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Pathogenic Germline Variants in 10,389 Adult Cancers.

Author(s): Huang, Kuan-Lin; Mashl, R Jay; Wu, Yige; Ritter, Deborah I; Wang, Jiayin; et al

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Abstract: We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, including novel associations of SDHA in melanoma and PALB2 in stomach adenocarcinoma. The 659 predisposition variants and 18 additional large deletions in tumor suppressors, including ATM, BRCA1, and NF1, showed low gene expression and frequent (43%) loss of heterozygosity or biallelic two-hit events. We also discovered 33 such variants in oncogenes, including missenses in MET, RET, and PTPN11 associated with high gene expression. We nominated 47 additional predisposition variants from prioritized VUSs supported by multiple evidences involving case-control frequency, loss of heterozygosity, expression effect, and co-localization with mutations and modified residues. Our integrative approach links rare predisposition variants to functional consequences, informing future guidelines of variant classification and germline genetic testing in cancer.
Publication Date: Apr-2018
Citation: Huang, Kuan-Lin, Mashl, R Jay, Wu, Yige, Ritter, Deborah I, Wang, Jiayin, Oh, Clara, Paczkowska, Marta, Reynolds, Sheila, Wyczalkowski, Matthew A, Oak, Ninad, Scott, Adam D, Krassowski, Michal, Cherniack, Andrew D, Houlahan, Kathleen E, Jayasinghe, Reyka, Wang, Liang-Bo, Zhou, Daniel Cui, Liu, Di, Cao, Song, Kim, Young Won, Koire, Amanda, McMichael, Joshua F, Hucthagowder, Vishwanathan, Kim, Tae-Beom, Hahn, Abigail, Wang, Chen, McLellan, Michael D, Al-Mulla, Fahd, Johnson, Kimberly J, Cancer Genome Atlas Research Network, Lichtarge, Olivier, Boutros, Paul C, Raphael, Benjamin, Lazar, Alexander J, Zhang, Wei, Wendl, Michael C, Govindan, Ramaswamy, Jain, Sanjay, Wheeler, David, Kulkarni, Shashikant, Dipersio, John F, Reimand, Jüri, Meric-Bernstam, Funda, Chen, Ken, Shmulevich, Ilya, Plon, Sharon E, Chen, Feng, Ding, Li. (2018). Pathogenic Germline Variants in 10,389 Adult Cancers.. Cell, 173 (2), 355 - 370.e14. doi:10.1016/j.cell.2018.03.039
DOI: doi:10.1016/j.cell.2018.03.039
ISSN: 0092-8674
EISSN: 1097-4172
Pages: 355 - 370.e14
Language: eng
Type of Material: Journal Article
Journal/Proceeding Title: Cell
Version: Final published version. This is an open access article.

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