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Article ; Online: Polygenic risk scores in cancer screening: a glass half full or half empty?

Pashayan, Nora / Easton, Douglas F / Michailidou, Kyriaki

2023 Volume 24, Issue 6, Page(s) 579–581

MeSH term(s)	Humans ; Early Detection of Cancer ; Neoplasms/diagnosis ; Neoplasms/genetics ; Risk Factors
Language	English
Publishing date	2023-05-10
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	2049730-1
ISSN	1474-5488 ; 1470-2045
ISSN (online)	1474-5488
ISSN	1470-2045
DOI	10.1016/S1470-2045(23)00217-6
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Article ; Online: Estimation of age of onset and progression of breast cancer by absolute risk dependent on polygenic risk score and other risk factors.

Bhatt, Rikesh / van den Hout, Ardo / Antoniou, Antonis C / Shah, Mitul / Ficorella, Lorenzo / Steggall, Emily / Easton, Douglas F / Pharoah, Paul D P / Pashayan, Nora

Cancer

2024 Volume 130, Issue 9, Page(s) 1590–1599

Abstract: Background: Genetic, lifestyle, reproductive, and anthropometric factors are associated with the risk of developing breast cancer. However, it is not yet known whether polygenic risk score (PRS) and absolute risk based on a combination of risk factors ... ...

Abstract	Background: Genetic, lifestyle, reproductive, and anthropometric factors are associated with the risk of developing breast cancer. However, it is not yet known whether polygenic risk score (PRS) and absolute risk based on a combination of risk factors are associated with the risk of progression of breast cancer. This study aims to estimate the distribution of sojourn time (pre-clinical screen-detectable period) and mammographic sensitivity by absolute breast cancer risk derived from polygenic proﬁle and the other risk factors. Methods: The authors used data from a population-based case-control study. Six categories of 10-year absolute risk based on different combinations of risk factors were derived using the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm. Women were classiﬁed into low, medium, and high-risk groups. The authors constructed a continuous-time multistate model. To calculate the sojourn time, they simulated the trajectories of subjects through the disease states. Results: There was little diﬀerence in sojourn time with a large overlap in the 95% conﬁdence interval (CI) between the risk groups across the six risk categories and PRS studied. However, the age of entry into the screen-detectable state varied by risk category, with the mean age of entry of 53.4 years (95% CI, 52.2-54.1) and 57.0 years (95% CI, 55.1-57.7) in the high-risk and low-risk women, respectively. Conclusion: In risk-stratiﬁed breast screening, the age at the start of screening, but not necessarily the frequency of screening, should be tailored to a woman's risk level. The optimal risk-stratiﬁed screening strategy that would improve the beneﬁt-to-harm balance and the cost-eﬀectiveness of the screening programs needs to be studied.
MeSH term(s)	Female ; Humans ; Middle Aged ; Breast Neoplasms/epidemiology ; Breast Neoplasms/genetics ; Breast Neoplasms/diagnosis ; Genetic Risk Score ; Case-Control Studies ; Age of Onset ; Risk Factors ; Risk Assessment ; Genetic Predisposition to Disease
Language	English
Publishing date	2024-01-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	1429-1
ISSN	1097-0142 ; 0008-543X ; 1934-662X
ISSN (online)	1097-0142
ISSN	0008-543X ; 1934-662X
DOI	10.1002/cncr.35183
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Article ; Online: Polygenic risk scores for prediction of breast cancer in Korean women.

Jee, Yon Ho / Ho, Weang-Kee / Park, Sohee / Easton, Douglas F / Teo, Soo-Hwang / Jung, Keum Ji / Kraft, Peter

International journal of epidemiology

2022 Volume 52, Issue 3, Page(s) 796–805

Abstract: Background: Polygenic risk scores (PRSs) for breast cancer, developed using European and Asian genome-wide association studies (GWAS), have been shown to have good discrimination in Asian women. However, prospective calibration of absolute risk ... ...

