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Britta Blümcke
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Robert Remy
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Anke Westerhoff
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | | | - Eléonore Frouin
- Université PSL, Paris, France; Clinical Bioinformatics Unit, Institut Curie, Paris, France
| | - Lisa Richters
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Lisa Golmard
- Institut Curie, Department of Genetics, Paris, France; Université PSL, Paris, France
| | - Nadine Kütting
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Chrystelle Colas
- Institut Curie, Department of Genetics, Paris, France; Université PSL, Paris, France; Institut Curie, Inserm U830, Paris, France
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Kerstin Rhiem
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Department of Genetics, Paris, France; Institut Curie, Inserm U830, Paris, France; Université Paris Cité, Paris, France
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Eric Hahnen
- Center for Familial Breast and Ovarian and Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital of Cologne, Cologne, Germany.
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Schreurs MAC, Ramón Y Cajal T, Adank MA, Collée JM, Hollestelle A, van Rooij J, Schmidt MK, Hooning MJ. The benefit of adding polygenic risk scores, lifestyle factors, and breast density to family history and genetic status for breast cancer risk and surveillance classification of unaffected women from germline CHEK2 c.1100delC families. Breast 2024; 73:103611. [PMID: 38039887 PMCID: PMC10730863 DOI: 10.1016/j.breast.2023.103611] [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: 09/25/2023] [Revised: 11/13/2023] [Accepted: 11/18/2023] [Indexed: 12/03/2023] Open
Abstract
To determine the changes in surveillance category by adding a polygenic risk score based on 311 breast cancer (BC)-associated variants (PRS311), questionnaire-based risk factors and breast density on personalized BC risk in unaffected women from Dutch CHEK2 c.1100delC families. In total, 117 unaffected women (58 heterozygotes and 59 non-carriers) from CHEK2 families were included. Blood-derived DNA samples were genotyped with the GSAMDv3-array to determine PRS311. Lifetime BC risk was calculated in CanRisk, which uses data from the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA). Women, were categorized into three surveillance groups. The surveillance advice was reclassified in 37.9 % of heterozygotes and 32.2 % of non-carriers after adding PRS311. Including questionnaire-based risk factors resulted in an additional change in 20.0 % of heterozygotes and 13.2 % of non-carriers; and a subanalysis showed that adding breast density on top shifted another 17.9 % of heterozygotes and 33.3 % of non-carriers. Overall, the majority of heterozygotes were reclassified to a less intensive surveillance, while non-carriers would require intensified surveillance. The addition of PRS311, questionnaire-based risk factors and breast density to family history resulted in a more personalized BC surveillance advice in CHEK2-families, which may lead to more efficient use of surveillance.
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Affiliation(s)
- Maartje A C Schreurs
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Teresa Ramón Y Cajal
- Familial Cancer Clinic, Medical Oncology Service, Hospital Sant Pau, Barcelona, Spain
| | - Muriel A Adank
- Department of Clinical Genetics, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - J Margriet Collée
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Marjanka K Schmidt
- Division of Molecular Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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Hanson H, Astiazaran-Symonds E, Amendola LM, Balmaña J, Foulkes WD, James P, Klugman S, Ngeow J, Schmutzler R, Voian N, Wick MJ, Pal T, Tischkowitz M, Stewart DR. Response to Stern. Genet Med 2024; 26:101030. [PMID: 38156990 DOI: 10.1016/j.gim.2023.101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024] Open
Affiliation(s)
- Helen Hanson
- Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom; Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Esteban Astiazaran-Symonds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD; Department of Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ
| | | | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain; Medical Oncology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Hospital Campus, Barcelona, Spain
| | - William D Foulkes
