How genome-wide SNP-SNP interactions relate to nasopharyngeal carcinoma susceptibility

Wen Hui Su, Yin Yao Shugart, Kai Ping Chang, Ngan Ming Tsang, Ka Po Tse, Yu Sun Chang

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Abstract

This study is the first to use genome-wide association study (GWAS) data to evaluate the multidimensional genetic architecture underlying nasopharyngeal cancer. Since analysis of data from GWAS confirms a close and consistent association between elevated risk for nasopharyngeal carcinoma (NPC) and major histocompatibility complex class 1 genes, our goal here was to explore lesser effects of gene-gene interactions. We conducted an exhaustive genome-wide analysis of GWAS data of NPC, revealing two-locus interactions occurring between single nucleotide polymorphisms (SNPs), and identified a number of suggestive interaction loci which were missed by traditional GWAS analyses. Although none of the interaction pairs we identified passed the genome-wide Bonferroni-adjusted threshold for significance, using independent GWAS data from the same population (Stage 2), we selected 66 SNP pairs in 39 clusters with P-11) which also show trans-expression quantitative loci (eQTL) association in Chinese population. We then detected a complicated cis-interaction pattern around the NPC-associated HLA-B locus, which is immediately adjacent to copy-number variations implicated in male susceptibility for NPC. While it remains to be seen exactly how and to what degree SNP-SNP interactions such as these affect susceptibility for nasopharyngeal cancer, future research on these questions holds great promise for increasing our understanding of this disease's genetic etiology, and possibly also that of other gene-related cancers.

Original languageEnglish (US)
Article numbere83034
JournalPLoS One
Volume8
Issue number12
DOIs
StatePublished - Dec 23 2013

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ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Su, W. H., Shugart, Y. Y., Chang, K. P., Tsang, N. M., Tse, K. P., & Chang, Y. S. (2013). How genome-wide SNP-SNP interactions relate to nasopharyngeal carcinoma susceptibility. PLoS One, 8(12), [e83034]. https://doi.org/10.1371/journal.pone.0083034