PDF file, 333KB, Figure 1a: Genome-wide Constitutive SNP Analysis with GBM Patient Overall Survival, Figure 1b: Association of Gene Expression in Tumors with Overall GBM Patient Survival.

PDF file, 406KB, Supplementary Table 1.115 TCGA SOC sample IDs used in the validation phase.; Supplementary Table 2. Proportionality tests based on the scaled Schoenfeld residules for the SNP effect in the log-additive Cox Proportional Hazards model adjusted for age and sex.; Supplementary Table 3. Validation of survival association with three SNPs in glioblastoma multiforme patients from three independent studies (Mayo Clinic10, GliomaSE11 and The Cancer Genome Atlas (TCGA17); Supplementary Table 4. Imputation analyiss of SSBP2 region:chr5: 80,680,000 -- 80,980,000, University of California, San Francisco Adult Glioma Study (AGS), Mayo Clinic, and The MACH, Hapmap 2, human genome build 18, 3 sites (University of California, San Francisco, Mayo Clinic and The Cancer Genome Atlas).

Genome-wide association studies have recently identified a cancer susceptibility locus at 10p12 mapping to MLLT10 associated with the onset of diverse tumors. We genotyped two tightly linked single-nucleotide polymorphisms (SNPs) at MLLT10 associated with meningioma (rs12770228) or ovarian cancer (rs1243180), and tested for associations among 295 meningioma cases, 606 glioma cases and 646 noncancer controls, all of European descent. The variant 'A' allele in MLLT10 rs12770228 was associated with an increased risk of meningioma (per allele odds ratio: 1.25; 95% confidence interval: 1.02, 1.53; P=0.031). Similar associations were observed for rs1243180. MLLT10 variants were unrelated to glioma. Functional investigation identified 22 candidate functional SNPs mapping to this region. The present study further validates 10p12 as a meningioma risk locus.

There is growing evidence that circadian disruption may alter risk and aggressiveness of cancer. We evaluated common genetic variants in the circadian gene pathway for associations with glioma risk and patient outcome in a US clinic-based case–control study.

Iron is essential for oxygen transport and oxidative metabolism; however, elevated iron stores can trigger overproduction of reactive oxygen species and induce DNA damage. Little is known about the association between body iron stores and glioma risk. This study examined the associations of iron levels measured in toenails and genetic variants linked to body iron stores with risk of glioma in a clinic-based case–control study.

Exposure to common infections in early life may stimulate immune development and reduce the risk for developing cancer. Birth order and family size are proxies for the timing of exposure to childhood infections with several studies showing a reduced risk of glioma associated with a higher order of birth (and presumed younger age at infection). The aim of this study was to examine whether birth order, family size, and other early life exposures are associated with the risk of glioma in adults using data collected in a large clinic-based US case-control study including 889 glioma cases and 903 community controls. A structured interviewer-administered questionnaire was used to collect information on family structure, childhood exposures and other potential risk factors. Logistic regression was used to calculate odds ratios (OR) and corresponding 95 % confidence intervals (CI) for the association between early life factors and glioma risk. Persons having any siblings were at significantly lower risk for glioma when compared to those reporting no siblings (OR = 0.64; 95 % CI 0.44–0.93; p = 0.020). Compared to first-borns, individuals with older siblings had a significantly lower risk (OR = 0.75; 95 % CI 0.61–0.91; p = 0.004). Birth weight, having been breast fed in infancy, and season of birth were not associated with glioma risk. The current findings lend further support to a growing body of evidence that early exposure to childhood infections reduces the risk of glioma onset in children and adults.