- Departments of Human Genetics, Oncology and Medicine, McGill University, Montréal, Québec, Canada
| | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia; Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Susan Klugman
- Division of Reproductive & Medical Genetics, Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Joanne Ngeow
- Genomic Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Rita Schmutzler
- Center of Integrated Oncology (CIO), University of Cologne, Cologne, Germany; Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Nicoleta Voian
- Providence Genetic Risk Clinic, Providence Cancer Institute, Portland, OR
| | - Myra J Wick
- Departments of Obstetrics and Gynecology and Clinical Genomics, Mayo Clinic, Rochester, MN
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
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Valentini V, Bucalo A, Conti G, Celli L, Porzio V, Capalbo C, Silvestri V, Ottini L. Gender-Specific Genetic Predisposition to Breast Cancer: BRCA Genes and Beyond. Cancers (Basel) 2024; 16:579. [PMID: 38339330 PMCID: PMC10854694 DOI: 10.3390/cancers16030579] [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: 12/21/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Among neoplastic diseases, breast cancer (BC) is one of the most influenced by gender. Despite common misconceptions associating BC as a women-only disease, BC can also occur in men. Additionally, transgender individuals may also experience BC. Genetic risk factors play a relevant role in BC predisposition, with important implications in precision prevention and treatment. The genetic architecture of BC susceptibility is similar in women and men, with high-, moderate-, and low-penetrance risk variants; however, some sex-specific features have emerged. Inherited high-penetrance pathogenic variants (PVs) in BRCA1 and BRCA2 genes are the strongest BC genetic risk factor. BRCA1 and BRCA2 PVs are more commonly associated with increased risk of female and male BC, respectively. Notably, BRCA-associated BCs are characterized by sex-specific pathologic features. Recently, next-generation sequencing technologies have helped to provide more insights on the role of moderate-penetrance BC risk variants, particularly in PALB2, CHEK2, and ATM genes, while international collaborative genome-wide association studies have contributed evidence on common low-penetrance BC risk variants, on their combined effect in polygenic models, and on their role as risk modulators in BRCA1/2 PV carriers. Overall, all these studies suggested that the genetic basis of male BC, although similar, may differ from female BC. Evaluating the genetic component of male BC as a distinct entity from female BC is the first step to improve both personalized risk assessment and therapeutic choices of patients of both sexes in order to reach gender equality in BC care. In this review, we summarize the latest research in the field of BC genetic predisposition with a particular focus on similarities and differences in male and female BC, and we also discuss the implications, challenges, and open issues that surround the establishment of a gender-oriented clinical management for BC.
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Affiliation(s)
- Virginia Valentini
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Agostino Bucalo
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Giulia Conti
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Ludovica Celli
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Virginia Porzio
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Carlo Capalbo
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
- Medical Oncology Unit, Sant’Andrea University Hospital, 00189 Rome, Italy
| | - Valentina Silvestri
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
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Greenwood HI, Dodelzon K. Screening in Women With BRCA Mutations Revisited. JOURNAL OF BREAST IMAGING 2024; 6:4-13. [PMID: 38166173 DOI: 10.1093/jbi/wbad093] [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: 07/27/2023] [Indexed: 01/04/2024]
Abstract
Patients with BRCA1 or BRCA2 gene mutations are at high risk for the development of breast cancer. This article reviews the current evidence for breast cancer screening of patients with BRCA1 or BRCA2 pathogenic gene mutations if they have not undergone prophylactic mastectomy. It will review the current evidence-based imaging recommendations for different modalities and ages of screening initiation in screening this patient population at high risk. Special considerations in transgender BRCA1 and BRCA2 mutation carriers are also discussed.