Abstract	Background: Polygenic risk scores (PRSs) for breast cancer, developed using European and Asian genome-wide association studies (GWAS), have been shown to have good discrimination in Asian women. However, prospective calibration of absolute risk prediction models, based on a PRS or PRS combined with lifestyle, clinical and environmental factors, in Asian women is limited. Methods: We consider several PRSs trained using European and/or Asian GWAS. For each PRS, we evaluate the discrimination and calibration of three absolute risk models among 41 031 women from the Korean Cancer Prevention Study (KCPS)-II Biobank: (i) a model using incidence, mortality and risk factor distributions (reference inputs) among US women and European relative risks; (ii) a recalibrated model, using Korean reference but European relative risks; and (iii) a fully Korean-based model using Korean reference and relative risk estimates from KCPS. Results: All Asian and European PRS improved discrimination over lifestyle, clinical and environmental (Qx) factors in Korean women. US-based absolute risk models overestimated the risks for women aged ≥50 years, and this overestimation was larger for models that only included PRS (expected-to-observed ratio E/O = 1.2 for women <50, E/O = 2.7 for women ≥50). Recalibrated and Korean-based risk models had better calibration in the large, although the risk in the highest decile was consistently overestimated. Absolute risk projections suggest that risk-reducing lifestyle changes would lead to larger absolute risk reductions among women at higher PRS. Conclusions: Absolute risk models incorporating PRS trained in European and Asian GWAS and population-appropriate average age-specific incidences may be useful for risk-stratified interventions in Korean women.
MeSH term(s)	Humans ; Female ; Breast Neoplasms/epidemiology ; Breast Neoplasms/genetics ; Genome-Wide Association Study ; Prospective Studies ; Genetic Predisposition to Disease ; Polymorphism, Single Nucleotide ; Risk Factors ; Republic of Korea/epidemiology ; Risk Assessment
Language	English
Publishing date	2022-11-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	187909-1
ISSN	1464-3685 ; 0300-5771
ISSN (online)	1464-3685
ISSN	0300-5771
DOI	10.1093/ije/dyac206
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Article ; Online: Letter to the editor: a response to Ming's study on machine learning techniques for personalized breast cancer risk prediction.

Giardiello, Daniele / Antoniou, Antonis C / Mariani, Luigi / Easton, Douglas F / Steyerberg, Ewout W

Breast cancer research : BCR

2020 Volume 22, Issue 1, Page(s) 17

MeSH term(s)	Breast ; Breast Neoplasms ; Humans ; Machine Learning ; Risk
Language	English
Publishing date	2020-02-10
Publishing country	England
Document type	Letter ; Comment
ZDB-ID	2015059-3
ISSN	1465-542X ; 1465-5411
ISSN (online)	1465-542X
ISSN	1465-5411
DOI	10.1186/s13058-020-1255-4
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Article ; Online: Detecting rare copy number variants from Illumina genotyping arrays with the CamCNV pipeline: Segmentation of z-scores improves detection and reliability.

Dennis, Joe / Walker, Logan / Tyrer, Jonathan / Michailidou, Kyriaki / Easton, Douglas F

Genetic epidemiology

2020 Volume 45, Issue 3, Page(s) 237–248

Abstract: The intensities from genotyping array data can be used to detect copy number variants (CNVs) but a high level of noise in the data and overlap between different copy-number intensity distributions produces unreliable calls, particularly when only a few ... ...

Abstract	The intensities from genotyping array data can be used to detect copy number variants (CNVs) but a high level of noise in the data and overlap between different copy-number intensity distributions produces unreliable calls, particularly when only a few probes are covered by the CNV. We present a novel pipeline (CamCNV) with a series of steps to reduce noise and detect more reliably CNVs covering as few as three probes. The pipeline aims to detect rare CNVs (below 1% frequency) for association tests in large cohorts. The method uses the information from all samples to convert intensities to z-scores, thus adjusting for variance between probes. We tested the sensitivity of our pipeline by looking for known CNVs from the 1000 Genomes Project in our genotyping of 1000 Genomes samples. We also compared the CNV calls for 1661 pairs of genotyped replicate samples. At the chosen mean z-score cut-off, sensitivity to detect the 1000 Genomes CNVs was approximately 85% for deletions and 65% for duplications. From the replicates, we estimate the false discovery rate is controlled at ∼10% for deletions (falling to below 3% with more than five probes) and ∼28% for duplications. The pipeline demonstrates improved sensitivity when compared to calling with PennCNV, particularly for short deletions covering only a few probes. For each called CNV, the mean z-score is a useful metric for controlling the false discovery rate.
MeSH term(s)	DNA Copy Number Variations ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Reproducibility of Results
Language	English
Publishing date	2020-10-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	605785-8
ISSN	1098-2272 ; 0741-0395
ISSN (online)	1098-2272
ISSN	0741-0395
DOI	10.1002/gepi.22367
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Article: Multi-gene panel testing and association analysis in Cypriot breast cancer cases and controls.

