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Barnekow E, Liu W, Helgadottir HT, Michailidou K, Dennis J, Bryant P, Thutkawkorapin J, Wendt C, Czene K, Hall P, Margolin S, Lindblom A. 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) 2022; 14:cancers14051206. [PMID: 35267517 PMCID: PMC8909613 DOI: 10.3390/cancers14051206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
(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.
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Affiliation(s)
- Elin Barnekow
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, 11883 Stockholm, Sweden; (C.W.); (S.M.)
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden;
- Correspondence: (E.B.); (A.L.); Tel.: +46-736-565-798 (E.B.); +46-852-485-248 (A.L.)
| | - Wen Liu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden; (W.L.); (H.T.H.); (P.B.); (J.T.)
- Department of Neuroscience, Uppsala University, 75237 Uppsala, Sweden
| | - Hafdis T. Helgadottir
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden; (W.L.); (H.T.H.); (P.B.); (J.T.)
- Department of Clinical Genetics, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Kyriaki Michailidou
- The Cyprus Institute of Neurology & Genetics, Cyprus School of Molecular Medicine, 1683 Nicosia, Cyprus;
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB18RN, UK;
| | - Patrick Bryant
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden; (W.L.); (H.T.H.); (P.B.); (J.T.)
- Department of Biochemistry and Biophysics, Stockholm University, 17165 Stockholm, Sweden
- Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Jessada Thutkawkorapin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden; (W.L.); (H.T.H.); (P.B.); (J.T.)
- Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Camilla Wendt
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, 11883 Stockholm, Sweden; (C.W.); (S.M.)
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden;
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17165 Stockholm, Sweden;
| | - Per Hall
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden;
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17165 Stockholm, Sweden;
| | - Sara Margolin
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, 11883 Stockholm, Sweden; (C.W.); (S.M.)
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden;
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden; (W.L.); (H.T.H.); (P.B.); (J.T.)
- Department of Clinical Genetics, Karolinska University Hospital, 17164 Stockholm, Sweden
- Correspondence: (E.B.); (A.L.); Tel.: +46-736-565-798 (E.B.); +46-852-485-248 (A.L.)
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Novel prostate cancer susceptibility gene SP6 predisposes patients to aggressive disease. Prostate Cancer Prostatic Dis 2021; 24:1158-1166. [PMID: 34012061 PMCID: PMC8616752 DOI: 10.1038/s41391-021-00378-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 03/17/2021] [Accepted: 04/28/2021] [Indexed: 02/04/2023]
Abstract
Prostate cancer (PrCa) is one of the most common cancers in men, but little is known about factors affecting its clinical outcomes. Genome-wide association studies have identified more than 170 germline susceptibility loci, but most of them are not associated with aggressive disease. We performed a genome-wide analysis of 185,478 SNPs in Finnish samples (2738 cases, 2400 controls) from the international Collaborative Oncological Gene-Environment Study (iCOGS) to find underlying PrCa risk variants. We identified a total of 21 common, low-penetrance susceptibility loci, including 10 novel variants independently associated with PrCa risk. Novel risk loci were located in the 8q24 (CASC8 rs16902147, OR 1.86, padj = 3.53 × 10-8 and rs58809953, OR 1.71, padj = 4.00 × 10-6; intergenic rs79012498, OR 1.81, padj = 4.26 × 10-8), 17q21 (SP6 rs2074187, OR 1.66, padj = 3.75 × 10-5), 11q13 (rs12795301, OR 1.42, padj = 2.89 × 10-5) and 8p21 (rs995432, OR 1.38, padj = 3.00 × 10-11) regions. Here, we describe SP6, a transcription factor gene, as a new, potentially high-risk gene for PrCa. The intronic variant rs2074187 in SP6 was associated not only with overall susceptibility to PrCa (OR 1.66) but also with a higher odds ratio for aggressive PrCa (OR 1.89) and lower odds for non-aggressive PrCa (OR 1.43). Furthermore, the new intergenic variant rs79012498 at 8q24 conferred risk for aggressive PrCa. Our findings highlighted the power of a population-stratified approach to identify novel, clinically actionable germline PrCa risk loci and strongly suggested SP6 as a new PrCa candidate gene that may be involved in the pathogenesis of PrCa.
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Su F, Zhang W, Zhang D, Zhang Y, Pang C, Huang Y, Wang M, Cui L, He L, Zhang J, Zou L, Zhang J, Li W, Li L, Shao J, Ma J, Xiao F, Liu M. Spatial Intratumor Genomic Heterogeneity within Localized Prostate Cancer Revealed by Single-nucleus Sequencing. Eur Urol 2018; 74:551-559. [DOI: 10.1016/j.eururo.2018.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/01/2018] [Indexed: 10/28/2022]
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Moses KA, Master VA, Underwood W. Race, Ethnicity, Marital Status, Literacy, and Prostate Cancer Outcomes in the United States. Prostate Cancer 2016. [DOI: 10.1016/b978-0-12-800077-9.00016-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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