501
|
Hilbers FS, van 't Hof PJ, Meijers CM, Mei H, Michailidou K, Dennis J, Hogervorst FBL, Nederlof PM, van Asperen CJ, Devilee P. Clustering of known low and moderate risk alleles rather than a novel recessive high-risk gene in non-BRCA1/2 sib trios affected with breast cancer. Int J Cancer 2020; 147:2708-2716. [PMID: 32383162 PMCID: PMC7540545 DOI: 10.1002/ijc.33039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/31/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022]
Abstract
Breast cancer risk is approximately twice as high in first‐degree relatives of female breast cancer cases than in women in the general population. Less than half of this risk can be attributed to the currently known genetic risk factors. Recessive risk alleles represent a relatively underexplored explanation for the remainder of familial risk. To address this, we selected 19 non‐BRCA1/2 breast cancer families in which at least three siblings were affected, while no first‐degree relatives of the previous or following generation had breast cancer. Germline DNA from one of the siblings was subjected to exome sequencing, while all affected siblings were genotyped using SNP arrays to assess haplotype sharing and to calculate a polygenic risk score (PRS) based on 160 low‐risk variants. We found no convincing candidate recessive alleles among exome sequencing variants in genomic regions for which all three siblings shared two haplotypes. However, we found two families in which all affected siblings carried the CHEK2*1100delC. In addition, the average normalized PRS of the “recessive” family probands (0.81) was significantly higher than that in both general population cases (0.35, P = .026) and controls (P = .0004). These findings suggest that the familial aggregation is, at least in part, explained by a polygenic effect of common low‐risk variants and rarer intermediate‐risk variants, while we did not find evidence of a role for novel recessive risk alleles. What's new? To find new breast cancer susceptibility alleles, these authors tested families in which at least three affected siblings had non‐BRCA1/2 breast cancer. No new susceptibility alleles emerged, but the analysis did reveal that on average, women from these families who had cancer had significantly higher polygenic risk scores than either sporadic cases or controls. This result highlights the importance of moderate risk alleles acting together in familial breast cancer.
Collapse
Affiliation(s)
- Florentine S Hilbers
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Peter J van 't Hof
- Sequence Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Caro M Meijers
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Hailiang Mei
- Sequence Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Frans B L Hogervorst
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands.,Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| |
Collapse
|
502
|
Yanes T, Kaur R, Meiser B, Scheepers-Joynt M, McInerny S, Barlow-Stewart K, Antill Y, Salmon L, Smyth C, James PA, Young MA. Women’s responses and understanding of polygenic breast cancer risk information. Fam Cancer 2020; 19:297-306. [DOI: 10.1007/s10689-020-00185-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
503
|
Lewis CM, Vassos E. Polygenic risk scores: from research tools to clinical instruments. Genome Med 2020; 12:44. [PMID: 32423490 PMCID: PMC7236300 DOI: 10.1186/s13073-020-00742-5] [Citation(s) in RCA: 577] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/01/2020] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies have shown unequivocally that common complex disorders have a polygenic genetic architecture and have enabled researchers to identify genetic variants associated with diseases. These variants can be combined into a polygenic risk score that captures part of an individual's susceptibility to diseases. Polygenic risk scores have been widely applied in research studies, confirming the association between the scores and disease status, but their clinical utility has yet to be established. Polygenic risk scores may be used to estimate an individual's lifetime genetic risk of disease, but the current discriminative ability is low in the general population. Clinical implementation of polygenic risk score (PRS) may be useful in cohorts where there is a higher prior probability of disease, for example, in early stages of diseases to assist in diagnosis or to inform treatment choices. Important considerations are the weaker evidence base in application to non-European ancestry and the challenges in translating an individual's PRS from a percentile of a normal distribution to a lifetime disease risk. In this review, we consider how PRS may be informative at different points in the disease trajectory giving examples of progress in the field and discussing obstacles that need to be addressed before clinical implementation.
Collapse
Affiliation(s)
- Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, de Crespigny Park, London, SE5 8AF, UK.
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK.
| | - Evangelos Vassos
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, de Crespigny Park, London, SE5 8AF, UK
| |
Collapse
|
504
|
Qing T, Mohsen H, Marczyk M, Ye Y, O'Meara T, Zhao H, Townsend JP, Gerstein M, Hatzis C, Kluger Y, Pusztai L. Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. Nat Commun 2020; 11:2438. [PMID: 32415133 PMCID: PMC7228928 DOI: 10.1038/s41467-020-16293-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/21/2020] [Indexed: 11/24/2022] Open
Abstract
Cancers harbor many somatic mutations and germline variants, we hypothesized that the combined effect of germline variants that alter the structure, expression, or function of protein-coding regions of cancer-biology related genes (gHFI) determines which and how many somatic mutations (sM) must occur for malignant transformation. We show that gHFI and sM affect overlapping genes and the average number of gHFI in cancer hallmark genes is higher in patients who develop cancer at a younger age (r = -0.77, P = 0.0051), while the average number of sM increases in increasing age groups (r = 0.92, P = 0.000073). A strong negative correlation exists between average gHFI and average sM burden in increasing age groups (r = -0.70, P = 0.017). In early-onset cancers, the larger gHFI burden in cancer genes suggests a greater contribution of germline alterations to the transformation process while late-onset cancers are more driven by somatic mutations.
Collapse
Affiliation(s)
- Tao Qing
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Hussein Mohsen
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Michal Marczyk
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Data Mining Division, Silesian University of Technology, Gliwice, Poland
| | - Yixuan Ye
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Tess O'Meara
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Hongyu Zhao
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA
| | - Jeffrey P Townsend
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
| | - Christos Hatzis
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Bristol-Myers Squibb, New York, NY, USA
| | - Yuval Kluger
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Pathology, School of Medicine, Yale University, New Haven, CT, USA
- Program of Applied Mathematics, Yale University, New Haven, CT, USA
| | - Lajos Pusztai
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA.
| |
Collapse
|
505
|
Zhou W, Chen X, Huang H, Liu S, Xie A, Lan L. Birth Weight and Incidence of Breast Cancer: Dose-Response Meta-analysis of Prospective Studies. Clin Breast Cancer 2020; 20:e555-e568. [PMID: 32665189 DOI: 10.1016/j.clbc.2020.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/13/2020] [Accepted: 04/23/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND Many studies have shown the association between birth weight and breast cancer (BC), but the evidence remains limited and inconsistent, especially in different menopause status. We sought to clarify the relationship and shape of the dose-response relation between birth weight and BC. METHODS The Web of Science, PubMed, and Embase databases were searched for prospective studies involving the relationship between birth weight and risk of BC published to November 2019. Random effects of generalized least squares regression models were used to estimate the quantitative dose-response association, and restricted cubic splines were used to model the association. RESULTS We included reports of 16 prospective studies describing 16,000 incident cases among 553,644 participants. We identified a modest-in-magnitude, but significant, association between birth weight and BC risk: risk increased by 2% (risk ratio, 1.02, 95% confidence interval, 1.01-1.03) and 9% (risk ratio, 1.09, 95% confidence interval, 1.04-1.15) with a per-500 g birth weight increment in all ages and premenopausal women, respectively. Our results showed a linear dose-response relationship between birth weight and BC risk (Pnonlinearity = .311) in premenopausal women, with statistical significance when birth weight was above about 3.5 kg. No significant association was found in postmenopausal women. CONCLUSION Higher birth weight has a relationship with increased risk of BC in premenopausal women, particularly when birth weight is above 3.5 kg.
Collapse
Affiliation(s)
- Wen Zhou
- Department of Health Management Center, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China
| | - Xu Chen
- Department of Health Services Section, The Eighth Affiliated Hospital Sun Yat-sen university, Shenzhen, China
| | - Hui Huang
- Department of Health Management Center, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China
| | - Shaoxia Liu
- Department of Health Management Center, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China
| | - Aixian Xie
- Department of Health Management Center, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China
| | - Liqin Lan
- Department of Health Management Center, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China.
| |
Collapse
|
506
|
Yang S, Zhou X. Accurate and Scalable Construction of Polygenic Scores in Large Biobank Data Sets. Am J Hum Genet 2020; 106:679-693. [PMID: 32330416 PMCID: PMC7212266 DOI: 10.1016/j.ajhg.2020.03.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/30/2020] [Indexed: 01/24/2023] Open
Abstract
Accurate construction of polygenic scores (PGS) can enable early diagnosis of diseases and facilitate the development of personalized medicine. Accurate PGS construction requires prediction models that are both adaptive to different genetic architectures and scalable to biobank scale datasets with millions of individuals and tens of millions of genetic variants. Here, we develop such a method called Deterministic Bayesian Sparse Linear Mixed Model (DBSLMM). DBSLMM relies on a flexible modeling assumption on the effect size distribution to achieve robust and accurate prediction performance across a range of genetic architectures. DBSLMM also relies on a simple deterministic search algorithm to yield an approximate analytic estimation solution using summary statistics only. The deterministic search algorithm, when paired with further algebraic innovations, results in substantial computational savings. With simulations, we show that DBSLMM achieves scalable and accurate prediction performance across a range of realistic genetic architectures. We then apply DBSLMM to analyze 25 traits in UK Biobank. For these traits, compared to existing approaches, DBSLMM achieves an average of 2.03%-101.09% accuracy gain in internal cross-validations. In external validations on two separate datasets, including one from BioBank Japan, DBSLMM achieves an average of 14.74%-522.74% accuracy gain. In these real data applications, DBSLMM is 1.03-28.11 times faster and uses only 7.4%-24.8% of physical memory as compared to other multiple regression-based PGS methods. Overall, DBSLMM represents an accurate and scalable method for constructing PGS in biobank scale datasets.