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Affiliation(s)
- Heather I Greenwood
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Katerina Dodelzon
- Department of Radiology, Weill Cornell Medical College, New York, NY, USA
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Baliakas P, Munters AR, Kämpe A, Tesi B, Bondeson ML, Ladenvall C, Eriksson D. Integrating a Polygenic Risk Score into a clinical setting would impact risk predictions in familial breast cancer. J Med Genet 2024; 61:150-154. [PMID: 37580114 PMCID: PMC10850617 DOI: 10.1136/jmg-2023-109311] [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: 04/02/2023] [Accepted: 07/28/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND Low-impact genetic variants identified in population-based genetic studies are not routinely measured as part of clinical genetic testing in familial breast cancer (BC). We studied the consequences of integrating an established Polygenic Risk Score (PRS) (BCAC 313, PRS313) into clinical sequencing of women with familial BC in Sweden. METHODS We developed an add-on sequencing panel to capture 313 risk variants in addition to the clinical screening of hereditary BC genes. Index patients with no pathogenic variant from 87 families, and 1000 population controls, were included in comparative PRS calculations. Including detailed family history, sequencing results and tumour pathology information, we used BOADICEA (Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm) V.6 to estimate contralateral and lifetime risks without and with PRS313. RESULTS Women with BC but no pathogenic variants in hereditary BC genes have a higher PRS313 compared with population controls (mean+0.78 SD, p<3e-9). Implementing PRS313 in the clinical risk estimation before their BC diagnosis would have changed the recommended follow-up in 24%-45% of women. CONCLUSIONS Our results show the potential impact of incorporating PRS313 directly in the clinical genomic investigation of women with familial BC.
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Affiliation(s)
- Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arielle R Munters
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders Kämpe
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Bianca Tesi
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska Institutet, Stockholm, Sweden
| | - Marie-Louise Bondeson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Claes Ladenvall
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Daniel Eriksson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Akademiska Sjukhuset, Uppsala, Sweden
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Recchia G, Moser KS, Freeman AL. What Affects Perceived Trustworthiness of Online Medical Information and Subsequent Treatment Decision Making? Randomized Trials on the Role of Uncertainty and Institutional Cues. MDM Policy Pract 2024; 9:23814683241226660. [PMID: 38370149 PMCID: PMC10870812 DOI: 10.1177/23814683241226660] [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: 08/07/2023] [Accepted: 12/09/2023] [Indexed: 02/20/2024] Open
Abstract
Background. Online, algorithmically driven prognostic tools are increasingly important in medical decision making. Institutions developing such tools need to be able to communicate the precision and accuracy of the information in a trustworthy manner, and so many attempt to communicate uncertainties but also use institutional logos to underscore their trustworthiness. Bringing together theories on trust, uncertainty, and psychological distance in a novel way, we tested whether and how the communication of uncertainty and the presence of institutional logos together affected trust in medical information, the prognostic tool itself, and treatment decisions. Methods. A pilot and 2 online experiments in which UK (experiment 1) and worldwide (experiment 2) participants (Ntotal = 4,724) were randomized to 1 of 12 arms in a 3 (uncertainty cue) × 4 (institutional cue) between-subjects design. The stimulus was based on an existing medical prognostic tool. Results. Institutional trust was consistently associated with trust in the prognostic tool itself, while uncertainty information had no consistent effect. Institutional trust predicted the amount of weight participants reported placing on institutional endorsements in their decision making and the likelihood of switching from passive to active treatment in a hypothetical scenario. There was also a significant effect of psychological distance to (perceived hypotheticality of) the scenario. Conclusions/Implications. These results underline the importance of institutions demonstrating trustworthiness and building trust with their users. They also suggest that users tend to be insensitive to communications of uncertainty and that communicators may need to be highly explicit when attempting to warn of low precision or quality of evidence. The effect of the perceived hypotheticality of the scenario underscores the importance of realistic decision-making scenarios for studies and the role of familiarity with the decision dilemma generally. Highlights In a world where information for medical decision making is increasingly going to be provided through digital, online tools, institutions providing such tools need guidance on how best to communicate about their trustworthiness and precision.We find that people are fairly insensitive to cues designed to communicate uncertainty around the outputs of such tools. Even putting "ATTENTION" in bold font or explicitly pointing out the weaknesses in the data did not appear to affect people's decision making using the tool's outputs. Institutions should take note, and further work is required to determine how best to communicate uncertainty in a way that elicits appropriate caution in lay users.People were much more sensitive to institutional logos associated with the outputs. Generalized institutional trust (rather than trust in the specific institution whose logo was shown) was associated with how trustworthy, accurate, and reliable the tool, its algorithm, and the numbers it produced were perceived to be. This underscores the role of societal trust in institutions at large.Finally, as a note to researchers, we found a significant effect of how hypothetical or believable participants felt the experimental scenario was. This is a variable that seems rarely controlled for in studies and yet played as much of a role as some of our variables of interest, so we suggest that it is measured in future experiments.