Greater adiposity has been linked to an increased risk and/or poorer survival in a variety of cancers. We examined whether prediagnostic body weight 1–5 years prior to diagnosis is associated with survival in patients with high grade glioma. The analysis was based on a series of patients with high-grade glioma (N = 853) enrolled in a US-based multicenter case–control study. Subjects reported height and weight 1–5 years prior to interview and at age 21. BMI was categorized according to WHO criteria as underweight (BMI <18.5 kg/m 2 ), normal weight (BMI 18.5–24.9 kg/m 2 ), overweight (BMI 25–29.9 kg/m 2 ) and obese (BMI ≥30 kg/m 2 ). Proportional hazards regression was used to estimate hazard ratios (HR) and 95 % confidence intervals (CIs) for glioma-related death according to body mass index (BMI, kg/m 2 ). Overall survival was reduced among patients underweight (median survival: 12.0 months) or obese (median: 13.6 months) when compared to patients of normal weight (median: 17.5 months) prior to glioma diagnosis ( p = 0.004). In a multivariate model controlling for other prognostic factors, an excess mortality was observed in patients reporting obese body weights 1–5 years prior to study interview when compared to patients with a normal BMI (HR = 1.32; 95 % CI 1.04–1.68). Consistent patterns of association with excess body weight were observed in men and women, and all findings were similar regardless of treatment for glioma. A lower than optimal body weight was associated with a nonsignificant excess mortality in multivariate analysis. Premorbid obesity was significantly associated with a poor patient outcome independent of treatment and established prognostic factors. Excess body weight may be an adverse prognostic factor in glioma, a relationship observed across a spectrum of cancer types. The current findings linking prediagnostic body weight with mortality in high-grade glioma warrant further research.

Abstract Background – Glioblastoma Multiforme (GBM) is a highly aggressive and heterogeneous disease in which survival of patients is measured only in months. Pathologic features associated with patient outcome are still incompletely understood. Until recently, phenotypic features of single cells have not been investigated due to technological limitations. However, with the advent of high-content slide scanning coupled with cognitive and scriptable algorithms, researchers are now positioned to identify and quantify single cell features that may provide unique insight on tumor behavior. In this project we sought to identify variations in cellular phenotypes which correlate with time of post diagnostic survival in patients with GBM. Methods – A total of 157 GBM patients were selected for study on the basis of short (SS) (median K-M survival = 6 months; N=81) or long (LS) (median K-M survival = 33 months, N=76) survival times. Median age was 56 years and all patients underwent current standard of care therapy for GBM (surgery, radiation and temozolomide). Among the 157 cases, 11 were excluded due to poor sample quality (final n=146). For each case, the diagnostic H&E slide was digitally scanned using the ScanScope XT (Aperio, Vista, CA, USA) with a 200x/0.8NA objective lens. Definiens TissueStudio v3.0 (Munich, Germany) was used to identify viable tumor regions. Individual cells were segmented in areas of viable tumor and twenty separate features extracted from each tumor cell (subcellular compartmentalization, nucleus to cytoplasm area ratio, nuclear size and shape, etc). In total, the 20 features were extracted in thousands of single cells for each GBM case. Output was evaluated by Matlab (The MathWorks, Inc,, Natick, MA) using a heatmap approach by first normalizing the scales of each feature to a range of 0-1, and assigning a color from green (0) to red (1) (5 classes) for each cell or compartment (x) and each feature (y). Results – This study was completed in a series of three stages including training followed by two replication sets. In the training set (N=50), four of the evaluated features associated with the size and shape of the cancer cell nuclei (i.e. width [μm], circularity, ellipticity and hematoxylin intensity), were found to distinguish the SS group (15/25) from the LS group (6/25) based on supervised classification. A similar pattern was observed in replication set 1 (15/24 and 8/28, respectively) and replication set 2 (15/23 and 8/21, respectively). Overall, 66% of cases were correctly classified with respect to survival time on the basis of these cellular features (p=0.0001). Conclusions – Quantitative image analysis may be useful in the identification of novel prognostic features in GBM with potential for gaining new biological insights on the behavior of these tumors. Citation Format: Mark C. Lloyd, Melissa H. Madden, L. Burton Nabors, Reid C. Thompson, Jeffrey J. Olson, Steven L. Carroll, James Browning, Tamir Epstein, Robert A. Gatenby, Kathleen M. Egan. Single cell phenotypic heterogeneity as a prognostic factor in glioblastoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 714. doi:10.1158/1538-7445.AM2013-714

