Fine Mapping of a Region of Chromosome 11q23.3 Reveals Independent Locus Associated with Risk of Glioma Hongyan Chen1, Bing Sun2, Yingjie Zhao1, Xiao Song1, Weiwei Fan1, Keke Zhou2, Liangfu Zhou2, Ying Mao2*., Daru Lu1*. 1 State Key Laboratory of Genetic Engineering, Fudan-VARI Genetic Epidemiology Center and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China, 2 Neurosurgery Department of Huashan Hospital, Fudan University, Shanghai, China Abstract Background: A single nucleotide polymorphism (SNP) at locus 11q23.3 (rs498872) in the near 59-UTR of the PHLDB1 gene was recently implicated as a risk factor for gliomas in a genome-wide association study, and this involvement was confirmed in three additional studies. Methodology/Principal Findings: To identify possible causal variants in the region, the authors genotyped 15 tagging SNPs in the 200 kb genomic region at 11q23.3 locus in a Chinese Han population-based case-control study with 983 cases and 1024 controls. We found evidence for an association between two independent loci (both the PHLDB1 and the ACRN1 genes) and a predisposition for gliomas. Among the multiple significant SNPs in the PHLDB1 gene region, the rs17749 SNP was the most significant [P = 1.3161026 in a recessive genetic model]. Additionally, two novel SNPs (rs2236661 and rs494560) that were independent of rs17749 were significantly associated with glioma risk in a recessive genetic model [P = 1.3161025 and P = 3.3261025, respectively]. The second novel locus was within the ARCN1 gene, and it was associated with a significantly reduced risk for glioma. Conclusions/Significance: Our data strongly support PHLDB1 as a susceptibility gene for glioma, also shedding light on a new potentially candidate gene, ARCN1. Citation: Chen H, Sun B, Zhao Y, Song X, Fan W, et al. (2012) Fine Mapping of a Region of Chromosome 11q23.3 Reveals Independent Locus Associated with Risk of Glioma. PLoS ONE 7(12): e52864. doi:10.1371/journal.pone.0052864 Editor: Hemant K. Paudel, McGill University Department of Neurology and Neurosurgery, Canada Received March 15, 2012; Accepted November 22, 2012; Published December 31, 2012 Copyright: ß 2012 Chen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was partially supported by Shanghai Science and Technology Research Program (09JC1402200), Natural Science Foundation of China (81001114), the Scientific Research Foundation for the Returned Overseas Chinese Scholars (State Education Ministry) and the Doctoral Fund of Ministry of Education of China. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] (DL); [email protected] (YM) . These authors jointly directed this work. Introduction individuals will develop gliomas, suggesting a genetic predisposi- tion for glioma occurrence. Gliomas that originate from glial cells are the most common An association between glioma risk and the rs498872 at 11q23.3 primary tumors of the central nervous system (CNS), representing was recently identified in a genome-wide association studies more than 40% of newly diagnosed brain tumors [1]. Asian (GWAS) [5]. This association was confirmed in three additional populations generally show lower incidence rates than populations studies [6,7,8], including our previous replication study in in Europe and North America. However, in the last few decades, a Chinese Han population. More importantly, the SNP, which is China has experienced rapid increases in malignant brain tumor mapped to the near 59-UTR of PHLDB1 (Pleckstrin homology-like incidence rates, especially in large cities. In 2000, the annual domain, family B, member 1) within a 101-kb LD block on incidence rate of brain tumors was less than 3.9 per 100,000 in 11q23.3, is frequently deleted in patients with neuroblastoma [9]. men and 2.8 per 100,000 in women in China [2]. According to Although there is no direct evidence of a role for this gene in the China’s Health Statistics Yearbook from 2009, the annual gliogenesis, based on all the available data, an association between mortality rate in 2004 and 2005 from gliomas was approximately 11q23.3 and glioma appears to be one of the most consistent 3.13 per 100,000 individuals [3]. Furthermore, glioblastoma genetic association findings in complex diseases to date. The multiforme (GBM) is the most common and the most malignant current data strongly suggest the presence of a glioma suscepti- astrocytic tumor, with a median survival of only 12–15 months bility locus at 11q23.3. under the current standard of care [4]. The etiology of gliomas is It is possible that other genetic variants near rs498872 in this largely unknown. High-dose ionizing radiation is known to region are responsible for the consistent risk in glioma observed for increase the risk. However, only a small proportion of exposed this SNP in previous studies. In