Collapse
Affiliation(s)
- Sheng Yang
- Department of Biostatistics, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
507
|
Harkness EF, Astley SM, Evans D. Risk-based breast cancer screening strategies in women. Best Pract Res Clin Obstet Gynaecol 2020; 65:3-17. [DOI: 10.1016/j.bpobgyn.2019.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/14/2019] [Accepted: 11/10/2019] [Indexed: 10/25/2022]
|
508
|
Shieh Y, Ziv E, Kerlikowske K. Interval breast cancers - insights into a complex phenotype. Nat Rev Clin Oncol 2020; 17:138-139. [PMID: 31965086 PMCID: PMC10365927 DOI: 10.1038/s41571-020-0327-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yiwey Shieh
- Division of General Internal Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Elad Ziv
- Division of General Internal Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Karla Kerlikowske
- Departments of Medicine and Epidemiology and Biostatistics, University of California, San Francisco, CA, USA. .,General Internal Medicine Section, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA.
| |
Collapse
|
509
|
Brentnall AR, van Veen EM, Harkness EF, Rafiq S, Byers H, Astley SM, Sampson S, Howell A, Newman WG, Cuzick J, Evans DGR. A case-control evaluation of 143 single nucleotide polymorphisms for breast cancer risk stratification with classical factors and mammographic density. Int J Cancer 2020; 146:2122-2129. [PMID: 31251818 PMCID: PMC7065068 DOI: 10.1002/ijc.32541] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/28/2019] [Indexed: 01/03/2023]
Abstract
Panels of single nucleotide polymorphisms (SNPs) stratify risk for breast cancer in women from the general population, but studies are needed assess their use in a fully comprehensive model including classical risk factors, mammographic density and more than 100 SNPs associated with breast cancer. A case-control study was designed (1,668 controls, 405 cases) in women aged 47-73 years attending routine screening in Manchester UK, and enrolled in a wider study to assess methods for risk assessment. Risk from classical questionnaire risk factors was assessed using the Tyrer-Cuzick model; mean percentage visual mammographic density was scored by two independent readers. DNA extracted from saliva was genotyped at selected SNPs using the OncoArray. A predefined polygenic risk score based on 143 SNPs was calculated (SNP143). The odds ratio (OR, and 95% confidence interval, CI) per interquartile range (IQ-OR) of SNP143 was estimated unadjusted and adjusted for Tyrer-Cuzick and breast density. Secondary analysis assessed risk by oestrogen receptor (ER) status. The primary polygenic risk score was well calibrated (O/E OR 1.10, 95% CI 0.86-1.34) and accuracy was retained after adjustment for Tyrer-Cuzick risk and mammographic density (IQ-OR unadjusted 2.12, 95% CI% 1.75-2.42; adjusted 2.06, 95% CI 1.75-2.42). SNP143 was a risk factor for ER+ and ER- breast cancer (adjusted IQ-OR, ER+ 2.11, 95% CI 1.78-2.51; ER- 1.81, 95% CI 1.16-2.84). In conclusion, polygenic risk scores based on a large number of SNPs improve risk stratification in combination with classical risk factors and mammographic density, and SNP143 was similarly predictive for ER-positive and ER-negative disease.
Collapse
Affiliation(s)
- Adam R. Brentnall
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Charterhouse Square, Barts and The LondonQueen Mary University of LondonLondonUnited Kingdom
| | - Elke M. van Veen
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Elaine F. Harkness
- Prevention Breast Cancer Centre and Nightingale Breast Screening CentreUniversity Hospital of South ManchesterManchesterUnited Kingdom
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUnited Kingdom
- Manchester Academic Health Science CentreUniversity of ManchesterManchesterUnited Kingdom
| | - Sajjad Rafiq
- School of Public Health, Epidemiology & BiostatisticsImperial College LondonLondonUnited Kingdom
| | - Helen Byers
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Susan M. Astley
- Prevention Breast Cancer Centre and Nightingale Breast Screening CentreUniversity Hospital of South ManchesterManchesterUnited Kingdom
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUnited Kingdom
- Manchester Academic Health Science CentreUniversity of ManchesterManchesterUnited Kingdom
- Manchester Breast Centre, Manchester Cancer Research CentreUniversity of ManchesterManchesterUnited Kingdom
| | - Sarah Sampson
- Prevention Breast Cancer Centre and Nightingale Breast Screening CentreUniversity Hospital of South ManchesterManchesterUnited Kingdom
| | - Anthony Howell
- Prevention Breast Cancer Centre and Nightingale Breast Screening CentreUniversity Hospital of South ManchesterManchesterUnited Kingdom
- The Christie NHS Foundation TrustManchesterUnited Kingdom
- Manchester Breast Centre, Manchester Cancer Research CentreUniversity of ManchesterManchesterUnited Kingdom
| | - William G. Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
- Manchester Centre for Genomic MedicineManchester University NHS Foundation TrustManchesterUnited Kingdom
- Manchester Breast Centre, Manchester Cancer Research CentreUniversity of ManchesterManchesterUnited Kingdom
| | - Jack Cuzick
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Charterhouse Square, Barts and The LondonQueen Mary University of LondonLondonUnited Kingdom
| | - Dafydd Gareth R. Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
- Prevention Breast Cancer Centre and Nightingale Breast Screening CentreUniversity Hospital of South ManchesterManchesterUnited Kingdom
- The Christie NHS Foundation TrustManchesterUnited Kingdom
- Manchester Centre for Genomic MedicineManchester University NHS Foundation TrustManchesterUnited Kingdom
- Manchester Breast Centre, Manchester Cancer Research CentreUniversity of ManchesterManchesterUnited Kingdom
| |
Collapse
|
510
|
Polygenic and clinical risk scores and their impact on age at onset and prediction of cardiometabolic diseases and common cancers. Nat Med 2020; 26:549-557. [DOI: 10.1038/s41591-020-0800-0] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/13/2020] [Indexed: 01/12/2023]
|
511
|
Al Ajmi K, Lophatananon A, Mekli K, Ollier W, Muir KR. Association of Nongenetic Factors With Breast Cancer Risk in Genetically Predisposed Groups of Women in the UK Biobank Cohort. JAMA Netw Open 2020; 3:e203760. [PMID: 32329772 PMCID: PMC7182796 DOI: 10.1001/jamanetworkopen.2020.3760] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
IMPORTANCE The association between noninherited factors, including lifestyle factors, and the risk of breast cancer (BC) in women and the association between BC and genetic makeup are only partly characterized. A study using data on current genetic stratification may help in the characterization. OBJECTIVE To examine the association between healthier lifestyle habits and BC risk in genetically predisposed groups. DESIGN, SETTING, AND PARTICIPANTS Data from UK Biobank, a prospective cohort comprising 2728 patients with BC and 88 489 women without BC, were analyzed. The data set used for the analysis was closed on March 31, 2019. The analysis was restricted to postmenopausal white women. Classification of healthy lifestyle was based on Cancer Research UK guidance (healthy weight, regular exercise, no use of hormone replacement therapy for more than 5 years, no oral contraceptive use, and alcohol intake <3 times/wk). Three groups were established: favorable (≥4 healthy factors), intermediate (2-3 healthy factors), and unfavorable (≤1 healthy factor). The genetic contribution was estimated using the polygenic risk scores of 305 preselected single-nucleotide variations. Polygenic risk scores were categorized into 3 tertiles (low, intermediate, and high). MAIN OUTCOMES AND MEASURES Cox proportional hazards regression was used to assess the hazard ratios (HRs) of the lifestyles and polygenic risk scores associated with a malignant neoplasm of the breast. RESULTS Mean (SD) age of the 2728 women with BC was 60.1 (5.5) years, and mean age of the 88 489 women serving as controls was 59.4 (4.9) years. The median follow-up time for the cohort was 10 years (maximum 13 years) (interquartile range, 9.44-10.82 years). Women with BC had a higher body mass index (relative risk [RR], 1.14; 95% CI, 1.05-1.23), performed less exercise (RR, 1.12; 95% CI, 1.01-1.25), used hormonal replacement therapy for longer than 5 years (RR, 1.23; 95% CI, 1.13-1.34), used more oral contraceptives (RR, 1.02; 95% CI, 0.93-1.12), and had greater alcohol intake (RR, 1.11; 95% CI, 1.03-1.19) compared with the controls. Overall, 20 657 women (23.3%) followed a favorable lifestyle, 60 195 women (68.0%) followed an intermediate lifestyle, and 7637 women (8.6%) followed an unfavorable lifestyle. The RR of the highest genetic risk group was 2.55 (95% CI, 2.28-2.84), and the RR of the most unfavorable lifestyle category was 1.44 (95% CI, 1.25-1.65). The association of lifestyle and BC within genetic subgroups showed lower HRs among women following a favorable lifestyle compared with intermediate and unfavorable lifestyles among all of the genetic groups: women with an unfavorable lifestyle had a higher risk of BC in the low genetic group (HR, 1.63; 95% CI, 1.13-2.34), intermediate genetic group (HR, 1.94; 95% CI, 1.46-2.58), and high genetic group (HR, 1.39; 95% CI, 1.11-1.74) compared with the reference group of favorable lifestyle. Intermediate lifestyle was also associated with a higher risk of BC among the low genetic group (HR, 1.40; 95% CI, 1.09-1.80) and the intermediate genetic group (HR, 1.37; 95% CI, 1.12-1.68). CONCLUSIONS AND RELEVANCE In this cohort study of data on women in the UK Biobank, a healthier lifestyle with more exercise, healthy weight, low alcohol intake, no oral contraceptive use, and no or limited hormonal replacement therapy use appeared to be associated with a reduced level of risk for BC, even if the women were at higher genetic risk for BC.
Collapse
Affiliation(s)
- Kawthar Al Ajmi
- Division of Population Health, Health Services Research and Primary Care, Faculty of Biology, Medicine and Health, Centre for Epidemiology, University of Manchester, Manchester, United Kingdom
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, Faculty of Biology, Medicine and Health, Centre for Epidemiology, University of Manchester, Manchester, United Kingdom
| | - Krisztina Mekli
- Cathie Marsh Institute for Social Research, School of Social Sciences, Faculty of Humanities, University of Manchester, Manchester, United Kingdom
| | - William Ollier
- Division of Population Health, Health Services Research and Primary Care, Faculty of Biology, Medicine and Health, Centre for Epidemiology, University of Manchester, Manchester, United Kingdom
- School of Healthcare Science, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, United Kingdom
| | - Kenneth R Muir
- Division of Population Health, Health Services Research and Primary Care, Faculty of Biology, Medicine and Health, Centre for Epidemiology, University of Manchester, Manchester, United Kingdom
| |
Collapse
|
512
|
High polygenic burden is associated with blood DNA methylation changes in individuals with suicidal behavior. J Psychiatr Res 2020; 123:62-71. [PMID: 32036075 DOI: 10.1016/j.jpsychires.2020.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/06/2020] [Accepted: 01/24/2020] [Indexed: 12/27/2022]
Abstract
Suicidal behavior is result of the interaction of several contributors, including genetic and environmental factors. The integration of approaches considering the polygenic component of suicidal behavior, such as polygenic risk scores (PRS) and DNA methylation is promising for improving our understanding of the complex interplay between genetic and environmental factors in this behavior. The aim of this study was the evaluation of DNA methylation differences between individuals with high and low genetic burden for suicidality. The present study was divided into two phases. In the first phase, genotyping with the Psycharray chip was performed in a discovery sample of 568 Mexican individuals, of which 149 had suicidal behavior (64 individuals with suicidal ideation, 50 with suicide attempt and 35 with completed suicide). Then, a PRS analysis based on summary statistics from the Psychiatric Genomic Consortium was performed in the discovery sample. In a second phase, we evaluated DNA methylation differences between individuals with high and low genetic burden for suicidality in a sub-sample of the discovery sample (target sample) of 94 subjects. We identified 153 differentially methylated sites between individuals with low and high-PRS. Among genes mapped to differentially methylated sites, we found genes involved in neurodevelopment (CHD7, RFX4, KCNA1, PLCB1, PITX1, NUMBL) and ATP binding (KIF7, NUBP2, KIF6, ATP8B1, ATP11A, CLCN7, MYLK, MAP2K5). Our results suggest that genetic variants might increase the predisposition to epigenetic variations in genes involved in neurodevelopment. This study highlights the possible implication of polygenic burden in the alteration of epigenetic changes in suicidal behavior.