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Affiliation(s)
- Gabriel Recchia
- Winton Centre for Risk & Evidence Communication, Department of Pure Maths and Mathematical Statistics, University of Cambridge, Cambridge, UK
| | - Karin S. Moser
- UniDistance Suisse, Faculty of Psychology, Brig, Switzerland
| | - Alexandra L.J. Freeman
- Winton Centre for Risk & Evidence Communication, Department of Pure Maths and Mathematical Statistics, University of Cambridge, Cambridge, UK
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Abu Shtaya A, Kedar I, Mattar S, Mahamid A, Basel-Salmon L, Farage Barhom S, Naftaly Nathan S, Magal N, Azulay N, Levy Zalcberg M, Chen-Shtoyerman R, Segol O, Seri M, Reznick Levi G, Shkedi-Rafid S, Vinkler C, Netzer I, Hagari Bechar O, Chamma L, Liberman S, Goldberg Y. The Diagnostic Yield and Implications of Targeted Founder Pathogenic Variant Testing in an Israeli Cohort. Cancers (Basel) 2023; 16:94. [PMID: 38201524 PMCID: PMC10777957 DOI: 10.3390/cancers16010094] [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: 11/10/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Founder pathogenic variants (PVs) are prevalent in Israel. This study investigated the current practice of offering cancer patients two-step genetic testing, starting with targeted testing for recurring founder PVs, followed, if negative, by next-generation sequencing. A total of 2128 subjects with cancer or a positive family history underwent oncogenetic testing with a panel of 51 recurring PVs at a tertiary medical center in March 2020-January 2023. Those with a known familial PV (n = 370) were excluded from the analysis. Among the remainder, 128/1758 (7%) were heterozygous for at least one variant, and 44 (34%) carried a PV of medium-high penetrance (MHPV). Cancer was diagnosed in 1519/1758 patients (86%). The diagnostic yield of founder MHPV testing was 2% in cancer patients and 4% in healthy individuals with a positive family history. It was higher in Ashkenazi Jews than non-Ashkenazi Jews and Arabs, but not over 10% for any type of cancer, and it was significantly higher in younger (<40 years) than older (>50 years) individuals (7% vs. 1%). Eighty-four of the heterozygotes (66%), mostly Ashkenazi Jews, harbored a low-penetrance variant (LPV) not associated with the diagnosed cancer, usually APC c.3902T>A. These findings question the advantage of two-step testing. LPVs should not be included in targeted testing because this can lead to an overestimation of the yield, and their detection does not preclude further comprehensive testing.
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Affiliation(s)
- Aasem Abu Shtaya
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
- Unit of Gastroenterology, Lady Davis Carmel Medical Center, Haifa 3436212, Israel;
| | - Inbal Kedar
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
| | - Samar Mattar
- Department of Surgery B, Carmel Medical Center, Haifa 3436212, Israel; (S.M.); (A.M.)
| | - Ahmad Mahamid
- Department of Surgery B, Carmel Medical Center, Haifa 3436212, Israel; (S.M.); (A.M.)
