A gender-specific association of CNV at 6p21.3 with NPC susceptibility

Ka Po Tse, Wen Hui Su, Min Lee Yang, Hsiao Yun Cheng, Ngan Ming Tsang, Kai Ping Chang, Sheng Po Hao, Yin Yao Shugart, Yu Sun Chang*

*Corresponding author for this work

Research output: Contribution to journalJournal Article peer-review

41 Scopus citations


Copy number variations (CNVs), a major source of human genetic polymorphism, have been suggested to have an important role in genetic susceptibility to common diseases such as cancer, immune diseases and neurological disorders. Nasopharyngeal carcinoma (NPC) is a multifactorial tumor closely associated with genetic background and with a male preponderance over female (3:1). Previous genome-wide associ- ation studies have identified single-nucleotide polymorphisms (SNPs) that are associated with NPC suscep- tibility. Here, we sought to explore the possible association of CNVs with NPC predisposition. Utilizing genome-wide SNP-based arrays and five CNV-prediction algorithms, we identified eight regions with CNV that were significantly overrepresented in NPC patients compared with healthy controls. These CNVs included six deletions (on chromosomes 3, 6, 7, 8 and 19), and two duplications (on chromosomes 7 and 12). Among them, the CNV located at chromosome 6p21.3, with single-copy deletion of the MICA and HCP5 genes, showed the highest association with NPC. Interestingly, it was more specifically associated with an increased NPC risk among males. This gender-specific association was replicated in an independent case-control sample using a self-established deletion-specific polymerase chain reaction strategy. To the best of our knowledge, this is the first study to explore the role of constitutional CNVs in NPC, using a genome-wide platform. Moreover, we identified eight novel candidate regions with CNV that merit future investigation, and our results suggest that similar to neuroblastoma and prostate cancer, genetic structural variations might contribute to NPC predisposition.

Original languageEnglish
Article numberddr191
Pages (from-to)2889-2896
Number of pages8
JournalHuman Molecular Genetics
Issue number14
StatePublished - 07 2011


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