Collapse
|
513
|
Li R, Chen Y, Ritchie MD, Moore JH. Electronic health records and polygenic risk scores for predicting disease risk. Nat Rev Genet 2020; 21:493-502. [PMID: 32235907 DOI: 10.1038/s41576-020-0224-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2020] [Indexed: 01/03/2023]
Abstract
Accurate prediction of disease risk based on the genetic make-up of an individual is essential for effective prevention and personalized treatment. Nevertheless, to date, individual genetic variants from genome-wide association studies have achieved only moderate prediction of disease risk. The aggregation of genetic variants under a polygenic model shows promising improvements in prediction accuracies. Increasingly, electronic health records (EHRs) are being linked to patient genetic data in biobanks, which provides new opportunities for developing and applying polygenic risk scores in the clinic, to systematically examine and evaluate patient susceptibilities to disease. However, the heterogeneous nature of EHR data brings forth many practical challenges along every step of designing and implementing risk prediction strategies. In this Review, we present the unique considerations for using genotype and phenotype data from biobank-linked EHRs for polygenic risk prediction.
Collapse
Affiliation(s)
- Ruowang Li
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yong Chen
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason H Moore
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
514
|
Maves H, Flodman P, Nathan D, Smith M. Ethnic disparities in the frequency of cancer reported in family histories. J Genet Couns 2020; 29:451-459. [DOI: 10.1002/jgc4.1264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/17/2020] [Accepted: 02/22/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Heather Maves
- Division of Genetic and Genomic Medicine Department of Pediatrics University of California, Irvine Irvine California
| | - Pamela Flodman
- Division of Genetic and Genomic Medicine Department of Pediatrics University of California, Irvine Irvine California
| | - Deepika Nathan
- Division of Genetic and Genomic Medicine Department of Pediatrics University of California, Irvine Irvine California
| | - Moyra Smith
- Division of Genetic and Genomic Medicine Department of Pediatrics University of California, Irvine Irvine California
| |
Collapse
|
515
|
Laner A, Benet-Pages A, Neitzel B, Holinski-Feder E. Analysis of 3297 individuals suggests that the pathogenic germline 5'-UTR variant BRCA1 c.-107A > T is not common in south-east Germany. Fam Cancer 2020; 19:211-213. [PMID: 32200540 DOI: 10.1007/s10689-020-00175-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/18/2020] [Indexed: 01/04/2023]
Abstract
In this study we aim to determine the prevalence of the recently identified pathogenic BRCA1 variant c.-107A > T in the south-east German population. This variant causes the epigenetic silencing of the BRCA1 promotor and has been detected in two independent families from the UK without a germline BRCA1 or BRCA2 pathogenic variant. A total of 3297 individuals with suspicion of hereditary breast and ovarian cancer and fulfilling the clinical criteria necessary for genetic testing in Germany were analyzed for presence of the variant by a Kompetitive Allele-Specific PCR (KASP) assay or direct Sanger sequencing. Since we did not detect an individual carrying the variant we conclude that BRCA1 c.-107A > T is not a common variant in the south-east German population.
Collapse
Affiliation(s)
- A Laner
- MGZ - Medizinisch Genetisches Zentrum, Bayerstr. 3-5, 80035, Munich, Germany.
| | - A Benet-Pages
- MGZ - Medizinisch Genetisches Zentrum, Bayerstr. 3-5, 80035, Munich, Germany.
| | - B Neitzel
- MGZ - Medizinisch Genetisches Zentrum, Bayerstr. 3-5, 80035, Munich, Germany
| | - E Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Bayerstr. 3-5, 80035, Munich, Germany.
| |
Collapse
|
516
|
Jia G, Lu Y, Wen W, Long J, Liu Y, Tao R, Li B, Denny JC, Shu XO, Zheng W. Evaluating the Utility of Polygenic Risk Scores in Identifying High-Risk Individuals for Eight Common Cancers. JNCI Cancer Spectr 2020; 4:pkaa021. [PMID: 32596635 PMCID: PMC7306192 DOI: 10.1093/jncics/pkaa021] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/14/2020] [Accepted: 03/06/2020] [Indexed: 12/13/2022] Open
Abstract
Background Genome-wide association studies have identified common genetic risk variants in many loci associated with multiple cancers. We sought to systematically evaluate the utility of these risk variants in identifying high-risk individuals for eight common cancers. Methods We constructed polygenic risk scores (PRS) using genome-wide association studies–identified risk variants for each cancer. Using data from 400 812 participants of European descent in a population-based cohort study, UK Biobank, we estimated hazard ratios associated with PRS using Cox proportional hazard models and evaluated the performance of the PRS in cancer risk prediction and their ability to identify individuals at more than a twofold elevated risk, a risk level comparable to a moderate-penetrance mutation in known cancer predisposition genes. Results During a median follow-up of 5.8 years, 14 584 incident case patients of cancers were identified (ranging from 358 epithelial ovarian cancer case patients to 4430 prostate cancer case patients). Compared with those at an average risk, individuals among the highest 5% of the PRS had a two- to threefold elevated risk for cancer of the prostate, breast, pancreas, colorectal, or ovary, and an approximately 1.5-fold elevated risk of cancer of the lung, bladder, or kidney. The areas under the curve ranged from 0.567 to 0.662. Using PRS, 40.4% of the study participants can be classified as having more than a twofold elevated risk for at least one site-specific cancer. Conclusions A large proportion of the general population can be identified at an elevated cancer risk by PRS, supporting the potential clinical utility of PRS for personalized cancer risk prediction.
Collapse
Affiliation(s)
- Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ying Liu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bingshan Li
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| |
Collapse
|
517
|
Abstract
Genome-wide association studies (GWASs) have identified at least 10 single-nucleotide polymorphisms (SNPs) associated with papillary thyroid cancer (PTC) risk. Most of these SNPs are common variants with small to moderate effect sizes. Here we assessed the combined genetic effects of these variants on PTC risk by using summarized GWAS results to build polygenic risk score (PRS) models in three PTC study groups from Ohio (1,544 patients and 1,593 controls), Iceland (723 patients and 129,556 controls), and the United Kingdom (534 patients and 407,945 controls). A PRS based on the 10 established PTC SNPs showed a stronger predictive power compared with the clinical factors model, with a minimum increase of area under the receiver-operating curve of 5.4 percentage points (P ≤ 1.0 × 10-9). Adding an extended PRS based on 592,475 common variants did not significantly improve the prediction power compared with the 10-SNP model, suggesting that most of the remaining undiscovered genetic risk in thyroid cancer is due to rare, moderate- to high-penetrance variants rather than to common low-penetrance variants. Based on the 10-SNP PRS, individuals in the top decile group of PRSs have a close to sevenfold greater risk (95% CI, 5.4-8.8) compared with the bottom decile group. In conclusion, PRSs based on a small number of common germline variants emphasize the importance of heritable low-penetrance markers in PTC.
Collapse
|
518
|
Abstract
Strategies to prevent cancer and diagnose it early when it is most treatable are needed to reduce the public health burden from rising disease incidence. Risk assessment is playing an increasingly important role in targeting individuals in need of such interventions. For breast cancer many individual risk factors have been well understood for a long time, but the development of a fully comprehensive risk model has not been straightforward, in part because there have been limited data where joint effects of an extensive set of risk factors may be estimated with precision. In this article we first review the approach taken to develop the IBIS (Tyrer-Cuzick) model, and describe recent updates. We then review and develop methods to assess calibration of models such as this one, where the risk of disease allowing for competing mortality over a long follow-up time or lifetime is estimated. The breast cancer risk model model and calibration assessment methods are demonstrated using a cohort of 132,139 women attending mammography screening in the State of Washington, USA.
Collapse
Affiliation(s)
- Adam R. Brentnall
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, Charterhouse square, London, EC1M 6BQ
| | - Jack Cuzick
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, Charterhouse square, London, EC1M 6BQ
| |
Collapse
|
519
|
Schneeweiss A, Hartkopf AD, Müller V, Wöckel A, Lux MP, Janni W, Ettl J, Belleville E, Huober J, Thill M, Fasching PA, Kolberg HC, Pöschke P, Welslau M, Overkamp F, Tesch H, Fehm TN, Lüftner D, Schütz F. Update Breast Cancer 2020 Part 1 - Early Breast Cancer: Consolidation of Knowledge About Known Therapies. Geburtshilfe Frauenheilkd 2020; 80:277-287. [PMID: 32139917 PMCID: PMC7056401 DOI: 10.1055/a-1111-2431] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 02/08/2023] Open
Abstract
This review is intended to present the latest developments in the prevention and treatment of early breast cancer. The risk of breast cancer can be increasingly better characterised with large epidemiological studies on genetic and non-genetic risk factors. Through new analyses, the evidence for high-penetrance genes as well as for low-penetrance genes was able to be improved. New data on denosumab and atezolizumab are available in the neoadjuvant situation as is a pooled appraisal of numerous studies on capecitabine in the curative situation. There is also an update to the overall survival data of pertuzumab in the adjuvant situation with a longer follow-up observation period. Finally, digital medicine is steadily finding its way into science. A recently conducted study on automated breast cancer detection using artificial intelligence establishes the basis for a future review in clinical studies.
Collapse
Affiliation(s)
- Andreas Schneeweiss
- National Center for Tumor Diseases, Division Gynecologic Oncology, University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Andreas D. Hartkopf
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
| | - Volkmar Müller
- Department of Gynecology, Hamburg-Eppendorf University Medical Center, Hamburg, Germany
| | - Achim Wöckel
- Department of Gynecology and Obstetrics, University Hospital Würzburg, Würzburg, Germany
| | - Michael P. Lux
- Klinik für Gynäkologie und Geburtshilfe, Frauenklinik St. Louise, Paderborn, St. Josefs-Krankenhaus, Salzkotten, Germany
| | - Wolfgang Janni
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Johannes Ettl
- Department of Obstetrics and Gynecology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | - Jens Huober
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Marc Thill
- Agaplesion Markus Krankenhaus, Frauenklinik, Frankfurt, Germany
| | - Peter A. Fasching
- Erlangen University Hospital, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Patrik Pöschke
- Erlangen University Hospital, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | | | - Hans Tesch
- Oncology Practice at Bethanien Hospital Frankfurt, Frankfurt, Germany
| | - Tanja N. Fehm
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Diana Lüftner
- Charité University Hospital, Campus Benjamin Franklin, Department of Hematology, Oncology and Tumour Immunology, Berlin, Germany
| | - Florian Schütz
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| |
Collapse
|
520
|
Hopper JL, Nguyen TL, Schmidt DF, Makalic E, Song YM, Sung J, Dite GS, Dowty JG, Li S. Going Beyond Conventional Mammographic Density to Discover Novel Mammogram-Based Predictors of Breast Cancer Risk. J Clin Med 2020; 9:jcm9030627. [PMID: 32110975 PMCID: PMC7141100 DOI: 10.3390/jcm9030627] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/15/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
This commentary is about predicting a woman’s breast cancer risk from her mammogram, building on the work of Wolfe, Boyd and Yaffe on mammographic density. We summarise our efforts at finding new mammogram-based risk predictors, and how they combine with the conventional mammographic density, in predicting risk for interval cancers and screen-detected breast cancers across different ages at diagnosis and for both Caucasian and Asian women. Using the OPERA (odds ratio per adjusted standard deviation) concept, in which the risk gradient is measured on an appropriate scale that takes into account other factors adjusted for by design or analysis, we show that our new mammogram-based measures are the strongest of all currently known breast cancer risk factors in terms of risk discrimination on a population-basis. We summarise our findings graphically using a path diagram in which conventional mammographic density predicts interval cancer due to its role in masking, while the new mammogram-based risk measures could have a causal effect on both interval and screen-detected breast cancer. We discuss attempts by others to pursue this line of investigation, the measurement challenge that allows different measures to be compared in an open and transparent manner on the same datasets, as well as the biological and public health consequences.