| | - Lina Basel-Salmon
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Felsenstein Medical Research Center, Petach Tikva 4920235, Israel
- Pediatric Genetics Unit, Schneider Children’s Medical Center of Israel, Petch Tikva 49202, Israel
| | - Sarit Farage Barhom
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
| | - Sofia Naftaly Nathan
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
| | - Nurit Magal
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
| | - Noy Azulay
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
| | | | - Rakefet Chen-Shtoyerman
- Adelson School of Medicine, Department of Molecular Biology, Ariel University, Ariel 40700, Israel;
- Kaplan Medical Center, Genetics Institute, Oncogenetic Clinic, Rehovot 7610001, Israel
| | - Ori Segol
- Unit of Gastroenterology, Lady Davis Carmel Medical Center, Haifa 3436212, Israel;
| | - Mor Seri
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
| | | | - Shiri Shkedi-Rafid
- Department of Genetics and Metabolic Diseases, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel;
| | - Chana Vinkler
- Institute for Medical Genetics, Wolfson Medical Center, Holon 5822012, Israel;
| | - Iris Netzer
- Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel;
| | - Ofir Hagari Bechar
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
| | - Liat Chamma
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
| | - Sari Liberman
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9112102, Israel
| | - Yael Goldberg
- Recanati Genetics Institute, Rabin Medical Center—Beilinson Hospital, Petach Tikva 4941492, Israel; (I.K.); (L.B.-S.); (N.M.); (M.S.); (O.H.B.); (Y.G.)
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
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Trainer AH, Goode E, Hoskins CN, Wheeler JCW, Best S. Calibrating variant curation by clinical context based on factors that influence patients' tolerance of uncertainty. Genet Med 2023; 25:100982. [PMID: 37724515 DOI: 10.1016/j.gim.2023.100982] [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: 03/27/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023] Open
Abstract
PURPOSE Shared decision making manages genomic uncertainty by integrating molecular and clinical uncertainties with patient values to craft a person-centered management plan. Laboratories seek genomic report consistency, agnostic to clinical context. Molecular reports often mask laboratory-managed uncertainties from clinical decision making. Better integration of these uncertainty management strategies requires a nuanced understanding of patients' perceptions and reactions to test uncertainties. We explored patients' tolerance to variant uncertainty in 3 parameters: (1) relative causal significance, (2) risk accuracy, and (3) classification validity. METHOD Deliberative forums were undertaken with 18 patients with predictive testing experience. Uncertainty deliberations were elicited for each parameter. A thematic framework was first developed, and then mapped to whether they justified tolerance to more or less parameter-specific uncertainty. RESULTS Six identified themes mapped to clinical and personal domains. These domains generated opposing forces when calibrating uncertainty. Personal themes justified tolerance of higher uncertainty and clinical themes lower uncertainty. Decision making in uncertainty focused on reducing management regret. Open communication increased tolerance of classification validity and risk accuracy uncertainty. Using these data, we have developed a nascent clinical algorithm integrating molecular uncertainty with clinical context through a targeted communication framework. CONCLUSION Maximizing test utility necessitates context-specific recalibration of uncertainty management and communication.
