Large-scale cross-cancer fine-mapping of the 5p15.33 region reveals multiple independent signals. Chen, H., Majumdar, A., Wang, L., Kar, S., Brown, K. M., Feng, H., Turman, C., Dennis, J., Easton, D., Michailidou, K., Simard, J., Breast Cancer Association Consortium (BCAC), Bishop, T., Cheng, I. C., Huyghe, J. R., Schmit, S. L., Colorectal Transdisciplinary Study (CORECT), Colon Cancer Family Registry Study (CCFR), Genetics, of Colorectal Cancer Consortium (GECCO), E., O'Mara, T. A., Spurdle, A. B., Endometrial Cancer Association Consortium (ECAC), Gharahkhani, P., Schumacher, J., Jankowski, J., Gockel, I., Esophageal Cancer GWAS Consortium, Bondy, M. L., Houlston, R. S., Jenkins, R. B., Melin, B., Glioma International Case Control Consortium (GICC), Lesseur, C., Ness, A. R., Diergaarde, B., Olshan, A. F., Head-Neck Cancer GWAS Consortium, Amos, C. I., Christiani, D. C., Landi, M. T., McKay, J. D., International Lung Cancer Consortium (ILCCO), Brossard, M., Iles, M. M., Law, M. H., MacGregor, S., Melanoma GWAS Consortium, Beesley, J., Jones, M. R., Tyrer, J., Winham, S. J., Ovarian Cancer Association Consortium (OCAC), Klein, A. P., Petersen, G., Li, D., Wolpin, B. M., Pancreatic Cancer Case-Control Consortium (PANC4), Pancreatic Cancer Cohort Consortium (PanScan), Eeles, R. A., Haiman, C. A., Kote-Jarai, Z., Schumacher, F. R., PRACTICAL consortium, CRUK, BPC3, CAPS, PEGASUS, Brennan, P., Chanock, S. J., Gaborieau, V., Purdue, M. P., Renal Cancer GWAS Consortium, Pharoah, P., Hung, R. J., Amundadottir, L. T., Kraft, P., Pasaniuc, B., & Lindström, S. HGG advances, 2(3):100041, July, 2021.
doi  abstract   bibtex   
Genome-wide association studies (GWASs) have identified thousands of cancer risk loci revealing many risk regions shared across multiple cancers. Characterizing the cross-cancer shared genetic basis can increase our understanding of global mechanisms of cancer development. In this study, we collected GWAS summary statistics based on up to 375,468 cancer cases and 530,521 controls for fourteen types of cancer, including breast (overall, estrogen receptor [ER]-positive, and ER-negative), colorectal, endometrial, esophageal, glioma, head/neck, lung, melanoma, ovarian, pancreatic, prostate, and renal cancer, to characterize the shared genetic basis of cancer risk. We identified thirteen pairs of cancers with statistically significant local genetic correlations across eight distinct genomic regions. Specifically, the 5p15.33 region, harboring the TERT and CLPTM1L genes, showed statistically significant local genetic correlations for multiple cancer pairs. We conducted a cross-cancer fine-mapping of the 5p15.33 region based on eight cancers that showed genome-wide significant associations in this region (ER-negative breast, colorectal, glioma, lung, melanoma, ovarian, pancreatic, and prostate cancer). We used an iterative analysis pipeline implementing a subset-based meta-analysis approach based on cancer-specific conditional analyses and identified ten independent cross-cancer associations within this region. For each signal, we conducted cross-cancer fine-mapping to prioritize the most plausible causal variants. Our findings provide a more in-depth understanding of the shared inherited basis across human cancers and expand our knowledge of the 5p15.33 region in carcinogenesis.