Collapse
|
521
|
Interactions between a Polygenic Risk Score and Non-genetic Risk Factors in Young-Onset Breast Cancer. Sci Rep 2020; 10:3242. [PMID: 32094468 PMCID: PMC7039983 DOI: 10.1038/s41598-020-60032-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
Most gene-environmental studies have focused on breast cancers generally, the preponderance of which occur after age 50. Young-onset breast cancers (YOBC) tend to be aggressive and may be etiologically different. The goal of this analysis was to assess interactions between an established 77-SNP polygenic risk score (PRS) and non-genetic risk factors for YOBC. We constructed the PRS using a family-based study of 1,291 women diagnosed with breast cancer before age 50 and their parents and unaffected sisters. We used conditional logistic regression to analyze interactions between the PRS and 14 established risk factors. In further analyses we assessed the same interactions, but for invasive cancer, estrogen receptor (ER) positive cancer and with broader inclusion of racial/ethnic groups. Results showed a decreased association between the PRS and YOBC risk for women who had ever used hormonal birth control (odds ratio [OR] = 2.20 versus 3.89) and a stronger association between the PRS and YOBC risk in pre-menopausal women (OR = 2.46 versus 1.23). Restricting the analysis to ER+ cancers or invasive cancers or using samples from all ethnic groups produced similar results. In conclusion, the PRS may interact with hormonal birth control use and with menopausal status on risk of YOBC.
Collapse
|
522
|
Bhattacharya A, García-Closas M, Olshan AF, Perou CM, Troester MA, Love MI. A framework for transcriptome-wide association studies in breast cancer in diverse study populations. Genome Biol 2020; 21:42. [PMID: 32079541 PMCID: PMC7033948 DOI: 10.1186/s13059-020-1942-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/21/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The relationship between germline genetic variation and breast cancer survival is largely unknown, especially in understudied minority populations who often have poorer survival. Genome-wide association studies (GWAS) have interrogated breast cancer survival but often are underpowered due to subtype heterogeneity and clinical covariates and detect loci in non-coding regions that are difficult to interpret. Transcriptome-wide association studies (TWAS) show increased power in detecting functionally relevant loci by leveraging expression quantitative trait loci (eQTLs) from external reference panels in relevant tissues. However, ancestry- or race-specific reference panels may be needed to draw correct inference in ancestrally diverse cohorts. Such panels for breast cancer are lacking. RESULTS We provide a framework for TWAS for breast cancer in diverse populations, using data from the Carolina Breast Cancer Study (CBCS), a population-based cohort that oversampled black women. We perform eQTL analysis for 406 breast cancer-related genes to train race-stratified predictive models of tumor expression from germline genotypes. Using these models, we impute expression in independent data from CBCS and TCGA, accounting for sampling variability in assessing performance. These models are not applicable across race, and their predictive performance varies across tumor subtype. Within CBCS (N = 3,828), at a false discovery-adjusted significance of 0.10 and stratifying for race, we identify associations in black women near AURKA, CAPN13, PIK3CA, and SERPINB5 via TWAS that are underpowered in GWAS. CONCLUSIONS We show that carefully implemented and thoroughly validated TWAS is an efficient approach for understanding the genetics underpinning breast cancer outcomes in diverse populations.
Collapse
Affiliation(s)
- Arjun Bhattacharya
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Andrew F. Olshan
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Melissa A. Troester
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, USA
| |
Collapse
|
523
|
Wong EM, Southey MC, Terry MB. Integrating DNA methylation measures to improve clinical risk assessment: are we there yet? The case of BRCA1 methylation marks to improve clinical risk assessment of breast cancer. Br J Cancer 2020; 122:1133-1140. [PMID: 32066913 PMCID: PMC7156506 DOI: 10.1038/s41416-019-0720-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/11/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Current risk prediction models estimate the probability of developing breast cancer over a defined period based on information such as family history, non-genetic breast cancer risk factors, genetic information from high and moderate risk breast cancer susceptibility genes and, over the past several years, polygenic risk scores (PRS) from more than 300 common variants. The inclusion of additional data such as PRS improves risk stratification, but it is anticipated that the inclusion of epigenetic marks could further improve model performance accuracy. Here, we present the case for including information on DNA methylation marks to improve the accuracy of these risk prediction models, and consider how this approach contrasts genetic information, as identifying DNA methylation marks associated with breast cancer risk differs inherently according to the source of DNA, approaches to the measurement of DNA methylation, and the timing of measurement. We highlight several DNA-methylation-specific challenges that should be considered when incorporating information on DNA methylation marks into risk prediction models, using BRCA1, a highly penetrant breast cancer susceptibility gene, as an example. Only after careful consideration of study design and DNA methylation measurement will prospective performance of the incorporation of information regarding DNA methylation marks into risk prediction models be valid.
Collapse
Affiliation(s)
- Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
| |
Collapse
|
524
|
Bafligil C, Thompson DJ, Lophatananon A, Smith MJ, Ryan NA, Naqvi A, Evans DG, Crosbie EJ. Association between genetic polymorphisms and endometrial cancer risk: a systematic review. J Med Genet 2020; 57:591-600. [PMID: 32066633 PMCID: PMC7476276 DOI: 10.1136/jmedgenet-2019-106529] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/24/2019] [Accepted: 12/15/2019] [Indexed: 12/21/2022]
Abstract
Introduction Endometrial cancer is one of the most commonly diagnosed cancers in women. Although there is a hereditary component to endometrial cancer, most cases are thought to be sporadic and lifestyle related. The aim of this study was to systematically review prospective and retrospective case–control studies, meta-analyses and genome-wide association studies to identify genomic variants that may be associated with endometrial cancer risk. Methods We searched MEDLINE, Embase and CINAHL from 2007 to 2019 without restrictions. We followed PRISMA 2009 guidelines. The search yielded 3015 hits in total. Following duplicate exclusion, 2674 abstracts were screened and 453 full-texts evaluated based on our pre-defined screening criteria. 149 articles were eligible for inclusion. Results We found that single nucleotide polymorphisms (SNPs) in HNF1B, KLF, EIF2AK, CYP19A1, SOX4 and MYC were strongly associated with incident endometrial cancer. Nineteen variants were reported with genome-wide significance and a further five with suggestive significance. No convincing evidence was found for the widely studied MDM2 variant rs2279744. Publication bias and false discovery rates were noted throughout the literature. Conclusion Endometrial cancer risk may be influenced by SNPs in genes involved in cell survival, oestrogen metabolism and transcriptional control. Larger cohorts are needed to identify more variants with genome-wide significance.
Collapse
Affiliation(s)
- Cemsel Bafligil
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Deborah J Thompson
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Miriam J Smith
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK
| | - Neil Aj Ryan
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Anie Naqvi
- University of Manchester Medical School, Manchester, UK
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, University of Manchester, Manchester, UK .,Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester, UK
| |
Collapse
|
525
|
Yanes T, Young MA, Meiser B, James PA. Clinical applications of polygenic breast cancer risk: a critical review and perspectives of an emerging field. Breast Cancer Res 2020; 22:21. [PMID: 32066492 PMCID: PMC7026946 DOI: 10.1186/s13058-020-01260-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 02/07/2020] [Indexed: 01/04/2023] Open
Abstract
Polygenic factors are estimated to account for an additional 18% of the familial relative risk of breast cancer, with those at the highest level of polygenic risk distribution having a least a twofold increased risk of the disease. Polygenic testing promises to revolutionize health services by providing personalized risk assessments to women at high-risk of breast cancer and within population breast screening programs. However, implementation of polygenic testing needs to be considered in light of its current limitations, such as limited risk prediction for women of non-European ancestry. This article aims to provide a comprehensive review of the evidence for polygenic breast cancer risk, including the discovery of variants associated with breast cancer at the genome-wide level of significance and the use of polygenic risk scores to estimate breast cancer risk. We also review the different applications of this technology including testing of women from high-risk breast cancer families with uninformative genetic testing results, as a moderator of monogenic risk, and for population screening programs. Finally, a potential framework for introducing testing for polygenic risk in familial cancer clinics and the potential challenges with implementing this technology in clinical practice are discussed.
Collapse
Affiliation(s)
- Tatiane Yanes
- Psychosocial Research Group, Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia. .,The University of Queensland Diamantina Institute, Dermatology Research Centre, University of Queensland, Brisbane, QLD, 4102, Australia.
| | - Mary-Anne Young
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Bettina Meiser
- Psychosocial Research Group, Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Paul A James
- Parkville Integrated Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| |
Collapse
|
526
|
Abd-Alhussain GK, Alatrakji MQYMA, Saleh WA, Fawzi HA, Mahmood AS. Effects of tamoxifen on the reproductive system of female breast cancer patients: an ultrasound-based cohort study. F1000Res 2020; 9:102. [DOI: 10.12688/f1000research.21481.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Background: Tamoxifen (TMX) is regarded as standard treatment for breast cancer (BC) patients. In recent years, several studies have reported gynecological side effects and due to TMX's estrogenic effects. Here, we evaluate the side effects of TMX on the endometrium and ovaries of female BC patients. Methods: This was an ultrasound-based cohort study conducted in three oncology centers in Baghdad, Iraq. A total of 255 female patients were included, 140 premenopausal (PreM) and 115 postmenopausal (PostM), with estrogen receptor (ER)-positive BC using TMX adjuvant hormonal treatment for at least three months after surgery and adjuvant chemo/radiotherapy. Ultrasound (US) on the endometrium and ovaries of the women following BC surgery/chemotherapy (baseline) and at 3, 6, 12, and 24 months following was performed. Data collected included age, menopausal status, co-morbid chronic illness and medications, including duration of TMX treatment. Results: Presence of ovarian cyst was significantly higher in the PreM compared to PostM women, while there were no significant differences for other gynecological findings. At baseline, endometrial thickness (ET) was significantly higher in the PreM compared to the PostM women. In both groups, women with increased ET became more frequent from baseline to 3 months, from 3 to 6 months, from 6 to 12 months, and from 12 to 24 months. At all time periods, women with increased ET was significantly higher in the PostM compared PreM women, resulting in a risk of ET increase by 6 folds (ranging from 3 – 11 folds) in PostM compared to PreM women. Conclusions: Longer duration of TMX is associated with increased ET. Duration of TMX did not appear to increase the risk of various gynecological outcomes, for example endometrial cancer rate was low. Finally, there was an increase in ET, which appeared to be six-folds higher in PostM compared to PreM women.
