Jianxin Shi, Weiyin Zhou, Bin Zhu, Paula L

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Rare Germline Copy Number Variations and Disease Susceptibility in Familial Melanoma Jianxin Shi, Weiyin Zhou, Bin Zhu, Paula L. Hyland, Hunter Bennett, Yanzi Xiao, Xijun Zhang, Laura S. Burke, Lei Song, Chih Hao Hsu, Chunhua Yan, Qingrong Chen, Daoud Meerzaman, Casey L. Dagnall, Laurie Burdette, Belynda Hicks, Neal D. Freedman, Stephen J. Chanock, Meredith Yeager, Margaret A. Tucker, Alisa M. Goldstein, Xiaohong R. Yang Journal of Investigative Dermatology Volume 136, Issue 12, Pages 2436-2443 (December 2016) DOI: 10.1016/j.jid.2016.07.023 Copyright © 2016 The Authors Terms and Conditions

Figure 1 Rare CNVs identified in melanoma-prone families. (a) A 1.3 Mb deletion on 1q42.12–13 by array-CGH (720k exon-focused); (b) a 10 kb deletion on 9p21.3 by array-CGH (390k 9p-focused); (c) a 112 kb deletion on 2q22.1 by array-CGH (720k exon-focused); (d) a 480 kb gain on 3p12.2 by an SNP array; (e) a 260 kb gain on 10q23.33 by array-CGH (720k exon-focused); (f) a 5–15 kb deletion on 8q24.3 by array-CGH (720k exon-focused). CGH, comparative genomic hybridization; CNV, copy number variation; SNP, single nucleotide polymorphism. Journal of Investigative Dermatology 2016 136, 2436-2443DOI: (10.1016/j.jid.2016.07.023) Copyright © 2016 The Authors Terms and Conditions

Figure 2 Families with identified copy number variations. Right half black panel: CMM only; left quarter black panel: DN only; three-quarter black panel: CMM with DN. Number under each person (square as male, circle as female) indicates individual ID, which is unique within a single family. (a) Family T. The melanoma case with the PARP1 deletion is indicated by an arrow. +: ZNF517 deletion carriers; −: ZNF517 deletion noncarriers. (b) Family Z. +: CDKN2A deletion carriers; −: CDKN2A deletion noncarriers; CMM cases 2003 and 2004 can be surmised to carry the deletion based on segregation. (c) Family D5. +: 2q22.1 deletion carriers; −: 2q22.1 deletion noncarriers. (d) Family F10. +: 3p12.2 deletion carriers; −: 3p12.2 deletion noncarriers. (e) Family A4. +: 10q23.33 duplication carriers; −: 10q23.33 duplication noncarriers. CMM, cutaneous malignant melanoma; DN, dysplastic nevi. Journal of Investigative Dermatology 2016 136, 2436-2443DOI: (10.1016/j.jid.2016.07.023) Copyright © 2016 The Authors Terms and Conditions

Figure 3 Expression levels of genes affected by copy number variations. Overall expression level for each gene was calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM) using RNASeq, which was performed using total RNA extracted from Epstein-Barr virus-transformed lymphoblastoid cell lines from 50 familial melanoma cases and 2 unrelated spouse controls. Journal of Investigative Dermatology 2016 136, 2436-2443DOI: (10.1016/j.jid.2016.07.023) Copyright © 2016 The Authors Terms and Conditions