this study, we performed a fine PLOS ONE | www.plosone.org 1 December 2012 | Volume 7 | Issue 12 | e52864 Fine Mapping 11q23.3 Region in Chinese Population mapping study to examine the association with glioma risk of all was considered the significance threshold using strict Bonferroni known common sequence variants in the vicinity of the rs498872 corrections [12,13]. In the single locus analyses, we observed SNP at 11q23.3. statistically significant differences between case patients and control participants in allele distributions for four SNPs Results (P = 2.8661024 for rs7115634, P = 3.3261026, for rs2236661, P = 2.9361025 for rs494560 and P = 3.0861025 for rs17748, To explore whether additional SNPs in the regions flanking respectively). Further logistic regression analyses revealed that SNP rs498872 are associated with glioma risk, we genotyped 15 patients with the rs7115634 G allele in the ARCN1 gene had a 21% tagging SNPs in the 200 kb genomic region at 11q23.3 in reduction of glioma risk (adjusted OR = 0.79, 95%CI = 0.70–0.89, a Chinese Han study population. The distribution of selected P = 2.1261024). Additionally, the rs2236661, rs494560 and characteristics between the 983 glioma cases and the 1,024 cancer- rs17748 in the PHLDB1 gene were statistically significantly free controls are summarized in Table 1. Because of the associated with glioma risk (adjusted P = 1.0661025, frequency-matching design of this study, the distributions of age P = 4.2361025 and P = 2.3661025, respectively). By tumor (age at diagnosis for case patients and age at inclusion for control subtypes, at a minimum separating the glioblastoma and other subjects) and sex were comparable between the case patients and gliomas, three SNPs (rs2236661, rs494560 and rs17748) were the control subjects. The mean age was 42.19 years for cases and significantly associated with other types (including astrocytic 42.22 for controls. Approximately 59% of both cases and controls glioma, oligodendrogliomas, ependymomas, ormixed gliomas) were male. Similar to the previous study [7,10,11], the cases were but not with GBM (adjusted P = 9.2261026, P = 1.0661024 and slightly more likely to report a family history of cancer (among P = 7.9061025, respectively). first-degree relatives) than controls (17.5% versus 13.1%; The LD plot of the chr11:117882577–118082577 region is P = 0.003). Among the cases, 306 had glioblastomas and 671 shown in Figure 1 (from hapmap data, release 21, Phases I and II, had low-grade gliomas (including 369 astrocytomas and 303 other CHB). Two separate clusters of glioma-associated SNPs were low-grade gliomas). found, including the previously reported PHLDB1 locus and The allele distributions of the 15 SNPs at 11q23.3 with their a novel locus (ARCN1). Among multiple significant SNPs at MAFs and associations with glioma risk are shown in Table 2. The PHLDB1 gene region, rs2236661 and rs494560 remained signif- genotype distribution in controls for all the variants were in icantly associated with glioma risk after adjusting for rs17748 Hardy-Weinberg equilibrium (P.0.01). To reduce the potential of 26 26 24 (adjusted P = 4.09610 and P = 8.73610 , respectively), sug- spurious findings due to multiple testing, P = 6.67610 (0.01/15) gesting these SNPs are independent from rs17748. Genotype frequency distributions of the four identified risk Table 1. Characteristics of the cases and controls in a Chinese SNPs between the cases and controls are detailed in Table 3. study population. Significant associations were observed for these four SNPs (P = 1.7561025 for rs2236661, P = 2.8261024 for rs494560 and P = 1.6861026 for rs17748) in a dominant model and for one SNP No. of P value for (P = 1.4861024 for rs7115634) in a recessive model, based on the 2 No. of Cases% Controls % x test best fit of the Akaike’s information criterion (Table 3). Further- Demographics more, we performed stratified analyses by glioma histological type. Total 983 1024 The rs2236661, rs494560 and rs17748 were strongly associated with non-GBM gliomas (adjusted P = 2.0861025, P = 2.6961024 Sex 0.545 and P = 1.6661026, respectively). Male 579 58.9 623 60.8 To understand the cumulative effects of these variants on Female 390 39.7 397 38.8 glioma risks, we created a variable to combine the effects of risk Missing 14 1.4 4 0.4 alleles per individual from the four independent risk variants Age 0.969 (rs7115634, rs2236661, rs494560 and rs71148). Overall, glioma Mean6SD 42.19615.77 42.22618.63 risk increased with increasing numbers of risk variant alleles. Individuals carrying 6–8 risk alleles had a 1.93-fold increased risk Smoke 0.012 of developing glioma compared with those who carried 0–2 risk Never 587 59.7 602 58.8 alleles (adjusted OR = 1.93, 95% CI = 1.46 to 2.55, Ever 317 32.2 412 40.2 P = 3.7061026, Table 4).