Collapse
|
527
|
Affiliation(s)
- Ian A Scott
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
- University of Queensland, Brisbane, QLD, Australia
| | - John Attia
- University of Newcastle, Callaghan, NSW, Australia
- John Hunter Hospital, Newcastle, NSW, Australia
| | - Ray Moynihan
- Institute for Evidence-Based Healthcare, Bond University, Robina, QLD, Australia
- Sydney Medical School-Public Health, University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
528
|
Mostafavi H, Harpak A, Agarwal I, Conley D, Pritchard JK, Przeworski M. Variable prediction accuracy of polygenic scores within an ancestry group. eLife 2020; 9:48376. [PMID: 31999256 DOI: 10.1101/629949] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 01/28/2020] [Indexed: 05/25/2023] Open
Abstract
Fields as diverse as human genetics and sociology are increasingly using polygenic scores based on genome-wide association studies (GWAS) for phenotypic prediction. However, recent work has shown that polygenic scores have limited portability across groups of different genetic ancestries, restricting the contexts in which they can be used reliably and potentially creating serious inequities in future clinical applications. Using the UK Biobank data, we demonstrate that even within a single ancestry group (i.e., when there are negligible differences in linkage disequilibrium or in causal alleles frequencies), the prediction accuracy of polygenic scores can depend on characteristics such as the socio-economic status, age or sex of the individuals in which the GWAS and the prediction were conducted, as well as on the GWAS design. Our findings highlight both the complexities of interpreting polygenic scores and underappreciated obstacles to their broad use.
Collapse
Affiliation(s)
| | - Arbel Harpak
- Department of Biological Sciences, Columbia University, New York, United States
| | - Ipsita Agarwal
- Department of Biological Sciences, Columbia University, New York, United States
| | - Dalton Conley
- Department of Sociology, Princeton University, Princeton, United States
- Office of Population Research, Princeton University, Princeton, United States
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, United States
- Department of Biology, Stanford University, Stanford, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, United States
- Department of Systems Biology, Columbia University, New York, United States
| |
Collapse
|
529
|
Mostafavi H, Harpak A, Agarwal I, Conley D, Pritchard JK, Przeworski M. Variable prediction accuracy of polygenic scores within an ancestry group. eLife 2020; 9:e48376. [PMID: 31999256 PMCID: PMC7067566 DOI: 10.7554/elife.48376] [Citation(s) in RCA: 215] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 01/28/2020] [Indexed: 12/13/2022] Open
Abstract
Fields as diverse as human genetics and sociology are increasingly using polygenic scores based on genome-wide association studies (GWAS) for phenotypic prediction. However, recent work has shown that polygenic scores have limited portability across groups of different genetic ancestries, restricting the contexts in which they can be used reliably and potentially creating serious inequities in future clinical applications. Using the UK Biobank data, we demonstrate that even within a single ancestry group (i.e., when there are negligible differences in linkage disequilibrium or in causal alleles frequencies), the prediction accuracy of polygenic scores can depend on characteristics such as the socio-economic status, age or sex of the individuals in which the GWAS and the prediction were conducted, as well as on the GWAS design. Our findings highlight both the complexities of interpreting polygenic scores and underappreciated obstacles to their broad use.
Collapse
Affiliation(s)
| | - Arbel Harpak
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Ipsita Agarwal
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Dalton Conley
- Department of Sociology, Princeton UniversityPrincetonUnited States
- Office of Population Research, Princeton UniversityPrincetonUnited States
| | - Jonathan K Pritchard
- Department of Genetics, Stanford UniversityStanfordUnited States
- Department of Biology, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Molly Przeworski
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
| |
Collapse
|
530
|
Dörk T, Park-Simon TW, Hillemanns P. Recommendations Related to Genetic Testing for Breast Cancer. JAMA 2020; 323:188. [PMID: 31935022 DOI: 10.1001/jama.2019.18214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Thilo Dörk
- Department of Gynaecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Tjoung-Won Park-Simon
- Department of Gynaecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Peter Hillemanns
- Department of Gynaecology and Obstetrics, Hannover Medical School, Hannover, Germany
| |
Collapse
|
531
|
Qassim A, Souzeau E, Siggs OM, Hassall MM, Han X, Griffiths HL, Frost NA, Vallabh NA, Kirwan JF, Menon G, Cree AJ, Galanopoulos A, Agar A, Healey PR, Graham SL, Landers J, Casson RJ, Gharahkhani P, Willoughby CE, Hewitt AW, Lotery AJ, MacGregor S, Craig JE. An Intraocular Pressure Polygenic Risk Score Stratifies Multiple Primary Open-Angle Glaucoma Parameters Including Treatment Intensity. Ophthalmology 2020; 127:901-907. [PMID: 32081492 DOI: 10.1016/j.ophtha.2019.12.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 11/27/2022] Open
Abstract
PURPOSE To examine the combined effects of common genetic variants associated with intraocular pressure (IOP) on primary open-angle glaucoma (POAG) phenotype using a polygenic risk score (PRS) stratification. DESIGN Cross-sectional study. PARTICIPANTS For the primary analysis, we examined the glaucoma phenotype of 2154 POAG patients enrolled in the Australian and New Zealand Registry of Advanced Glaucoma, including patients recruited from the United Kingdom. For replication, we examined an independent cohort of 624 early POAG patients. METHODS Using IOP genome-wide association study summary statistics, we developed a PRS derived solely from IOP-associated variants and stratified POAG patients into 3 risk tiers. The lowest and highest quintiles of the score were set as the low- and high-risk groups, respectively, and the other quintiles were set as the intermediate risk group. MAIN OUTCOME MEASURES Clinical glaucoma phenotype including maximum recorded IOP, age at diagnosis, number of family members affected by glaucoma, cup-to-disc ratio, visual field mean deviation, and treatment intensity. RESULTS A dose-response relationship was found between the IOP PRS and the maximum recorded IOP, with the high genetic risk group having a higher maximum IOP by 1.7 mmHg (standard deviation [SD], 0.62 mmHg) than the low genetic risk group (P = 0.006). Compared with the low genetic risk group, the high genetic risk group had a younger age of diagnosis by 3.7 years (SD, 1.0 years; P < 0.001), more family members affected by 0.46 members (SD, 0.11 members; P < 0.001), and higher rates of incisional surgery (odds ratio, 1.5; 95% confidence interval, 1.1-2.0; P = 0.007). No statistically significant difference was found in mean deviation. We further replicated the maximum IOP, number of family members affected by glaucoma, and treatment intensity (number of medications) results in the early POAG cohort (P ≤ 0.01). CONCLUSIONS The IOP PRS was correlated positively with maximum IOP, disease severity, need for surgery, and number of affected family members. Genes acting via IOP-mediated pathways, when considered in aggregate, have clinically important and reproducible implications for glaucoma patients and their close family members.
Collapse
Affiliation(s)
- Ayub Qassim
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia.
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Owen M Siggs
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Mark M Hassall
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Helen L Griffiths
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - N Andrew Frost
- Department of Ophthalmology, Torbay Hospital, Torquay, Devon, United Kingdom
| | - Neeru A Vallabh
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - James F Kirwan
- Department of Ophthalmology, Portsmouth Hospitals, Portsmouth, United Kingdom
| | - Geeta Menon
- Department of Ophthalmology, Frimley Park Hospital NHS Foundation Trust, Frimley, United Kingdom
| | - Angela J Cree
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Anna Galanopoulos
- South Australian Institute of Ophthalmology, Royal Adelaide Hospital, Adelaide, Australia
| | - Ashish Agar
- Department of Ophthalmology, Prince of Wales Hospital, Randwick, Australia
| | - Paul R Healey
- Centre for Vision Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Stuart L Graham
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - John Landers
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Robert J Casson
- South Australian Institute of Ophthalmology, University of Adelaide, Adelaide, Australia
| | | | - Colin E Willoughby
- Biomedical Sciences Research Institute, Ulster University, Coleraine, United Kingdom; Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Andrew J Lotery
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| |
Collapse
|
532
|
Mota NR, Franke B. 30-year journey from the start of the Human Genome Project to clinical application of genomics in psychiatry: are we there yet? Lancet Psychiatry 2020; 7:7-9. [PMID: 31860458 DOI: 10.1016/s2215-0366(19)30477-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 11/25/2022]
Affiliation(s)
- Nina Roth Mota
- Department of Human Genetics and Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, Netherlands
| | - Barbara Franke
- Department of Human Genetics and Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, Netherlands.
| |
Collapse
|
533
|
Berger MJ, Williams HE, Barrett R, Zimmer AD, McKennon W, Hong H, Ginsberg J, Zhou AY, Neben CL. Color Data v2: a user-friendly, open-access database with hereditary cancer and hereditary cardiovascular conditions datasets. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5979743. [PMID: 33181822 PMCID: PMC7661094 DOI: 10.1093/database/baaa083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 11/14/2022]
Abstract
Publicly available genetic databases promote data sharing and fuel scientific discoveries for the prevention, treatment and management of disease. In 2018, we built Color Data, a user-friendly, open access database containing genotypic and self-reported phenotypic information from 50 000 individuals who were sequenced for 30 genes associated with hereditary cancer. In a continued effort to promote access to these types of data, we launched Color Data v2, an updated version of the Color Data database. This new release includes additional clinical genetic testing results from more than 18 000 individuals who were sequenced for 30 genes associated with hereditary cardiovascular conditions as well as polygenic risk scores for breast cancer, coronary artery disease and atrial fibrillation. In addition, we used self-reported phenotypic information to implement the following four clinical risk models: Gail Model for 5-year risk of breast cancer, Claus Model for lifetime risk of breast cancer, simple office-based Framingham Coronary Heart Disease Risk Score for 10-year risk of coronary heart disease and CHARGE-AF simple score for 5-year risk of atrial fibrillation. These new features and capabilities are highlighted through two sample queries in the database. We hope that the broad dissemination of these data will help researchers continue to explore genotype–phenotype correlations and identify novel variants for functional analysis, enabling scientific discoveries in the field of population genomics. Database URL: https://data.color.com/
Collapse
Affiliation(s)
- Mark J Berger
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Hannah E Williams
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Ryan Barrett
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Anjali D Zimmer
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Wendy McKennon
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Huy Hong
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Jeremy Ginsberg
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Alicia Y Zhou
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Cynthia L Neben
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| |
Collapse
|
534
|
Gierach GL, Choudhury PP, García-Closas M. Toward Risk-Stratified Breast Cancer Screening: Considerations for Changes in Screening Guidelines. JAMA Oncol 2020; 6:31-33. [PMID: 31725821 PMCID: PMC8170848 DOI: 10.1001/jamaoncol.2019.3820] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Gretchen L Gierach
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Parichoy Pal Choudhury
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Montserrat García-Closas
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| |
Collapse
|
535
|
Muller C, Yurgelun M, Kupfer SS. Precision Treatment and Prevention of Colorectal Cancer-Hope or Hype? Gastroenterology 2020; 158:441-446. [PMID: 31622623 PMCID: PMC6957699 DOI: 10.1053/j.gastro.2019.09.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Charles Muller
- Section of Gastroenterology, Hepatology and Nutrition, University of Chicago, Chicago, Illinois
| | | | - Sonia S Kupfer
- Section of Gastroenterology, Hepatology and Nutrition, University of Chicago, Chicago, Illinois.