Abstract Elevated iron stores can trigger overproduction of reactive oxygen species and induce oxidative DNA damage. To our knowledge, no studies have investigated the association of body iron stores with the risk of glioma. In this investigation, we examined single nucleotide polymorphisms (SNPs) identified as markers of iron status in genome-wide association studies, and also measured iron stores in toenail samples in a clinic-based case-control study conducted at medical centers in the southeastern US. Genotyping was performed in 622 newly diagnosed, nonrecurrent glioma cases (including 341 WHO grade IV glioblastomas (GBM); 146 WHO grade II or III astrocytomas, 94 mixed oligoastrocytomas (MOAs) and oligodendrogliomas, and 41 gliomas with unspecified histology) and 628 healthy controls with no history of brain tumors. Illumina GoldenGate and Taqman OpenArray assays were used to genotype oral DNA samples. A total of 24 SNPs associated with markers of iron status were genotyped. Iron levels in toenail samples were measured in 200 glioma cases and 200 controls using neutron-activation analysis. Logistic regression was used to estimate age and gender-adjusted odds ratios (OR) and 95% confidence intervals (CI) for glioma risk according to examined genotypes and toenail iron levels. Proportional hazards regression was used to estimate age and gender-adjusted hazard ratios (HR) for glioma-related death among 320 patients with GBM or high grade astrocytomas all treated with the current standard of care for high grade glioma (eg. surgery, radiation and temozolomide) (248 deaths; median Kaplan-Meier survival: 15.0 months). We observed no overall association with glioma risk or patient outcome for SNPs in ARSB, BTN1A1, C7ORF10, FLJ43390, GHR, GTSCR1, HFE, HIST1H2BJ, KRT18P33, LRRC16, SCGN, SLC17A1, TOPBP1, and WTAP. Among non-GBM astrocytomas, borderline risk associations were observed for rs236918 in PCSK7 (G>C; minor allele frequency (MAF) = 0.11) (per variant allele OR = 0.50; 95% CI: 0.29 to 0.88; p for trend = 0.01) and with rs1049296 in TF (C>T; MAF = 0.17) (recessive model OR = 3.03; 95% CI: 1.11 to 8.27; p = 0.03). Among oligodendrogliomas/MOAs, risk associations were observed for rs4820268 in TMPRSS6 (A>G; MAF = 0.43) (recessive model OR = 1.91; 95% CI: 1.14 to 3.22; p = 0.01) and rs12216125 in TRIM38 (C>T; MAF = 0.35) (dominant model OR = 1.67; 95% CI: 1.03 to 2.72; p = 0.04). No SNPs were associated with the risk of GBM. One SNP, rs972275 in RSPO3 (G>C; MAF = 0.38), was associated with shorter patient survival (dominant model HR = 1.40; 95% CI: 1.06, 1.87; p=0.02). Increasing levels of toenail iron was associated with a non-significant decrease in glioma risk (OR = 0.88; 95% CI: 0.77 to 1.02; p = 0.08). Iron levels were not associated with survival. To our knowledge this is the first report suggesting that genetically determined variation in iron status may affect glioma risk and patient outcome. Further studies are needed to confirm these results. Citation Format: Gabriella M. Anic, Reid C. Thompson, L. Burton Nabors, Jeffrey J. Olson, Melissa H. Madden, James E. Browning, John D. Brockman, Peter A. Forsyth, Kathleen M. Egan. Toenail iron, genetic variation in iron status, and the risk and outcome of glioma . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 104. doi:10.1158/1538-7445.AM2013-104

Increased height and greater adiposity have been linked to an increased risk of many cancer types, though few large studies have examined these associations in glioma. We examined body weight and height as potential risk factors for glioma in a large US-based case–control study.

