(1) Background: The heritability of breast cancer is partly explained but much of the genetic contribution remains to be identified. Haplotypes are often used as markers of ethnicity as they are preserved through generations. We have previously demonstrated that haplotype analysis, in addition to standard SNP association studies, could give novel and more detailed information on genetic cancer susceptibility. (2) Methods: In order to examine the association of a SNP or a haplotype to breast cancer risk, we performed a genome wide haplotype association study, using sliding window analysis of window sizes 1–25 and 50 SNPs, in 3200 Swedish breast cancer cases and 5021 controls. (3) Results: We identified a novel breast cancer susceptibility locus in 8p21.1 (OR 2.08; p 3.92 × 10⁻⁸), confirmed three known loci in 10q26.13, 11q13.3, 16q12.1-2 and further identified novel subloci within these three loci. Altogether 76 risk SNPs, 3302 risk haplotypes of window size 2–25 and 113 risk haplotypes of window size 50 at p < 5 × 10⁻⁸ on chromosomes 8, 10, 11 and 16 were identified. In the known loci haplotype analysis reached an OR of 1.48 in overall breast cancer and in familial cases OR 1.68. (4) Conclusions: Analyzing haplotypes, rather than single variants, could detect novel susceptibility loci even in small study populations but the method requires a fairly homogenous study population.

Most breast cancer heritability is unexplained. We hypothesized that analysis of unrelated familial cases in a GWAS context could enable the identification of novel susceptibility loci. In order to examine the association of a haplotype with breast cancer risk, we performed a genome-wide haplotype association study using a sliding window analysis of window sizes 1–25 SNPs in 650 familial invasive breast cancer cases and 5021 controls. We identified five novel risk loci on 9p24.3 (OR 3.4; p 4.9 × 10⁻¹¹), 11q22.3 (OR 2.4; p 5.2 × 10⁻⁹), 15q11.2 (OR 3.6; p 2.3 × 10⁻⁸), 16q24.1 (OR 3; p 3 × 10⁻⁸) and Xq21.31 (OR 3.3; p 1.7 × 10⁻⁸) and confirmed three well-known loci on 10q25.13, 11q13.3, and 16q12.1. In total, 1593 significant risk haplotypes and 39 risk SNPs were distributed on the eight loci. In comparison with unselected breast cancer cases from a previous study, the OR was increased in the familial analysis in all eight loci. Analyzing familial cancer cases and controls enabled the identification of novel breast cancer susceptibility loci.

Genome-wide association studies [GWAS] have identified a limited number of endometrial cancer risk loci by analyzing single nucleotide polymorphisms [SNPs]. We hypothesized that analyzing haplotypes rather than SNPs could provide novel and more detailed information on genetic cancer susceptibility loci. To examine the association of a SNP or haplotype with endometrial cancer risk we performed a two-stage haplotype GWAS. The discovery GWAS included a sub-cohort of 1,116 Swedish endometrial cancer cases and 5,021 controls from previously published GWAS data. A sliding window analysis was employed with window sizes of 1-25 SNPs using a logistic regression model. The Swedish haplotype analysis identified 15 novel candidate risk loci (2q31.1, 4p16.1, 4p15.31, 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 and p-values from 4.25 × 10⁻⁸ to 9.86 × 10⁻¹⁵. A second replication haplotype analysis of the Swedish novel loci was performed using two cohorts from Belgium and Germany. In spite of small sample sizes in the replication cohorts, there was still support for most loci with positive ORs. In addition, the findings in the two European cohorts motivates further studies to search for founder haplotypes. These novel findings suggested that endometrial cancer loci, identified through haplotype analysis, conferred a higher risk compared to previous single-variant GWAS.

Background: To find support for risk-modifying genes in breast cancer, a haplotype GWAS in sporadic breast cancer cases was undertaken. The results were compared with the results from previous analyses in familial cases and all cases from the same Swedish cohort. Methods: In total, 2550 women with sporadic invasive breast cancer and 5021 healthy controls were included in a sliding-window haplotype GWAS using PLINK 1.07. Results: The analysis of sporadic cases confirmed the loci on chromosomes 10q26.13, 11q13.3, and 16q12.1 and suggested one novel locus on chromosome 12p11.21 (OR = 1.42 p = 4.55 × 10⁻⁸). A comparison between these loci and the same loci in the analyses of familial cases and all breast cancer cases was undertaken. Conclusions: Haplotype GWAS in sporadic cases of Swedish breast cancer cases supported known risk loci and suggested another risk locus. The loci identified in the analysis of sporadic and all breast cancer cases were suggested to act as modifiers of the risk of breast cancer. Haplotype analysis identified other loci with higher odds ratios than single-variant analysis. Further studies are needed to find out how to best include the findings in breast cancer prevention.

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 papersI. 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/ijms24054468II. 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/cancers14051206III. 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/genes15121616IV. 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.0316086V. 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...

Breast and endometrial cancer are prevalent and share both hormonal and environmental risk factors. This study aimed to identify shared germline genetic risk loci for these cancers. In total, 1116 endometrial cancer cases, 3200 breast cancer cases, and 5021 healthy controls were included in a merged sliding window haplotype genome-wide association study (GWAS). This analysis employed a logistic regression model in PLINK v1.07. The results from this merged analysis were compared with previous individual analyses of the same samples. The analysis identified three loci that influenced both the risk of breast and endometrial cancer: 8p21.1 (OR 2.1; p 1.6 × 10⁻⁸), 16q24.3 (OR 2.4; p 3.8 × 10⁻⁸) and 17q11.2 (OR 1.3; p 4.3 × 10⁻⁸). This combined haplotype GWAS of endometrial and breast cancers identified three loci associated with shared genetic risk, two of which were novel: 16q24.3 and 17q11.2. Further studies are warranted to replicate these findings and to determine its pathophysiological role and future clinical implications.