| |
Collapse
|
536
|
Giardiello D, Steyerberg EW, Hauptmann M, Adank MA, Akdeniz D, Blomqvist C, Bojesen SE, Bolla MK, Brinkhuis M, Chang-Claude J, Czene K, Devilee P, Dunning AM, Easton DF, Eccles DM, Fasching PA, Figueroa J, Flyger H, García-Closas M, Haeberle L, Haiman CA, Hall P, Hamann U, Hopper JL, Jager A, Jakubowska A, Jung A, Keeman R, Kramer I, Lambrechts D, Le Marchand L, Lindblom A, Lubiński J, Manoochehri M, Mariani L, Nevanlinna H, Oldenburg HSA, Pelders S, Pharoah PDP, Shah M, Siesling S, Smit VTHBM, Southey MC, Tapper WJ, Tollenaar RAEM, van den Broek AJ, van Deurzen CHM, van Leeuwen FE, van Ongeval C, Van't Veer LJ, Wang Q, Wendt C, Westenend PJ, Hooning MJ, Schmidt MK. Prediction and clinical utility of a contralateral breast cancer risk model. Breast Cancer Res 2019; 21:144. [PMID: 31847907 PMCID: PMC6918633 DOI: 10.1186/s13058-019-1221-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/29/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Breast cancer survivors are at risk for contralateral breast cancer (CBC), with the consequent burden of further treatment and potentially less favorable prognosis. We aimed to develop and validate a CBC risk prediction model and evaluate its applicability for clinical decision-making. METHODS We included data of 132,756 invasive non-metastatic breast cancer patients from 20 studies with 4682 CBC events and a median follow-up of 8.8 years. We developed a multivariable Fine and Gray prediction model (PredictCBC-1A) including patient, primary tumor, and treatment characteristics and BRCA1/2 germline mutation status, accounting for the competing risks of death and distant metastasis. We also developed a model without BRCA1/2 mutation status (PredictCBC-1B) since this information was available for only 6% of patients and is routinely unavailable in the general breast cancer population. Prediction performance was evaluated using calibration and discrimination, calculated by a time-dependent area under the curve (AUC) at 5 and 10 years after diagnosis of primary breast cancer, and an internal-external cross-validation procedure. Decision curve analysis was performed to evaluate the net benefit of the model to quantify clinical utility. RESULTS In the multivariable model, BRCA1/2 germline mutation status, family history, and systemic adjuvant treatment showed the strongest associations with CBC risk. The AUC of PredictCBC-1A was 0.63 (95% prediction interval (PI) at 5 years, 0.52-0.74; at 10 years, 0.53-0.72). Calibration-in-the-large was -0.13 (95% PI: -1.62-1.37), and the calibration slope was 0.90 (95% PI: 0.73-1.08). The AUC of Predict-1B at 10 years was 0.59 (95% PI: 0.52-0.66); calibration was slightly lower. Decision curve analysis for preventive contralateral mastectomy showed potential clinical utility of PredictCBC-1A between thresholds of 4-10% 10-year CBC risk for BRCA1/2 mutation carriers and non-carriers. CONCLUSIONS We developed a reasonably calibrated model to predict the risk of CBC in women of European-descent; however, prediction accuracy was moderate. Our model shows potential for improved risk counseling, but decision-making regarding contralateral preventive mastectomy, especially in the general breast cancer population where limited information of the mutation status in BRCA1/2 is available, remains challenging.
Collapse
Affiliation(s)
- Daniele Giardiello
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Ewout W Steyerberg
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Michael Hauptmann
- Institute of Biometry and Registry Research, Brandenburg Medical School, Neuruppin, Germany
- Department of Epidemiology and Biostatistics, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Muriel A Adank
- The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Family Cancer Clinic, Amsterdam, The Netherlands
| | - Delal Akdeniz
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Oncology, Örebro University Hospital, Örebro, Sweden
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mariël Brinkhuis
- East-Netherlands, Laboratory for Pathology, Hengelo, The Netherlands
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, 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
| | - Diana M Eccles
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Peter A Fasching
- Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Edinburgh, UK
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Montserrat García-Closas
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Lothar Haeberle
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Audrey Jung
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Iris Kramer
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Loic Le Marchand
- University of Hawaii Cancer Center, Epidemiology Program, Honolulu, HI, USA
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Luigi Mariani
- Unit of Clinical Epidemiology and Trial Organization, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Hester S A Oldenburg
- Department of Surgical Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Saskia Pelders
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Paul D P Pharoah
- 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
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Sabine Siesling
- Department of Research, Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Vincent T H B M Smit
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexandra J van den Broek
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | | | - Flora E van Leeuwen
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Chantal van Ongeval
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Laura J Van't Veer
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Camilla Wendt
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | | | - Maartje J Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands.
| |
Collapse
|
537
|
Öfverholm A, Einbeigi Z, Wigermo A, Holmberg E, Karsson P. Increased Overall Mortality Even after Risk Reducing Surgery for BRCA-Positive Women in Western Sweden. Genes (Basel) 2019; 10:genes10121046. [PMID: 31888263 PMCID: PMC6947302 DOI: 10.3390/genes10121046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/02/2019] [Accepted: 12/12/2019] [Indexed: 11/16/2022] Open
Abstract
Women with BRCA variants have a high lifetime risk of developing breast and ovarian cancer. The aim of this study was to investigate the standard incidence ratios (SIR) for breast and ovarian cancer and standard mortality ratios (SMR) in a population-based cohort of women in Western Sweden, under surveillance and after risk reducing surgery. Women who tested positive for a BRCA variant between 1995–2016 (n = 489) were prospectively registered and followed up for cancer incidence, risk reducing surgery and mortality. The Swedish Cancer Register was used to compare breast and ovarian cancer incidence and mortality with and without risk reducing surgery for women with BRCA variants in comparison to women in the general population. SIR for breast cancer under surveillance until risk-reducing mastectomy (RRM) was 14.0 (95% CI 9.42–20.7) and decreased to 1.93 (95% CI 0.48–7.7) after RRM. The SIR for ovarian cancer was 124.6 (95% CI 59.4–261.3) under surveillance until risk reducing salpingo-oophorectomy (RRSO) and decreased to 13.5 (95% CI 4.34–41.8) after RRSO. The SMR under surveillance before any risk reducing surgery was 5.56 (95% 2.09–14.8) and after both RRM and RRSO 4.32 (95% CI 1.62–11.5). Women with cancer diagnoses from the pathology report after risk reducing surgery were excluded from the analyses. Risk reducing surgery reduced the incidence of breast and ovarian cancer in women with BRCA variants. However, overall mortality was significantly increased in comparison to the women in the general population and remained elevated even after risk reducing surgery. These findings warrant further research regarding additional measures for these women.
Collapse
Affiliation(s)
- Anna Öfverholm
- Department of Oncology, Institution of Clinical Sciences, Sahlgrenska Academy, Sahlgrenska University Hospital, University of Gothenburg, 413 45 Gothenburg, Sweden; (A.Ö.); (Z.E.); (E.H.)
| | - Zakaria Einbeigi
- Department of Oncology, Institution of Clinical Sciences, Sahlgrenska Academy, Sahlgrenska University Hospital, University of Gothenburg, 413 45 Gothenburg, Sweden; (A.Ö.); (Z.E.); (E.H.)
| | | | - Erik Holmberg
- Department of Oncology, Institution of Clinical Sciences, Sahlgrenska Academy, Sahlgrenska University Hospital, University of Gothenburg, 413 45 Gothenburg, Sweden; (A.Ö.); (Z.E.); (E.H.)
| | - Per Karsson
- Department of Oncology, Institution of Clinical Sciences, Sahlgrenska Academy, Sahlgrenska University Hospital, University of Gothenburg, 413 45 Gothenburg, Sweden; (A.Ö.); (Z.E.); (E.H.)
- Correspondence:
| |
Collapse
|
538
|
Treff NR, Eccles J, Lello L, Bechor E, Hsu J, Plunkett K, Zimmerman R, Rana B, Samoilenko A, Hsu S, Tellier LCAM. Utility and First Clinical Application of Screening Embryos for Polygenic Disease Risk Reduction. Front Endocrinol (Lausanne) 2019; 10:845. [PMID: 31920964 PMCID: PMC6915076 DOI: 10.3389/fendo.2019.00845] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022] Open
Abstract
For over 2 decades preimplantation genetic testing (PGT) has been in clinical use to reduce the risk of miscarriage and genetic disease in patients with advanced maternal age and risk of transmitting disease. Recently developed methods of genome-wide genotyping and machine learning algorithms now offer the ability to genotype embryos for polygenic disease risk with accuracy equivalent to adults. In addition, contemporary studies on adults indicate the ability to predict polygenic disorders with risk equivalent to monogenic disorders. Existing biobanks provide opportunities to model the clinical utility of polygenic disease risk reduction among sibling adults. Here, we provide a mathematical model for the use of embryo screening to reduce the risk of type 1 diabetes. Results indicate a 45-72% reduced risk with blinded genetic selection of one sibling. The first clinical case of polygenic risk scoring in human preimplantation embryos from patients with a family history of complex disease is reported. In addition to these data, several common and accepted practices place PGT for polygenic disease risk in the applicable context of contemporary reproductive medicine. In addition, prediction of risk for PCOS, endometriosis, and aneuploidy are of particular interest and relevance to patients with infertility and represent an important focus of future research on polygenic risk scoring in embryos.