Zanti, Maria / Loizidou, Maria A / O'Mahony, Denise G / Dorling, Leila / Dennis, Joe / Devilee, Peter / Easton, Douglas F / Panayiotidis, Mihalis I / Hadjisavvas, Andreas / Michailidou, Kyriaki

Frontiers in genetics

2023 Volume 14, Page(s) 1248492

Abstract: Introduction: ...

Abstract	Introduction:
Language	English
Publishing date	2023-09-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1248492
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Article ; Online: Exploring the barriers to and facilitators of implementing CanRisk in primary care: a qualitative thematic framework analysis.

Archer, Stephanie / Donoso, Francisca Stutzin / Carver, Tim / Yue, Adelaide / Cunningham, Alex P / Ficorella, Lorenzo / Tischkowitz, Marc / Easton, Douglas F / Antoniou, Antonis C / Emery, Jon / Usher-Smith, Juliet / Walter, Fiona M

The British journal of general practice : the journal of the Royal College of General Practitioners

2023 Volume 73, Issue 733, Page(s) e586–e596

Abstract: Background: The CanRisk tool enables the collection of risk factor information and calculation of estimated future breast cancer risks based on the multifactorial Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm ( ... ...

Abstract	Background: The CanRisk tool enables the collection of risk factor information and calculation of estimated future breast cancer risks based on the multifactorial Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) model. Despite BOADICEA being recommended in National Institute for Health and Care Excellence (NICE) guidelines and CanRisk being freely available for use, the CanRisk tool has not yet been widely implemented in primary care. Aim: To explore the barriers to and facilitators of the implementation of the CanRisk tool in primary care. Design and setting: A multi-methods study was conducted with primary care practitioners (PCPs) in the East of England. Method: Participants used the CanRisk tool to complete two vignette-based case studies; semi-structured interviews gained feedback about the tool; and questionnaires collected demographic details and information about the structural characteristics of the practices. Results: Sixteen PCPs (eight GPs and eight nurses) completed the study. The main barriers to implementation included: time needed to complete the tool; competing priorities; IT infrastructure; and PCPs' lack of confidence and knowledge to use the tool. Main facilitators included: easy navigation of the tool; its potential clinical impact; and the increasing availability of and expectation to use risk prediction tools. Conclusion: There is now a greater understanding of the barriers and facilitators that exist when using CanRisk in primary care. The study has highlighted that future implementation activities should focus on reducing the time needed to complete a CanRisk calculation, integrating the CanRisk tool into existing IT infrastructure, and identifying appropriate contexts in which to conduct a CanRisk calculation. PCPs may also benefit from information about cancer risk assessment and CanRisk-specific training.
MeSH term(s)	Humans ; Female ; Breast Neoplasms/prevention & control ; Risk Factors ; Primary Health Care ; England ; Case-Control Studies ; Qualitative Research
Language	English
Publishing date	2023-07-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1043148-2
ISSN	1478-5242 ; 0035-8797 ; 0960-1643
ISSN (online)	1478-5242
ISSN	0035-8797 ; 0960-1643
DOI	10.3399/BJGP.2022.0643
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Article ; Online: Prediction of breast cancer risk for sisters of women attending screening.

Mao, Xinhe / He, Wei / Eriksson, Mikael / Lindström, Linda S / Holowko, Natalie / Bajalica-Lagercrantz, Svetlana / Hammarström, Mattias / Grassmann, Felix / Humphreys, Keith / Easton, Douglas / Hall, Per / Czene, Kamila

Journal of the National Cancer Institute

2023 Volume 115, Issue 11, Page(s) 1310–1317

Abstract: Background: Risk assessment is important for breast cancer prevention and early detection. We aimed to examine whether common risk factors, mammographic features, and breast cancer risk prediction scores of a woman were associated with breast cancer ... ...

