Allele Hazard Ratio Research Articles

Abstract 2691: Genome-wide association study identifies two susceptibility loci that modify radiation-related risk for breast cancer after childhood cancer: A report from the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort

Abstract Background: Childhood cancer survivors treated with chest radiotherapy have substantially elevated risk for developing breast cancer. Although numerous breast cancer susceptibility variants have been established, genetic predisposition for breast cancer after childhood cancer remains poorly understood. Methods: We conducted the first genome-wide association study of subsequent breast cancer in female childhood cancer survivors within two large-scale cohorts with detailed treatment data and systematic, long-term follow-up: the Childhood Cancer Survivor Study [CCSS; 178 breast cancer cases, 2200 controls (survivors without subsequent neoplasm) of European descent] and the St. Jude Lifetime Cohort (SJLIFE; 29 cases, 574 controls). Genotyping on the Illumina HumanOmni5MExome (CCSS) or Affymetrix 6.0 (SJLIFE) array and imputation based on the 1000 Genomes Project yielded >16 million high quality genotyped or imputed variants available in both studies. Assuming an additive genetic model, we used multivariate Cox regression to quantify the effect of each variant in the overall population and stratified by receipt of ≥10 Gray (Gy) or <10 Gy radiation exposure to the chest. Results: We identified two loci associated with breast cancer risk among children who received ≥10 Gy radiation to the chest (131 cases, 493 controls): one at 1q41 [rs4342822, risk allele frequency (RAF) = 0.46 in controls, pooled per allele hazard ratio (HR) = 1.94, 95% confidence interval (CI) = 1.50-2.51, Pexact = 1.20×10−8] and another at 11q23 (rs74949440, RAF = 0.02 in controls, HR = 3.71, 95%CI = 2.18-6.32, Pexact = 2.00×10−9). Neither locus was associated with breast cancer risk among children who received <10 Gy radiation to the chest (69 cases, 2144 controls; rs4342822: HR = 1.03, 95%CI = 0.75-1.44; rs74949440: HR = 1.21, 0.41-3.54). Results were consistent in the two studies, and the associations did not appear to be related to type of first primary childhood cancer. Both loci fall in or near biologically plausible candidate genes: the variant rs4342822 lies near PROX1, which is amplified in >10% of breast cancers in The Cancer Genome Atlas data. The variant rs74949440 is intronic to TAGLN, whose expression levels have been associated with breast cancer prognosis and altered cell death resistance following irradiation in human carcinoma cell lines. Conclusion: These findings represent the first evidence outside of identified high-risk cancer susceptibility genes that certain individuals are genetically predisposed to developing breast cancer after radiotherapy and suggest that radiation exposure may interact with germline genetics to modify breast cancer risk. Citation Format: Lindsay M. Morton, Joshua N. Sampson, Gregory T. Armstrong, Ting-Huei Chen, Melissa Hudson, Eric Karlins, Casey L. Dagnall, Shenchao Li, Carmen L. Wilson, Kumar Srivastava, Wei Liu, Guolian Kang, Kevin Oeffinger, Tara O. Henderson, Chaya S. Moskowitz, Todd M. Gibson, Diana M. Merino, Jeannette R. Wong, Sue Hammond, Joseph P. Neglia, Lucie M. Turcotte, Jeremy Miller, Laura Bowen, William A. Wheeler, Wendy M. Leisenring, John A. Whitton, Laurie Burdette, Belynda D. Hicks, Mitchell J. Machiela, Aurelie Vogt, Zhaoming Wang, Meredith Yeager, Geoffrey Neale, Matthew Lear, Louise C. Strong, Yutaka Yasui, Marilyn Stovall, Rita E. Weathers, Susan A. Smith, Rebecca Howell, Stella M. Davies, Gretchen A. Radloff, Amy Berrington de González, Peter D. Inskip, Preetha Rajaraman, Joseph F. Fraumeni, Smita Bhatia, Stephen J. Chanock, Margaret A. Tucker, Leslie L. Robison. Genome-wide association study identifies two susceptibility loci that modify radiation-related risk for breast cancer after childhood cancer: A report from the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2691.

Polymorphisms of cystathionine beta-synthase gene are associated with susceptibility to sepsis.

Sepsis is the systemic inflammatory host response to infection. Cystathionine beta-synthase (CBS)-dependent homocysteine (Hcy) pathway was demonstrated to affect disease severity and mortality in patients with severe sepsis/septic shock. Independent studies identified a single-nucleotide polymorphism (SNP, rs6586282, hg19 chr21:g.44478497C>T) in intron 14 of the CBS-coding gene (CBS) associated with Hcy plasma levels. We aimed to describe the association of this SNP and variants of a splice donor-affecting variable-number tandem repeat (VNTR, NG_008938.1:g.22763_22793[16_22]) 243 bp downstream of rs6586282 with severe human sepsis. We analyzed the VNTR structure and genotyped variants of rs6586282 and a neighboring SNP (rs34758144, hg19 chr21:g.44478582G>A) in two case-control studies including patients with severe sepsis/septic shock from Germany (n=168) and Greece (n=237). In both studies, we consistently observed an association of CBS VNTR alleles with sepsis susceptibility. Risk linearly increased with number of tandem repeats (per allele odds ratio in the adjusted analysis 1.34; 95% confidence interval (CI)=1.17-1.55; P<0.001). Association had also been shown for rs34758144 whose risk allele is in linkage disequilibrium with one long VNTR allele (19 repeat). In contrast, we observed no evidence for an effect on 28-day survival in patients with severe sepsis/septic shock (per allele hazard ratio in the adjusted analysis for VNTR 1.10; 95% CI=0.95-1.28; P=0.20). In a minigene approach, we demonstrated alternative splicing in distinct VNTR alleles, which, however, was independent of the number of tandem units. In conclusion, there is no ordinary conjunction between human CBS and severe sepsis/septic shock, but CBS genotypes are involved in disease susceptibility.