SSBP2 variants are associated with survival in glioblastoma patients Yuanyuan Xiao, Paul A. Decker, Terri Rice, Lucie S. McCoy, Ivan Smirnov, Joseph S. Patoka, Helen M. Hansen, Joe L. Wiemels, Tarik Tihan, Michael D. Prados, Susan M. Chang, Mitchel S. Berger, Matthew L. Kosel, Brooke L. Fridley, Daniel H. Lachance, Brian Patrick O’Neill, Jan C. Buckner, Reid C. Thompson, L. B. Nabors, Jeffrey J. Olson, Steve Brem, Melissa H. Madden, James E. Browning, John K. Wiencke, Kathleen M. Egan, Robert B. Jenkins, Margaret R. Wrensch

Validation of a recent finding linking a rare variant in TP53 to the risk of glioma, the most common primary brain tumour, is reported here. This study genotyped the single nucleotide polymorphism (SNP) rs78378222 in 566 glioma cases and 603 controls. The variant 'C' allele (with an allelic frequency of 1.1% in controls) was associated with a 3.5-fold excess in glioma risk (odds ratio 3.54; p=0.0001). Variant carriers had significantly improved survival (hazard ratio 0.52; p=0.009) when compared to non-carriers. The rs78378222 SNP is the first confirmed rare susceptibility variant in glioma. Results may shed light on the aetiology and progression of these tumours.

Abstract Experimental and clinical evidence suggest that vitamin D protects against several types of cancer by promoting cell differentiation and apoptosis and by inhibiting cell proliferation and angiogenesis. In vitro evidence supports a similar protective function in glioma; however, no study has examined whether common genetic variants in the vitamin D pathway are related to glioma risk or patient outcome. We evaluated these potential associations in a clinic-based case-control study conducted at medical centers in the southeastern US. Genotyping was performed in 623 newly diagnosed (eg. nonrecurrent) glioma cases (including 343 WHO grade IV glioblastomas (GBM); 148 WHO grade II or III astrocytomas, 95 oligoastrocytomas and oligodendrogliomas, and 37 gliomas with unspecified histology) and 631 healthy controls with no history of brain tumors. A total of 7 candidate tagging single nucleotide polymorphisms (SNPs) were genotyped in the vitamin D receptor (VDR at 12q13) including rs2107301, rs2238135, rs4516035, rs731236 (Taq1), rs1544410 (Bsm1), rs11568820 (Cdx2), and rs2228570 (Fok1). SNPs associated with serum concentrations of 25-hydroxy vitamin D in genome-wide association studies (GWAS) were also evaluated including rs1155563, rs12512631, rs2282679, and rs7041 in GC (4q12-q13), rs10741657 in CYP2R1 (11p15), rs6013897 in CYP24A1 (20q13), rs3829251 in NADSYN1 (11q13), and rs6599638 at C10orf88 (10q26). Genotyping was performed in oral DNA samples using Illumina GoldenGate and Taqman OpenArray assays. Logistic regression was used to estimate age and gender-adjusted odds ratios (OR) and 95% confidence intervals (CI) for glioma risk according to vitamin D genotypes. Proportional hazards regression was used to estimate age and gender-adjusted hazard ratios (HR) for glioma-related death among 439 patients with high grade tumors including GBM and high grade astrocytomas (331 deaths; median Kaplan-Meier survival: 15.0 months). GWAS SNPs in NADSYN1, GC, and C10ORF88 were not associated with glioma risk or patient survival. Risk associations limited to GBM were observed for rs2238135 in the VDR (G>C; minor allele frequency (MAF) = 0.20) (per variant allele OR = 1.31; 95% CI: 1.01 to 1.71; p for trend = 0.04) and for GWAS SNP rs10741657 located near CYP2R1 (G>A; MAF = 0.40) (per variant allele OR = 0.79; 95% CI: 0.63 to 0.98; p for trend = 0.03). The variant allele in CYP24A1 rs6013897 (T>A; MAF = 0.20) was associated with prolonged survival among patients with high grade tumors (per variant allele HR = 0.79; 95% CI: 0.59 to 0.97; p for trend = 0.03) in patients uniformly treated with the current standard of care (surgery, radiation and temozolomide). To our knowledge this is the first report suggesting that genetic variation in vitamin D related genes may be a determinant of glioma risk and outcome. Further studies are needed to confirm these results and identify the putative causal variant. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2629. doi:1538-7445.AM2012-2629

