Limitations in next-generation sequencing-based genotyping of breast cancer polygenic risk score loci

Considering polygenic risk scores (PRSs) in individual risk prediction is increasingly becoming the standard in genetic testing for hereditary breast cancer (BC). To calculate individual BC risks, the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) with inclusion of the BCAC 313 or the BRIDGES 306 BC PRS is commonly used. Meaningful incorporation of PRSs relies on reproducing the allele frequencies (AFs), and hence, the distribution of PRS values, expected by the algorithm. Here, the 324 loci of the BCAC 313 and the BRIDGES 306 BC PRS were examined in population-specific database gnomAD and in real-world data sets of five centers of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC), to determine whether these expected AFs are achieved with next-generation sequencing-based genotyping. Four PRS loci were non-existent in gnomAD v3.1.2 non-Finnish Europeans, further 24 loci showed noticeably deviating AFs. In real-world data, between 16 and up to 22 loci were reported with noticeably deviating AFs, and were shown to have effects on final risk prediction. Deviations depended on sequencing approach, variant caller and calling mode (forced versus unforced) employed. Therefore, this study demonstrates the necessity to apply quality assurance not only in terms of sequencing coverage but also observed AFs in a sufficiently large sample, when implementing PRSs in a routine diagnostic setting. Furthermore, future PRS design should be guided by reproducibility of expected AFs in addition to the observed effect sizes. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement RR and RF received funding from the German Federal Ministry of Health within the genomDE initiative. MD received funding from the German Cancer Aid () in the HerediVar project. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: IMGAG: The use of aggregate statistics of human subject genetics data was approved by the ethics committee of the Medical Faculty of the University of Tübingen, Germany (Genome+, ClinicalTrial.gov-Nr: [NCT04315727][1]; #066/2021BO2 for retrospective data analysis). ICG, IHG-M, CFBOC, IHG-R: Written informed consent was obtained from all patients and ethical approval was granted by the ethics committee of the Technische University Dresden, ethics committee of the Medical Association Westfalen-Lippe, ethics committee of the Medical Faculty of the University of Cologne (19-1360_4), the ethics committee of the University of Regensburg (21-2192-103). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data generated or analyzed during this study are included in this published article [and its supplementary files]. [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT04315727&atom=%2Fmedrxiv%2Fearly%2F2023%2F12%2F17%2F2023.12.15.23298835.atom