Collapse
Affiliation(s)
- Nathan R. Treff
- Genomic Prediction Inc., North Brunswick, NJ, United States
- Genomic Prediction Clinical Laboratory, North Brunswick, NJ, United States
| | - Jennifer Eccles
- Genomic Prediction Inc., North Brunswick, NJ, United States
- Genomic Prediction Clinical Laboratory, North Brunswick, NJ, United States
| | - Lou Lello
- Genomic Prediction Inc., North Brunswick, NJ, United States
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, United States
| | - Elan Bechor
- Genomic Prediction Inc., North Brunswick, NJ, United States
| | - Jeffrey Hsu
- Genomic Prediction Inc., North Brunswick, NJ, United States
| | - Kathryn Plunkett
- Genomic Prediction Inc., North Brunswick, NJ, United States
- Genomic Prediction Clinical Laboratory, North Brunswick, NJ, United States
| | - Raymond Zimmerman
- Genomic Prediction Inc., North Brunswick, NJ, United States
- Genomic Prediction Clinical Laboratory, North Brunswick, NJ, United States
| | - Bhavini Rana
- Genomic Prediction Inc., North Brunswick, NJ, United States
- Genomic Prediction Clinical Laboratory, North Brunswick, NJ, United States
| | | | - Steven Hsu
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, United States
| | - Laurent C. A. M. Tellier
- Genomic Prediction Inc., North Brunswick, NJ, United States
- Genomic Prediction Clinical Laboratory, North Brunswick, NJ, United States
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, United States
| |
Collapse
|
539
|
Udler MS, McCarthy MI, Florez JC, Mahajan A. Genetic Risk Scores for Diabetes Diagnosis and Precision Medicine. Endocr Rev 2019; 40:1500-1520. [PMID: 31322649 PMCID: PMC6760294 DOI: 10.1210/er.2019-00088] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022]
Abstract
During the last decade, there have been substantial advances in the identification and characterization of DNA sequence variants associated with individual predisposition to type 1 and type 2 diabetes. As well as providing insights into the molecular, cellular, and physiological mechanisms involved in disease pathogenesis, these risk variants, when combined into a polygenic score, capture information on individual patterns of disease predisposition that have the potential to influence clinical management. In this review, we describe the various opportunities that polygenic scores provide: to predict diabetes risk, to support differential diagnosis, and to understand phenotypic and clinical heterogeneity. We also describe the challenges that will need to be overcome if this potential is to be fully realized.
Collapse
Affiliation(s)
- Miriam S Udler
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Headington, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jose C Florez
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
540
|
Homburger JR, Neben CL, Mishne G, Zhou AY, Kathiresan S, Khera AV. Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores. Genome Med 2019; 11:74. [PMID: 31771638 PMCID: PMC6880438 DOI: 10.1186/s13073-019-0682-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/01/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Inherited susceptibility to common, complex diseases may be caused by rare, pathogenic variants ("monogenic") or by the cumulative effect of numerous common variants ("polygenic"). Comprehensive genome interpretation should enable assessment for both monogenic and polygenic components of inherited risk. The traditional approach requires two distinct genetic testing technologies-high coverage sequencing of known genes to detect monogenic variants and a genome-wide genotyping array followed by imputation to calculate genome-wide polygenic scores (GPSs). We assessed the feasibility and accuracy of using low coverage whole genome sequencing (lcWGS) as an alternative to genotyping arrays to calculate GPSs. METHODS First, we performed downsampling and imputation of WGS data from ten individuals to assess concordance with known genotypes. Second, we assessed the correlation between GPSs for 3 common diseases-coronary artery disease (CAD), breast cancer (BC), and atrial fibrillation (AF)-calculated using lcWGS and genotyping array in 184 samples. Third, we assessed concordance of lcWGS-based genotype calls and GPS calculation in 120 individuals with known genotypes, selected to reflect diverse ancestral backgrounds. Fourth, we assessed the relationship between GPSs calculated using lcWGS and disease phenotypes in a cohort of 11,502 individuals of European ancestry. RESULTS We found imputation accuracy r2 values of greater than 0.90 for all ten samples-including those of African and Ashkenazi Jewish ancestry-with lcWGS data at 0.5×. GPSs calculated using lcWGS and genotyping array followed by imputation in 184 individuals were highly correlated for each of the 3 common diseases (r2 = 0.93-0.97) with similar score distributions. Using lcWGS data from 120 individuals of diverse ancestral backgrounds, we found similar results with respect to imputation accuracy and GPS correlations. Finally, we calculated GPSs for CAD, BC, and AF using lcWGS in 11,502 individuals of European ancestry, confirming odds ratios per standard deviation increment ranging 1.28 to 1.59, consistent with previous studies. CONCLUSIONS lcWGS is an alternative technology to genotyping arrays for common genetic variant assessment and GPS calculation. lcWGS provides comparable imputation accuracy while also overcoming the ascertainment bias inherent to variant selection in genotyping array design.
Collapse
Affiliation(s)
| | - Cynthia L Neben
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Gilad Mishne
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Alicia Y Zhou
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | | | - Amit V Khera
- Center for Genomic Medicine and Cardiology Division, Department of Medicine, Massachusetts General Hospital, Simches Research Building | CPZN 6.256, Boston, MA, 02114, USA.
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
541
|
Janssens ACJW. Validity of polygenic risk scores: are we measuring what we think we are? Hum Mol Genet 2019; 28:R143-R150. [PMID: 31504522 PMCID: PMC7013150 DOI: 10.1093/hmg/ddz205] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
Polygenic risk scores (PRSs) have become the standard for quantifying genetic liability in the prediction of disease risks. PRSs are generally constructed as weighted sum scores of risk alleles using effect sizes from genome-wide association studies as their weights. The construction of PRSs is being improved with more appropriate selection of independent single-nucleotide polymorphisms (SNPs) and optimized estimation of their weights but is rarely reflected upon from a theoretical perspective, focusing on the validity of the risk score. Borrowing from psychometrics, this paper discusses the validity of PRSs and introduces the three main types of validity that are considered in the evaluation of tests and measurements: construct, content, and criterion validity. This introduction is followed by a discussion of three topics that challenge the validity of PRS, namely, their claimed independence of clinical risk factors, the consequences of relaxing SNP inclusion thresholds and the selection of SNP weights. This discussion of the validity of PRS reminds us that we need to keep questioning if weighted sums of risk alleles are measuring what we think they are in the various scenarios in which PRSs are used and that we need to keep exploring alternative modeling strategies that might better reflect the underlying biological pathways.
Collapse
Affiliation(s)
- A Cecile J W Janssens
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, USA
| |
Collapse
|
542
|
Flügge F, Figge L, Duhm-Harbeck P, Kammler R, Habermann JK. How clinical biobanks can support precision medicine: from standardized preprocessing to treatment guidance. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2019. [DOI: 10.1080/23808993.2019.1690395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Friedemann Flügge
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
| | - Lena Figge
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
| | | | - Rosita Kammler
- Translational Research Coordination for International Breast Cancer Study Group and European Thoracic Oncology Platform, Bern, Switzerland
- European, Middle Eastern and African Society for Biopreservation and Biobanking, Brussels, Belgium
| | - Jens K. Habermann
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
- European, Middle Eastern and African Society for Biopreservation and Biobanking, Brussels, Belgium
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein (UKSH), Lübeck, Germany
| |
Collapse
|
543
|
Nguyen TL, Li S, Dite GS, Aung YK, Evans CF, Trinh HN, Baglietto L, Stone J, Song YM, Sung J, English DR, Jenkins MA, Dugué PA, Milne RL, Southey MC, Giles GG, Pike MC, Hopper JL. Interval breast cancer risk associations with breast density, family history and breast tissue aging. Int J Cancer 2019; 147:375-382. [PMID: 31609476 PMCID: PMC7318124 DOI: 10.1002/ijc.32731] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/16/2019] [Accepted: 09/27/2019] [Indexed: 01/04/2023]
Abstract
Interval breast cancers (those diagnosed between recommended mammography screens) generally have poorer outcomes and are more common among women with dense breasts. We aimed to develop a risk model for interval breast cancer. We conducted a nested case-control study within the Melbourne Collaborative Cohort Study involving 168 interval breast cancer patients and 498 matched control subjects. We measured breast density using the CUMULUS software. We recorded first-degree family history by questionnaire, measured body mass index (BMI) and calculated age-adjusted breast tissue aging, a novel measure of exposure to estrogen and progesterone based on the Pike model. We fitted conditional logistic regression to estimate odds ratio (OR) or odds ratio per adjusted standard deviation (OPERA) and calculated the area under the receiver operating characteristic curve (AUC). The stronger risk associations were for unadjusted percent breast density (OPERA = 1.99; AUC = 0.66), more so after adjusting for age and BMI (OPERA = 2.26; AUC = 0.70), and for family history (OR = 2.70; AUC = 0.56). When the latter two factors and their multiplicative interactions with age-adjusted breast tissue aging (p = 0.01 and 0.02, respectively) were fitted, the AUC was 0.73 (95% CI 0.69-0.77), equivalent to a ninefold interquartile risk ratio. In summary, compared with using dense breasts alone, risk discrimination for interval breast cancers could be doubled by instead using breast density, BMI, family history and hormonal exposure. This would also give women with dense breasts, and their physicians, more information about the major consequence of having dense breasts-an increased risk of developing an interval breast cancer.
Collapse
Affiliation(s)
- Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Ye K Aung
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Christopher F Evans
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Ho N Trinh
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Jennifer Stone
- Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, WA, Australia
| | - Yun-Mi Song
- Department of Family Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Joohon Sung
- Department of Epidemiology School of Public Health, Seoul National University, Seoul, South Korea.,Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Dallas R English
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Pierre-Antoine Dugué
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, 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
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, 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
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, 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
| | - Malcolm C Pike
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
544
|
Guan Z, Raut JR, Weigl K, Schöttker B, Holleczek B, Zhang Y, Brenner H. Individual and joint performance of DNA methylation profiles, genetic risk score and environmental risk scores for predicting breast cancer risk. Mol Oncol 2019; 14:42-53. [PMID: 31677238 PMCID: PMC6944111 DOI: 10.1002/1878-0261.12594] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 08/30/2019] [Accepted: 10/24/2019] [Indexed: 12/24/2022] Open
Abstract
DNA methylation patterns in the blood, genetic risk scores (GRSs), and environmental risk factors can potentially improve breast cancer (BC) risk prediction. We assessed the individual and joint predictive performance of methylation, GRS, and environmental risk factors for BC incidence in a prospective cohort study. In a cohort of 5462 women aged 50–75 from Germany, 101 BC cases were identified during 14 years of follow‐up and were compared to 263 BC‐free controls in a nested case–control design. Three previously suggested methylation risk scores (MRSs) based on methylation of 423, 248, and 131 cytosine‐phosphate‐guanine (CpG) loci, and a GRS based on the risk alleles from 269 recently identified single nucleotide polymorphisms were constructed. Additionally, multiple previously proposed environmental risk scores (ERSs) were built based on environmental variables. Areas under the receiver operating characteristic curves (AUCs) were estimated for evaluating BC risk prediction performance. MRS and ERS showed limited accuracy in predicting BC incidence, with AUCs ranging from 0.52 to 0.56 and from 0.52 to 0.59, respectively. The GRS predicted BC incidence with a higher accuracy (AUC = 0.61). Adjusted odds ratios per standard deviation increase (95% confidence interval) were 1.07 (0.84–1.36) and 1.40 (1.09–1.80) for the best performing MRS and ERS, respectively, and 1.48 (1.16–1.90) for the GRS. A full risk model combining the MRS, GRS, and ERS predicted BC incidence with the highest accuracy (AUC = 0.64) and might be useful for identifying high‐risk populations for BC screening.