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Affiliation(s)
- Alison H Trainer
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Department of Medicine, University of Melbourne, Melbourne, VIC, Australia; Department of Genomic Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
| | - Erin Goode
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Department of Genomic Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Cass N Hoskins
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Department of Genomic Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Jack C W Wheeler
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Department of Genomic Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Stephanie Best
- Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre Alliance, Melbourne, VIC, Australia; Australian Genomics, Murdoch Childrens Research Institute, Melbourne, VIC, Australia
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Badran AR, Youngs A, Forman A, Elms M, Chang LL, Lebbe F, Reekie A, Short J, Hlaing MT, Watts E, Hipps D, Snape K. Proactive familial cancer risk assessment: a service development study in UK primary care. BJGP Open 2023; 7:BJGPO.2023.0076. [PMID: 37591554 PMCID: PMC11176673 DOI: 10.3399/bjgpo.2023.0076] [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: 04/28/2023] [Revised: 07/31/2023] [Accepted: 08/11/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Family history assessment can identify individuals above population-risk for cancer to enable targeted Screening, Prevention, and Early Detection (SPED). Family History Questionnaire Service (FHQS) is a resource-efficient patient-facing online tool to facilitate this. In the UK, cancer risk assessment is usually only offered to concerned individuals proactively self-presenting to their GP, leading to inequity in accessing SPED in the community. AIM To improve access to community cancer genetic risk assessment and explore barriers to uptake. DESIGN & SETTING Service development project of a digital pathway using the FHQS for cancer risk assessment across four general practices within the clinical remit of the South West Thames Centre for Genomics (SWTCG). METHOD 3100 individuals aged 38-50 years were invited to complete the FHQS through either text message or email. A random selection of 100 non-responders were contacted to determine barriers to uptake. RESULTS In total, n = 304/3100 (10%) registered for the FHQS. Responders were more likely to be British (63% vs 47%, P<0.001), speak English as their main language (92% vs 76%, P<0.001), and not require an interpreter (99.6% vs 94.9%, P = 0.001). Of 304 responders, 158 (52%) were automatically identified as at population-risk without full family history review. Of the remaining 146 responders, 52 (36%) required either additional screening referral (n = 23), genetics referral (n = 15), and/or advice to relatives (n = 18). Of 100 non-responders contacted, eight had incorrect contact details and 53 were contactable. Reasons for not responding included not receiving invitation details (n = 26), losing the invitation (n = 5), or forgetting (n = 4). CONCLUSION The FHQS can be used as part of a low-resource primary care pathway to identify individuals in the community above population-risk for cancer requiring action. This study highlighted barriers to uptake requiring consideration to maximise impact and minimise inequity.
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Affiliation(s)
- Abdul Rahman Badran
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
- Fieldway Medical Centre, Danebury, New Addington, Croydon, UK
| | - Alice Youngs
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Andrea Forman
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Marisa Elms
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | | | - Fiyaz Lebbe
- Fieldway Medical Centre, Danebury, New Addington, Croydon, UK
| | - Adam Reekie
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - John Short
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Min Theik Hlaing
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Emma Watts
- Shere Surgery, Gomshall Lane, Guildford, UK
| | - Deborah Hipps
- The Exchange Surgery, Gracefield Gardens, London, UK
| | - Katie Snape
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
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Sowamber R, Lukey A, Huntsman D, Hanley G. Ovarian Cancer: From Precursor Lesion Identification to Population-Based Prevention Programs. Curr Oncol 2023; 30:10179-10194. [PMID: 38132375 PMCID: PMC10742141 DOI: 10.3390/curroncol30120741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is a heterogeneous group of malignancies, including high-grade serous ovarian cancer (HGSC). HGSC is often diagnosed at advanced stages and is linked to TP53 variants. While BRCA variants elevate risk, most HGSC cases occur in individuals without known genetic variants, necessitating prevention strategies for people without known high-risk genetic variants. Effective prevention programs are also needed due to the lack of traditional screening options. An emerging primary prevention strategy is opportunistic salpingectomy, which involves removing fallopian tubes during another planned pelvic surgery. Opportunistic salpingectomy offers a safe and cost-effective preventative option that is gaining global adoption. With the publication of the first cohort study of patients who underwent salpingectomy, specifically for cancer prevention, attention has turned to broadening opportunities for salpingectomy in addition to more targeted approaches. Prevention opportunities are promising with increasing adoption of salpingectomy and the increased understanding of the etiology of the distinct histotypes of ovarian cancer. Yet, further research on targeted risk-reducing salpingectomy with thoughtful consideration of equity is necessary to reduce death and suffering from ovarian cancer.