Experimental and epidemiological evidence shows a beneficial role of vitamin D in cancer. In vitro evidence is consistent with a similar protective function in glioma; however, no study has yet examined the potential role of vitamin D in glioma.We evaluated the association between common genetic variants in the vitamin D pathway and glioma risk and patient outcome in 622 newly diagnosed glioma cases and 628 healthy controls enrolled in a clinic-based case-control study. Subjects were genotyped for 7 candidate and tagging single nucleotide polymorphisms in the vitamin D receptor and 8 additional variants in NADSYN1, GC, CYP24A1, CYP2R1, and C10ORF88 linked in genome-wide association studies to serum concentrations of vitamin D. Unconditional logistic regression was used to estimate age- and gender-adjusted odds ratios and 95 % confidence intervals for glioma risk according to vitamin D genotypes. Proportional hazards regression was used to estimate hazard ratios for glioma-related death among 320 patients diagnosed with high-grade tumors. P values were uncorrected for multiple comparisons.Risk of astrocytic tumors was associated with variant alleles in rs3829251 (NADSYN1), rs10741657 (CYP2R1), rs2228570 (Fok1, VDR), and rs731236 (Taq1, VDR). No risk associations were found among oligodendroglial tumors. Survival associations were observed according to variant status for rs1544410 (Bsm1, VDR) and rs6013897 (CYP24A1).This exploratory analysis provides limited evidence of a role for genetic variation in vitamin D pathway genes with glioma risk and survival.

Abstract Purpose: Glioblastoma is a devastating, incurable disease with few known prognostic factors. Here, we present the first genome-wide survival and validation study for glioblastoma. Experimental Design: Cox regressions for survival with 314,635 inherited autosomal single-nucleotide polymorphisms (SNP) among 315 San Francisco Adult Glioma Study patients for discovery and three independent validation data sets [87 Mayo Clinic, 232 glioma patients recruited from several medical centers in Southeastern United States (GliomaSE), and 115 The Cancer Genome Atlas patients] were used to identify SNPs associated with overall survival for Caucasian glioblastoma patients treated with the current standard of care, resection, radiation, and temozolomide (total n = 749). Tumor expression of the gene that contained the identified prognostic SNP was examined in three separate data sets (total n = 619). Genotype imputation was used to estimate hazard ratios (HR) for SNPs that had not been directly genotyped. Results: From the discovery and validation analyses, we identified a variant in single-stranded DNA-binding protein 2 (SSBP2) on 5q14.1 associated with overall survival in combined analyses (HR, 1.64; P = 1.3 × 10−6). Expression of SSBP2 in tumors from three independent data sets also was significantly related to patient survival (P = 5.3 × 10−4). Using genotype imputation, the SSBP2 SNP rs17296479 had the strongest statistically significant genome-wide association with poorer overall patient survival (HR, 1.79; 95% CI, 1.45-2.22; P = 1.0 × 10−7). Conclusion: The minor allele of SSBP2 SNP rs17296479 and the increased tumor expression of SSBP2 were statistically significantly associated with poorer overall survival among glioblastoma patients. With further confirmation, previously unrecognized inherited variations influencing survival may warrant inclusion in clinical trials to improve randomization. Unaccounted for genetic influence on survival could produce unwanted bias in such studies. Clin Cancer Res; 18(11); 3154–62. ©2012 AACR.

