Breast and endometrial cancer susceptibility, genome-wide haplotype association studies

The heritability of BC and EC is partially understood; however, a significant portion of its genetic contribution remains to be identified. Haplotypes are frequently utilized as markers of ethnicity due to their preservation through generations and there are known Swedish, Icelandic and Jewish founder haplotypes in BRCA genes. In the past decade, germline variants for BC and EC have primarily been discovered through GWAS focusing on SNPs in large global populations. We have previously demonstrated that haplotype-based GWAS on Swedish samples, can reveal novel susceptibility loci for colorectal cancer, achieving promising results even with a relatively small study population. To build on earlier epidemiological findings of overrepresentation of EC cases in families affected of BC, the overall aim of this thesis was to identify novel genetic candidate risk loci for BC and EC, either separately or as a putative syndrome. Various strategies utilizing the haplotype-based GWAS approach were applied to Swedish samples that were previously included in the large BCAC (Breast Cancer Association Consortium) and ECAC (Endometrial Cancer Association Consortium).

Study I identified one novel BC candidate risk locus at 8p21.2 (odds ratio (OR) 2.08; p 3.92x10-8) and confirmed three known BC susceptibility loci (10q26.13, 11q13.3, and 16q12.1) based on 3,200 unselected BC cases (both with and without family history) and 5,021 controls. Within the three known loci, relatively separated subloci were identified, indicating diverse variants may occur in the Swedish population in these regions. Subgroup analysis of familial cases in the four loci demonstrated higher OR in all four loci (non-significant for 8p21.2). Thus, haplotype-based GWAS is a robust method, and a novel BC locus could be detected. The selected familial analysis of the loci provided support for a direct genetic contribution to the association. Study II identified five novel BC candidate risk loci (9p24.3, 11q22.3, 15q11.2, 16q24.1, and Xq21.31) with OR ranging from 2.4 to 3.6 and confirmed three well-known BC susceptibility loci (10q26.13, 11q13.3, and 16q12.1) based on analysis of 650 familial BC cases and 5021 controls. Comparison of data from study I demonstrated higher OR in all eight loci for the familial analysis. Thus, selected analysis of familial cases (with enriched genetic contribution) could identify novel loci and again supported the direct genetic contribution for the association. Study III identified one novel risk locus at 12p11.21 (OR 1.42; p 4.55 x 10-8) and confirmed three well-known loci (10q26.13, 11q13.3, and 16q12.1, the latter with two separate haplotypes) based on 2,550 sporadic BC cases (without family history) and 5,021 controls. The novel locus on chromosome 12p11.21 exhibited a higher OR in the analysis of sporadic cases compared to familial cases and unselected cases (data from study I and II). Thus, the novel locus may represent a genetic effect-modifier, maybe influenced by environmental factors. Study IV identified 15 novel EC candidate risk loci (2q1.1, 4p16.1, 6q13, 7p21.1, 9p13.3, 10q26.3, 11q21, 12q13.11, 13q12.11, 15q13.3, 16q24.3, 19q13.32, 20p12.3 and 22q13.2) with OR ranging from 1.6 to 3.3 based on 1,116 EC cases and 5,021 controls. None of these loci were known. Therefore, a replication analysis of the novel Swedish loci was conducted using two smaller cohorts from Belgium (528 EC- cases; 1,266 controls) and Germany (221 EC-cases; 251 controls). Despite the modest sample sizes in the replication cohorts, there was support for most loci, which exhibited positive ORs. Furthermore, potential European founder haplotypes were suggested. Study V identified three candidate risk loci associated with shared risk for EC and BC at 8p21.2 (OR 2.05; p 1.58x10-8), 16q24.3 (OR 2.4; p 3.88x10-8) and 17q11.2 (OR 1.27; p 4.3x10-8) based on 4,316 EC cases and 5,021 controls.

In conclusion, the five studies presented in this thesis identified novel susceptibility loci for BC and EC individually, as well as loci with shared genetic risks. Further studies are warranted to explore how these findings can be integrated into future preventive strategies. This knowledge contributes to the ongoing move towards more personalized prevention.

List of scientific papers

I. Barnekow, E., Hasslow, J., Liu, W., Bryant, P., Thutkawkorapin, J., Wendt, C., Czene, K., Hall, P., Margolin, S., & Lindblom, A. (2023). A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31. Int J Mol Sci, 24(5). https://doi.org/10.3390/ijms24054468

II. Barnekow, E., Liu, W., Helgadottir, H. T., Michailidou, K., Dennis, J., Bryant, P., Thutkawkorapin, J., Wendt, C., Czene, K., Hall, P., Margolin, S., & Lindblom, A. (2022). A Swedish Genome-Wide Haplotype Association Analysis Identifies a Novel Breast Cancer Susceptibility Locus in 8p21.2 and Characterizes Three Loci on Chromosomes 10, 11 and 16. Cancers (Basel), 14(5). https://doi.org/10.3390/cancers14051206

III. Vermani, L., Barnekow, E., Liu, W., Wendt, C., Hall, P., Margolin, S., & Lindblom, A. (2024). Swedish Genome-Wide Haplotype Association Analysis Suggests Breast Cancer Loci with Varying Risk-Modifying Effects. Genes (Basel), 15(12). https://doi.org/10.3390/genes15121616

IV. Barnekow, E., Liu, W., Andersson, E., Wang, X., Helgadottir, H. T., Thutkawkorapin, J., Barilla, S., Vermani, L., Mints, M., Tham, E., Fasching, P. A., Lambrechts, D., Amant, F., Spurdle, A. B., Hall, P., O'Mara, T. A., Margolin, S., & Lindblom, A. (2025). A Swedish genome-wide haplotype association analysis identifies novel candidate loci associated with endometrial cancer risk. PLoS One, 20(3). https://doi.org/10.1371/journal.pone.0316086

V. Barnekow, E., Liu, W., Andersson Franko, M., von Wachenfeldt, A., Wendt, C., Tham, E., Mints, M., Tracy, A. O'Mara, Hall, P., Margolin, S., Lindblom A. Novel shared heritable candidate risk loci for breast and endometrial cancer, a Swedish haplotype genome-wide association study. [Manuscript]