@article{chen_large-scale_2021,
	title = {Large-scale cross-cancer fine-mapping of the 5p15.33 region reveals multiple independent signals},
	volume = {2},
	issn = {2666-2477},
	doi = {10.1016/j.xhgg.2021.100041},
	abstract = {Genome-wide association studies (GWASs) have identified thousands of cancer risk loci revealing many risk regions shared across multiple cancers. Characterizing the cross-cancer shared genetic basis can increase our understanding of global mechanisms of cancer development. In this study, we collected GWAS summary statistics based on up to 375,468 cancer cases and 530,521 controls for fourteen types of cancer, including breast (overall, estrogen receptor [ER]-positive, and ER-negative), colorectal, endometrial, esophageal, glioma, head/neck, lung, melanoma, ovarian, pancreatic, prostate, and renal cancer, to characterize the shared genetic basis of cancer risk. We identified thirteen pairs of cancers with statistically significant local genetic correlations across eight distinct genomic regions. Specifically, the 5p15.33 region, harboring the TERT and CLPTM1L genes, showed statistically significant local genetic correlations for multiple cancer pairs. We conducted a cross-cancer fine-mapping of the 5p15.33 region based on eight cancers that showed genome-wide significant associations in this region (ER-negative breast, colorectal, glioma, lung, melanoma, ovarian, pancreatic, and prostate cancer). We used an iterative analysis pipeline implementing a subset-based meta-analysis approach based on cancer-specific conditional analyses and identified ten independent cross-cancer associations within this region. For each signal, we conducted cross-cancer fine-mapping to prioritize the most plausible causal variants. Our findings provide a more in-depth understanding of the shared inherited basis across human cancers and expand our knowledge of the 5p15.33 region in carcinogenesis.},
	language = {eng},
	number = {3},
	journal = {HGG advances},
	author = {Chen, Hongjie and Majumdar, Arunabha and Wang, Lu and Kar, Siddhartha and Brown, Kevin M. and Feng, Helian and Turman, Constance and Dennis, Joe and Easton, Douglas and Michailidou, Kyriaki and Simard, Jacques and {Breast Cancer Association Consortium (BCAC)} and Bishop, Timothy and Cheng, Iona C. and Huyghe, Jeroen R. and Schmit, Stephanie L. and {Colorectal Transdisciplinary Study (CORECT)} and {Colon Cancer Family Registry Study (CCFR)} and {Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO)} and O'Mara, Tracy A. and Spurdle, Amanda B. and {Endometrial Cancer Association Consortium (ECAC)} and Gharahkhani, Puya and Schumacher, Johannes and Jankowski, Janusz and Gockel, Ines and {Esophageal Cancer GWAS Consortium} and Bondy, Melissa L. and Houlston, Richard S. and Jenkins, Robert B. and Melin, Beatrice and {Glioma International Case Control Consortium (GICC)} and Lesseur, Corina and Ness, Andy R. and Diergaarde, Brenda and Olshan, Andrew F. and {Head-Neck Cancer GWAS Consortium} and Amos, Christopher I. and Christiani, David C. and Landi, Maria T. and McKay, James D. and {International Lung Cancer Consortium (ILCCO)} and Brossard, Myriam and Iles, Mark M. and Law, Matthew H. and MacGregor, Stuart and {Melanoma GWAS Consortium} and Beesley, Jonathan and Jones, Michelle R. and Tyrer, Jonathan and Winham, Stacey J. and {Ovarian Cancer Association Consortium (OCAC)} and Klein, Alison P. and Petersen, Gloria and Li, Donghui and Wolpin, Brian M. and {Pancreatic Cancer Case-Control Consortium (PANC4)} and {Pancreatic Cancer Cohort Consortium (PanScan)} and Eeles, Rosalind A. and Haiman, Christopher A. and Kote-Jarai, Zsofia and Schumacher, Fredrick R. and {PRACTICAL consortium} and {CRUK} and {BPC3} and {CAPS} and {PEGASUS} and Brennan, Paul and Chanock, Stephen J. and Gaborieau, Valerie and Purdue, Mark P. and {Renal Cancer GWAS Consortium} and Pharoah, Paul and Hung, Rayjean J. and Amundadottir, Laufey T. and Kraft, Peter and Pasaniuc, Bogdan and Lindström, Sara},
	month = jul,
	year = {2021},
	pmid = {34355204},
	pmcid = {PMC8336922},
	pages = {100041},
}
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