Background: The human SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays essential roles in a variety of cellular processes and has been implicated in human cancer. However, the role of germline genetic variants in this complex in relation to cancer risk is not well studied. Methods: We assessed the association of 16 variants in the catalytic subunits (SMARCA2 and SMARCA4) of the SWI/SNF complex with the risk of glioma subtypes (lower grade astrocytoma, oligodendroglioma and glioblastoma [GBM]) and with mortality from high-grade tumors (GBM) in a multicenter US case–control study that included 561 cases and 574 controls. Associations were estimated with odds ratios (OR, for risk) or hazards ratios (HR, for mortality) with 95% confidence intervals (CI). False discovery rate (FDR-q) was used to control for multiple testing in risk associations. Results: None of the investigated SNPs was associated with overall glioma risk. However, analyses according to histological subtypes revealed a statistically significant increased risk of oligodendroglioma in association with SMARCA2 rs2296212 (OR=4.05, 95%CI=1.11–14.80, P=0.030, q=0.08) and rs4741651 (OR=4.68, 95%CI=1.43–15.30, P=0.011, q=0.08) and SMARCA4 rs11672232 (OR=1.90, 95%CI=1.01–3.58, P=0.048, q=0.08) and rs12232780 (OR=2.14, 95%CI=1.06–4.33, P=0.035, q=0.08). No significant risk associations were observed for GBM or lower grade astrocytoma. Suggestive associations with GBM mortality were not validated in the Cancer Genome Atlas. Conclusion: Our findings suggest that genetic variants in SMARCA2 and SMARCA4 influence the risk of oligodendroglioma. Further research is warranted on the SWI/SNF complex genes and epigenetic mechanisms more generally in the development of glioma in adults.

Abstract Natural killer (NK) cells play a key role in the immune response to certain infections and neoplasms. A major activating receptor of NK lymphocytes is NKG2D. In cancer, NKG2D ligands on transformed cells transmit danger signals to NKG2D-activated NK T cells culminating in cytolysis of malignant cells. A role for NK host defense in glioma is suggested by the expression of NKG2D ligands on glioma cells though not normal brain and correlation of NKG2D ligand expression with increasing WHO grade of malignancy. Genetic variation in NKG2D and its ligands has been associated with susceptibility to cancer and autoimmune diseases. We examined single nucleotide polymorphisms (SNPs) in genes affecting NK cell-mediated immune response for association with glioma risk and outcome in a case-control study encompassing 563 newly diagnosed glioma cases (including 324 WHO grade IV glioblastomas (GBM); 145 WHO grade II or III astrocytomas and 94 oligoastrocytomas and oligodendrogliomas) and 629 healthy controls with no history of brain cancer. DNA was isolated from saliva samples. A total of 24 candidate SNPs were genotyped using the Illumina Goldengate assay in critical genes linked to NK immunosurveillance including KLRK1 (encoding NKG2D), key NKG2D ligands (MICA, MICB and RAET1E), and genes linked to tumor immunoresistance (IDO1, IDO2). Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) for glioma risk in relation to individual SNPs adjusting for age and gender. Proportional hazards regression was used to estimate age and gender-adjusted hazard ratios (HR) for GBM-related death (203 deaths; median follow up: 11.2 months) for each examined SNP. A haplotype associated with low NK activity in peripheral lymphocytes, identified by SNPs in the NK complex gene region on 12p13-p12 and marked by rs1049174 in the 3’UTR of KLRK1 (minor allele frequency (MAF) in controls: 26%), was associated with an increased glioma risk (per variant “C” allele OR: 1.22; 95% CI: 1.02-1.46; p=0.030); associations with this SNP were most prominent among oligodendroglioma patients (per allele OR: 1.69; 95% CI: 1.20-2.38; p=0.0027). A putatively functional nonsynonymous SNP in MICA (rs1051794; Lys196Glu; MAF: 27%) had a borderline association with risk for GBM (per variant “A” allele OR: 1.24; 95% CI: 1.00-1.53; p=0.048) though not other glioma subtypes; the variant rs1051794 allele was associated with increased GBM mortality (per allele HR: 1.31; 95% CI: 1.04-1.65; p=0.020). An intronic SNP in IDO2 (rs2543072) associated with risk of astrocytic tumors (per variant “T” allele OR: 1.65; 95% CI: 1.19-2.30; p=0.003; MAF: 21%) was also associated with GBM mortality (per allele HR: 1.28; 95% CI: 1.00-1.62; p=0.046). These results provide evidence that genetic variation in NK immunosurveillance influences glioma susceptibility and may contribute to GBM aggressiveness. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 875. doi:10.1158/1538-7445.AM2011-875