Abstract	Background: Risk assessment is important for breast cancer prevention and early detection. We aimed to examine whether common risk factors, mammographic features, and breast cancer risk prediction scores of a woman were associated with breast cancer risk for her sisters. Methods: We included 53 051 women from the Karolinska Mammography Project for Risk Prediction of Breast Cancer (KARMA) study. Established risk factors were derived using self-reported questionnaires, mammograms, and single nucleotide polymorphism genotyping. Using the Swedish Multi-Generation Register, we identified 32 198 sisters of the KARMA women (including 5352 KARMA participants and 26 846 nonparticipants). Cox models were used to estimate the hazard ratios of breast cancer for both women and their sisters, respectively. Results: A higher breast cancer polygenic risk score, a history of benign breast disease, and higher breast density in women were associated with an increased risk of breast cancer for both women and their sisters. No statistically significant association was observed between breast microcalcifications and masses in women and breast cancer risk for their sisters. Furthermore, higher breast cancer risk scores in women were associated with an increased risk of breast cancer for their sisters. Specifically, the hazard ratios for breast cancer per 1 standard deviation increase in age-adjusted KARMA, Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA), and Tyrer-Cuzick risk scores were 1.16 (95% confidence interval [CI] = 1.07 to 1.27), 1.23 (95% CI = 1.12 to 1.35), and 1.21 (95% CI = 1.11 to 1.32), respectively. Conclusion: A woman's breast cancer risk factors are associated with her sister's breast cancer risk. However, the clinical utility of these findings requires further investigation.
MeSH term(s)	Female ; Humans ; Breast Neoplasms/diagnostic imaging ; Breast Neoplasms/epidemiology ; Breast Neoplasms/genetics ; Early Detection of Cancer ; Breast/diagnostic imaging ; Mammography ; Breast Density ; Risk Factors ; Risk Assessment
Language	English
Publishing date	2023-05-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2992-0
ISSN	1460-2105 ; 0027-8874 ; 0198-0157
ISSN (online)	1460-2105
ISSN	0027-8874 ; 0198-0157
DOI	10.1093/jnci/djad101
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Article ; Online: More on Co-Occurrence of COMT and BRCA1/2 Variants in a Population.

Spurdle, Amanda B / Goldgar, David E / Easton, Douglas F

The New England journal of medicine

2017 Volume 377, Issue 8, Page(s) 795

MeSH term(s)	Breast Neoplasms ; Humans
Language	English
Publishing date	2017--24
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJMc1708425
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Article ; Online: Evaluation of SNPs associated with mammographic density in European women with mammographic density in Asian women from South-East Asia.

Mariapun, Shivaani / Ho, Weang Kee / Eriksson, Mikael / Tai, Mei Chee / Mohd Taib, Nur Aishah / Yip, Cheng Har / Rahmat, Kartini / Li, Jingmei / Hartman, Mikael / Hall, Per / Easton, Douglas F / Lindstrom, Sara / Teo, Soo-Hwang

Breast cancer research and treatment

2023 Volume 201, Issue 2, Page(s) 237–245

Abstract: Purpose: Mammographic density (MD), after accounting for age and body mass index (BMI), is a strong heritable risk factor for breast cancer. Genome-wide association studies (GWAS) have identified 64 SNPs in 55 independent loci associated with MD in ... ...

Abstract	Purpose: Mammographic density (MD), after accounting for age and body mass index (BMI), is a strong heritable risk factor for breast cancer. Genome-wide association studies (GWAS) have identified 64 SNPs in 55 independent loci associated with MD in women of European ancestry. Their associations with MD in Asian women, however, are largely unknown. Method: Using linear regression adjusting for age, BMI, and ancestry-informative principal components, we evaluated the associations of previously reported MD-associated SNPs with MD in a multi-ethnic cohort of Asian ancestry. Area and volumetric mammographic densities were determined using STRATUS (N = 2450) and Volpara™ (N = 2257). We also assessed the associations of these SNPs with breast cancer risk in an Asian population of 14,570 cases and 80,870 controls. Results: Of the 61 SNPs available in our data, 21 were associated with MD at a nominal threshold of P value < 0.05, all in consistent directions with those reported in European ancestry populations. Of the remaining 40 variants with a P-value of association > 0.05, 29 variants showed consistent directions of association as those previously reported. We found that nine of the 21 MD-associated SNPs in this study were also associated with breast cancer risk in Asian women (P < 0.05), seven of which showed a direction of associations that was consistent with that reported for MD. Conclusion: Our study confirms the associations of 21 SNPs (19/55 or 34.5% out of all known MD loci identified in women of European ancestry) with area and/or volumetric densities in Asian women, and further supports the evidence of a shared genetic basis through common genetic variants for MD and breast cancer risk.
MeSH term(s)	Female ; Humans ; Breast Density/genetics ; Breast Neoplasms/diagnostic imaging ; Breast Neoplasms/genetics ; Breast Neoplasms/epidemiology ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Risk Factors ; Asia, Eastern ; Mammography
Language	English
Publishing date	2023-06-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	604563-7
ISSN	1573-7217 ; 0167-6806
ISSN (online)	1573-7217
ISSN	0167-6806
DOI	10.1007/s10549-023-06984-2
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