Collapse
Affiliation(s)
- Zhong Guan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Medical Faculty Heidelberg, University of Heidelberg, Germany
| | - Janhavi R Raut
- Medical Faculty Heidelberg, University of Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Network Aging Research, University of Heidelberg, Germany
| | | | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
545
|
Esquivel-Sada D, Lévesque E, Hagan J, Knoppers BM, Simard J. Envisioning Implementation of a Personalized Approach in Breast Cancer Screening Programs: Stakeholder Perspectives. Healthc Policy 2019; 15:39-54. [PMID: 32077844 PMCID: PMC7020798 DOI: 10.12927/hcpol.2019.26072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Advances in genomics and epidemiology can foster the implementation of a risk-based approach to current age-based breast cancer screening programs. This personalized approach would challenge the trajectory for women in the healthcare system by adding both a risk-assessment step (including a genomic test) and screening options. OBJECTIVE The aim of this study is to explore, from an organizational perspective, the acceptability of different proposals for each step of the trajectory for women in the healthcare system should a personalized approach be implemented in the province of Quebec. METHODS We interviewed 20 professional stakeholders who are either involved in the current breast cancer screening program in Quebec or who are likely to play a role in the future implementation of a personalized risk-based approach. RESULTS|DISCUSSION Preferences are split between proposals supporting self-management by the women themselves (e.g., solicitation through media campaign, self-collection of information and sample and results provided by letter) and proposals prioritizing more interaction between women and healthcare providers (e.g., solicitation by health professionals, collection of information and samples by a nurse and results provided by health professionals).
Collapse
Affiliation(s)
- Daphne Esquivel-Sada
- Sociologist, Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC
| | - Emmanuelle Lévesque
- Lawyer and Academic Associate, Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC
| | - Julie Hagan
- Academic Associate, Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine McGill University, Montreal, QC
| | - Bartha Maria Knoppers
- Professor, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Director, Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC
| | - Jacques Simard
- Professor, Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec City, QC
| |
Collapse
|
546
|
Daly MB, Ross E. Breast Cancer Chemoprevention—Can We Make a Case for Precision Medicine? JAMA Oncol 2019; 5:1542-1544. [DOI: 10.1001/jamaoncol.2019.3785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Eric Ross
- Population Studies Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| |
Collapse
|
547
|
Roberts MR, Sordillo JE, Kraft P, Asgari MM. Sex-Stratified Polygenic Risk Score Identifies Individuals at Increased Risk of Basal Cell Carcinoma. J Invest Dermatol 2019; 140:971-975. [PMID: 31682843 DOI: 10.1016/j.jid.2019.09.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/16/2019] [Accepted: 09/03/2019] [Indexed: 12/13/2022]
Abstract
The incidence of basal cell carcinoma (BCC) is higher among men than women. Susceptibility loci for BCC have been identified through genome-wide association studies, and two previous studies have found polygenic risk scores (PRS) to be significantly associated with the risk of BCC. However, to our knowledge, sex-stratified PRS analyses examining the genetic contribution to BCC risk among men and women have not been previously reported. To quantify the contribution of genetic variability on the BCC risk by sex, we derived a polygenic risk score and estimated the genetic relative risk distribution for men and women. Using 29 published single nucleotide polymorphisms, we found that the estimated relative risk of BCC increases with higher percentiles of the polygenic risk score. For men, the estimated risk of BCC is twice the average population risk at the 88th percentile, while for women, this occurs at the 99th percentile. Our findings indicate that there is a significant impact of genetic variation on the risk of developing BCC and that this impact may be greater for men than for women. Polygenic risk scores may be clinically useful tools for risk stratification, particularly in combination with other known risk factors for BCC development.
Collapse
Affiliation(s)
- Michelle R Roberts
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
| | - Joanne E Sordillo
- Department of Population Medicine, Harvard Pilgrim Healthcare Institute, Boston, Massachusetts
| | - Peter Kraft
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Maryam M Asgari
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts; Department of Population Medicine, Harvard Pilgrim Healthcare Institute, Boston, Massachusetts.
| |
Collapse
|
548
|
Lammert J, Skandarajah AR, Shackleton K, Calder P, Thomas S, Lindeman GJ, Mann GB. Outcomes of women at high familial risk for breast cancer: An 8-year single-center experience. Asia Pac J Clin Oncol 2019; 16:e27-e37. [PMID: 31657879 DOI: 10.1111/ajco.13274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/04/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The value of a high-risk surveillance program for mutation carriers and women at high familial breast cancer risk has not been extensively studied. A Breast and Ovarian Cancer Risk Management Clinic (BOCRMC) was established at the Royal Melbourne Hospital in 2010 to provide multimodality screening and risk management strategies for this group of women. The aims of this study were to evaluate the program and describe breast cancer diagnoses for BRCA1, BRCA2, and other germline mutation carriers as well as high-risk noncarriers attending the BOCRMC. METHODS Clinical data from mutation carriers and noncarriers with a ≥25% lifetime risk of developing breast cancer who attended between 2010 and 2018 were extracted from clinic records and compared. The pattern and mode of detection of cancer were determined. RESULTS A total of 206 mutation carriers and 305 noncarriers attended the BOCRMC and underwent screening on at least one occasion. Median age was 37 years. After a median follow-up of 34 months, 15 (seven invasive) breast cancers were identified in mutation carriers, with seven (six invasive) breast cancers identified in noncarriers. Of these, 20 (90.9%) were detected by annual screening, whereas two (9.1%) were detected as interval cancers (both in BRCA1 mutation carriers). Median size of the invasive breast cancers was 11 mm (range: 1.5-30 mm). The majority (76.9%) were axillary node negative. In women aged 25-49 years, the annualized cancer incidence was 1.6% in BRCA1, 1.4% in BRCA2 mutation carriers, and 0.5% in noncarriers. This compares to 0.06% annualized cancer incidence in the general Australian population. CONCLUSIONS Screening was effective at detecting early-stage cancers. The incidence of events in young noncarriers was substantially higher than in the general population. This potentially justifies ongoing management through a specialty clinic, although further research to better personalize risk assessment in noncarriers is required.
Collapse
Affiliation(s)
- Jacqueline Lammert
- Department of Gynecology and Center for Hereditary Breast and Ovarian Cancer, University Hospital rechts der Isar, Technical University of Munich (TUM), Munich, Germany
| | - Anita R Skandarajah
- Breast Service, The Royal Melbourne and Royal Women's Hospitals, Parkville, Victoria, Australia.,Department of Surgery, The University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Kylie Shackleton
- Breast Service, The Royal Melbourne and Royal Women's Hospitals, Parkville, Victoria, Australia.,Familial Cancer Centre, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Patricia Calder
- Familial Cancer Centre, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Susan Thomas
- Breast Service, The Royal Melbourne and Royal Women's Hospitals, Parkville, Victoria, Australia.,Familial Cancer Centre, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Geoffrey J Lindeman
- Breast Service, The Royal Melbourne and Royal Women's Hospitals, Parkville, Victoria, Australia.,Familial Cancer Centre, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medicine, The University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Gregory Bruce Mann
- Breast Service, The Royal Melbourne and Royal Women's Hospitals, Parkville, Victoria, Australia.,Department of Surgery, The University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
| |
Collapse
|
549
|
Glentis S, Dimopoulos AC, Rouskas K, Ntritsos G, Evangelou E, Narod SA, Mes-Masson AM, Foulkes WD, Rivera B, Tonin PN, Ragoussis J, Dimas AS. Exome Sequencing in BRCA1- and BRCA2-Negative Greek Families Identifies MDM1 and NBEAL1 as Candidate Risk Genes for Hereditary Breast Cancer. Front Genet 2019; 10:1005. [PMID: 31681433 PMCID: PMC6813924 DOI: 10.3389/fgene.2019.01005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/20/2019] [Indexed: 12/30/2022] Open
Abstract
Approximately 10% of breast cancer (BC) cases are hereditary BC (HBC), with HBC most commonly encountered in the context of hereditary breast and ovarian cancer (HBOC) syndrome. Although thousands of loss-of-function (LoF) alleles in over 20 genes have been associated with HBC susceptibility, the genetic etiology of approximately 50% of cases remains unexplained, even when polygenic risk models are considered. We focused on one of the least-studied European populations and applied whole-exome sequencing (WES) to 52 individuals from 17 Greek HBOC families, in which at least one patient was negative for known HBC risk variants. Initial screening revealed pathogenic variants in known cancer genes, including BARD1:p.Trp91* detected in a cancer-free individual, and MEN1:p.Glu260Lys detected in a BC patient. Gene- and variant-based approaches were applied to exome data to identify candidate risk variants outside of known risk genes. Findings were verified in a collection of Canadian HBOC patients of European ancestry (FBRCAX), in an independent group of Canadian BC patients (CHUM-BC) and controls (CARTaGENE), as well as in individuals from The Cancer Genome Atlas (TCGA) and the UK Biobank (UKB). Rare LoF variants were uncovered in MDM1 and NBEAL1 in Greek and Canadian HBOC patients. We also report prioritized missense variants SETBP1:c.4129G > C and C7orf34:c.248C > T. These variants comprise promising candidates whose role in cancer pathogenicity needs to be explored further.
Collapse
Affiliation(s)
- Stavros Glentis
- Division of Molecular Biology and Genetics, Biomedical Sciences Research Center Al. Fleming, Vari, Greece
| | - Alexandros C Dimopoulos
- Division of Molecular Biology and Genetics, Biomedical Sciences Research Center Al. Fleming, Vari, Greece
| | - Konstantinos Rouskas
- Division of Molecular Biology and Genetics, Biomedical Sciences Research Center Al. Fleming, Vari, Greece
| | - George Ntritsos
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece.,Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Steven A Narod
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.,Women's College Research Institute, Women's College Hospital, Toronto, ON, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
| | - William D Foulkes
- Department of Oncology, McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Department of Medical Genetics, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Barbara Rivera
- Department of Oncology, McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Patricia N Tonin
- Department of Medicine, McGill University, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada.,Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Oncology, McGill University, Montreal, QC, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Antigone S Dimas
- Division of Molecular Biology and Genetics, Biomedical Sciences Research Center Al. Fleming, Vari, Greece
| |
Collapse
|
550
|
A systems approach to clinical oncology uses deep phenotyping to deliver personalized care. Nat Rev Clin Oncol 2019; 17:183-194. [DOI: 10.1038/s41571-019-0273-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2019] [Indexed: 02/06/2023]
|