The Notch signaling network is an evolutionarily conserved intercellular signaling pathway that plays a fundamental role during cell-fate specification in the developing mammalian nervous system. Mounting evidence suggest that this signaling network plays a critical oncogenic role in the development and progression of glioma. Stem-like cells in brain tumors require Notch for their survival and growth. Moreover, Notch-1 and its ligands, Delta-like-1 and Jagged-1 are overexpressed in both glioma cell lines and primary human gliomas. Down-regulation of Notch-1, Delta-like-1, or Jagged-1 by RNA interference induces apoptosis and inhibits proliferation in multiple glioma cell lines. Finally, pretreatment of glioma cells with Notch-1 or Delta-like-1 small interfering RNA significantly prolongs survival in experimental models of brain tumors. In the present study, we tested whether single nucleotide polymorphisms (SNPs) in the genes encoding Notch-1 (NOTCH1 at 9q34) and its ligands, Delta-like-1 (DLL1 at 6q27) and Jagged-1 (JAG1 at 20p12-p11) are associated with the risk of glioma onset in a clinic-based case-control study conducted at medical centers in the southeastern US. A total of 29 candidate and haplotype tagging SNPs (10 SNPs in NOTCH1; 2 in DLL1 and 17 in JAG1) were genotyped using the Illumina Goldengate assay in 563 newly diagnosed (eg. nonrecurrent) glioma cases (including 324 WHO grade IV glioblastomas (GBM); 145 WHO grade II or III astrocytomas and 94 oligoastrocytomas and oligodendrogliomas) and 629 healthy controls with no history of brain tumor. DNA was isolated from saliva samples. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) for individual SNPs adjusting for age and gender. No consistent associations were observed for either examined variant in DLL1. An intronic SNP (rs3013300) in NOTCH1 located 9.2kb from the start codon was associated with an increased risk of astrocytomas (per variant “T” allele OR: 1.48; 95% CI: 1.12-1.96; p=0.006; MAF: 0.31), though not other glioma subtypes. Another intronic SNP in NOTCH1 (rs11574903) in weak linkage with the rs3013300 variant (r2: 0.10) was significantly associated with risk of oligodendrogliomas (per variant ‘T” allele OR: 1.68; 95% CI: 1.18-2.40; p=0.004; MAF: 0.22). This SNP is located 62bp downstream of a nonsynonymous SNP (rs115563691; V1671I) in NOTCH1. A SNP in the 3’UTR of the NOTCH1 ligand, JAG1 (rs8708), located in a putative micro-RNA binding site, was significantly associated with the risk of GBM (per variant “A” allele OR: 1.30; 95% CI: 1.06-1.59; p=0.010; MAF: 0.45). To our knowledge, this is the first study implicating genetic variants in the Notch stem cell signaling network with cancer risk. Further research is needed to confirm these findings and to elucidate putative causal variants in this pathway. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 874. doi:10.1158/1538-7445.AM2011-874