Genome-wide Association Study Reveals Multiple Nasopharyngeal Carcinoma- Associated Loci within the HLA Region at Chromosome 6p21.3 Ka-Po Tse, Wen-Hui.

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Genome-wide Association Study Reveals Multiple Nasopharyngeal Carcinoma- Associated Loci within the HLA Region at Chromosome 6p21.3 Ka-Po Tse, Wen-Hui Su, Kai-Ping Chang, Ngan-Ming Tsang, Chia-Jung Yu, Petrus Tang, Lee-Chu See, Chuen Hsueh, Min-Lee Yang, Sheng-Po Hao, Hong-Yi Li, Ming-Hsi Wang, Li-Ping Liao, Lih-Chyang Chen, Sheue-Rong Lin, Timothy J. Jorgensen, Yu-Sun Chang, Yin Yao Shugart The American Journal of Human Genetics Volume 85, Issue 2, Pages 194-203 (August 2009) DOI: 10.1016/j.ajhg.2009.07.007 Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 1 Summary of GWAS Results, Based on Chromosome Associations with NPC were determined for 480,365 SNPs among 277 cases and 285 controls. The x axis represents the position on each chromosome from the p terminus to the q terminus, and the y axis depicts p values on a minus logarithmic scale. Analysis was adjusted for age and gender with the use of a logistic regression model. Chromosomes are shown in alternating colors for clarity. Red dots indicate SNPs with significant p values in the combined data from three stages (Table 1). Data on the X chromosome are not presented, due to gender adjustment during statistical analysis. The American Journal of Human Genetics 2009 85, 194-203DOI: (10.1016/j.ajhg.2009.07.007) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 2 Association Analyses of SNPs at Chromosome 6p21.3 Top: Blue dots indicate the p values for association testing drawn from first-stage GWAS on a minus logarithmic scale. Red dots depict SNPs with significant p values in combined (three stages) data. Bottom: Detailed LD structure depicted in HaploView. Analysis was adjusted for age and gender with the use of a logistic regression model. The corresponding location of genes is shown below. Pairwise linkage disequilibrium estimated in 285 control samples depicted in HaploView is shown at the bottom. Increasing intensities of red represent higher r2 values. The American Journal of Human Genetics 2009 85, 194-203DOI: (10.1016/j.ajhg.2009.07.007) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 3 GABAB Receptor 1 Protein Expression in NPC Tumor Cells GABAB receptor 1 protein was detected in NPC tumor cells (A), infiltrating leukocytes (C, indicated by arrowheads), and endothelial cells (D, indicated by “V”) by immunohistochemical staining. Distribution of NPC tumor cells is depicted with positive nuclear EBER signals (B). Expression of GABBR1 transcripts (E) and protein (F) was detected in NPC cell lines and in the normal nasopharyngeal epithelial cell line, NP69. The American Journal of Human Genetics 2009 85, 194-203DOI: (10.1016/j.ajhg.2009.07.007) Copyright © 2009 The American Society of Human Genetics Terms and Conditions