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Affiliation(s)
- Ramlogan Sowamber
- Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V6T 1Z4, Canada
| | - Alexandra Lukey
- School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - David Huntsman
- Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V6T 1Z4, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Gillian Hanley
- Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
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Narod SA. Choices for cancer prevention for women with a BRCA1 mutation? a personal view. Hered Cancer Clin Pract 2023; 21:26. [PMID: 38031144 PMCID: PMC10685461 DOI: 10.1186/s13053-023-00271-3] [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: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
With widespread testing for susceptibility genes, increasing numbers of women are being identified to carry a mutation in one of many genes which renders them susceptible to cancer. The first gene to be identified (in 1994) was BRCA1 which increases a woman's risk for breast cancer (70%) and ovarian cancer (40%). The prevalence of BRCA1 gene mutations has been studied widely and in many countries, mostly in women affected with cancer. In many settings testing is offered routinely to women with serous ovarian cancer or early-onset or triple-negative breast cancer. It is preferable to identify a mutation in a healthy women prior to the diagnosis of cancer. The basic strategies for prevention include surgical prevention, chemoprevention and screening (early detection). Much progress has been made in the past two decades evaluating the benefits of these three approaches. In this commentary I provide my personal views regarding these various interventions in the context of counselling a newly diagnosed health woman with a BRCA1 mutation.
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Affiliation(s)
- Steven A Narod
- Women's College Research Institute, University of Toronto, 790 Bay Street, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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Brincat MR, Mira AR, Lawrence A. Current and Emerging Strategies for Tubo-Ovarian Cancer Diagnostics. Diagnostics (Basel) 2023; 13:3331. [PMID: 37958227 PMCID: PMC10647517 DOI: 10.3390/diagnostics13213331] [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: 09/04/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Tubo-ovarian cancer is the most lethal gynaecological cancer. More than 75% of patients are diagnosed at an advanced stage, which is associated with poorer overall survival. Symptoms at presentation are vague and non-specific, contributing to late diagnosis. Multimodal risk models have improved the diagnostic accuracy of adnexal mass assessment based on patient risk factors, coupled with findings on imaging and serum-based biomarker tests. Newly developed ultrasonographic assessment algorithms have standardised documentation and enable stratification of care between local hospitals and cancer centres. So far, no screening test has proven to reduce ovarian cancer mortality in the general population. This review is an update on the evidence behind ovarian cancer diagnostic strategies.
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Affiliation(s)
- Mark R. Brincat
- Department of Gynaecological Oncology, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK
| | - Ana Rita Mira
- Department of Gynaecological Oncology, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK
- Hospital Garcia de Orta, 2805-267 Almada, Portugal
| | - Alexandra Lawrence
- Department of Gynaecological Oncology, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK
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Balasubramanian JB, Choudhury PP, Mukhopadhyay S, Ahearn T, Chatterjee N, García-Closas M, Almeida JS. Wasm-iCARE: a portable and privacy-preserving web module to build, validate, and apply absolute risk models. ARXIV 2023:arXiv:2310.09252v1. [PMID: 37873020 PMCID: PMC10593073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Objective Absolute risk models estimate an individual's future disease risk over a specified time interval. Applications utilizing server-side risk tooling, such as the R-based iCARE (R-iCARE), to build, validate, and apply absolute risk models, face serious limitations in portability and privacy due to their need for circulating user data in remote servers for operation. Our objective was to overcome these limitations. Materials and Methods We refactored R-iCARE into a Python package (Py-iCARE) then compiled it to WebAssembly (Wasm-iCARE): a portable web module, which operates entirely within the privacy of the user's device. Results We showcase the portability and privacy of Wasm-iCARE through two applications: for researchers to statistically validate risk models, and to deliver them to end-users. Both applications run entirely on the client-side, requiring no downloads or installations, and keeps user data on-device during risk calculation. Conclusions Wasm-iCARE fosters accessible and privacy-preserving risk tools, accelerating their validation and delivery.
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Affiliation(s)
| | - Parichoy Pal Choudhury
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- American Cancer Society, Atlanta, GA, USA
| | - Srijon Mukhopadhyay
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- The Cancer Epidemiology and Prevention Research Unit, The Institute of Cancer Research, London, England
| | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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