A retrospective observational study of the relationship between single nucleotide polymorphisms associated with the risk of developing colorectal cancer and survival.

BackgroundThere is variability in clinical outcome for patients with apparently the same stage colorectal cancer (CRC). Single nucleotide polymorphisms (SNPs) mapping to chromosomes 1q41, 3q26.2, 6p21, 8q23.3, 8q24.21, 10p14, 11q13, 11q23.1, 12q13.13, 14q22, 14q22.2, 15q13.3, 16q22.1, 18q21.1, 19q13.11, 20p12, 20p12.3, 20q13.33 and Xp22 have robustly been shown to be associated with the risk of developing CRC. Since germline variation can also influence patient outcome the relationship between these SNPs and patient survivorship from CRC was examined.MethodsAll enrolled into the National Study of Colorectal Cancer Genetics (NSCCG) were genotyped for 1q41, 3q26.2, 6p21, 8q23.3, 8q24.21, 10p14, 11q13, 11q23.1, 12q13.13, 14q22, 14q22.2, 15q13.3, 16q22.1, 18q21.1, 19q13.11, 20p12, 20p12.3, 20q13.33 and xp22 SNPs. Linking this information to the National Cancer Data Repository allowed patient genotype to be related to survival.ResultsThe linked dataset consisted of 4,327 individuals. 14q22.22 genotype defined by the SNP rs4444235 showed a significant association with overall survival. Specifically, the C allele was associated with poorer observed survival (per allele hazard ratio 1.13, 95% confidence interval 1.05–1.22, P = 0.0015).ConclusionThe CRC susceptibility SNP rs4444235 also appears to exert an influence in modulating patient survival and warrants further evaluation as a potential prognostic marker.

Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with prognosis of estrogen receptor-negative breast cancer after chemotherapy.

IntroductionTumor lymphocyte infiltration is associated with clinical response to chemotherapy in estrogen receptor (ER) negative breast cancer. To identify variants in immunosuppressive pathway genes associated with prognosis after adjuvant chemotherapy for ER-negative patients, we studied stage I-III invasive breast cancer patients of European ancestry, including 9,334 ER-positive (3,151 treated with chemotherapy) and 2,334 ER-negative patients (1,499 treated with chemotherapy).MethodsWe pooled data from sixteen studies from the Breast Cancer Association Consortium (BCAC), and employed two independent studies for replications. Overall 3,610 single nucleotide polymorphisms (SNPs) in 133 genes were genotyped as part of the Collaborative Oncological Gene-environment Study, in which phenotype and clinical data were collected and harmonized. Multivariable Cox proportional hazard regression was used to assess genetic associations with overall survival (OS) and breast cancer-specific survival (BCSS). Heterogeneity according to chemotherapy or ER status was evaluated with the log-likelihood ratio test.ResultsThree independent SNPs in TGFBR2 and IL12B were associated with OS (P <10−3) solely in ER-negative patients after chemotherapy (267 events). Poorer OS associated with TGFBR2 rs1367610 (G > C) (per allele hazard ratio (HR) 1.54 (95% confidence interval (CI) 1.22 to 1.95), P = 3.08 × 10−4) was not found in ER-negative patients without chemotherapy or ER-positive patients with chemotherapy (P for interaction <10−3). Two SNPs in IL12B (r2 = 0.20) showed different associations with ER-negative disease after chemotherapy: rs2546892 (G > A) with poorer OS (HR 1.50 (95% CI 1.21 to 1.86), P = 1.81 × 10−4), and rs2853694 (A > C) with improved OS (HR 0.73 (95% CI 0.61 to 0.87), P = 3.67 × 10−4). Similar associations were observed with BCSS. Association with TGFBR2 rs1367610 but not IL12B variants replicated using BCAC Asian samples and the independent Prospective Study of Outcomes in Sporadic versus Hereditary Breast Cancer Study and yielded a combined HR of 1.57 ((95% CI 1.28 to 1.94), P = 2.05 × 10−5) without study heterogeneity.ConclusionsTGFBR2 variants may have prognostic and predictive value in ER-negative breast cancer patients treated with adjuvant chemotherapy. Our findings provide further insights into the development of immunotherapeutic targets for ER-negative breast cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/s13058-015-0522-2) contains supplementary material, which is available to authorized users.

Dietary folate and related micronutrients, folate-metabolising genes, and ovarian cancer survival

ObjectiveFolate is essential for DNA synthesis and methylation and is implicated in tumour progression. Few studies have examined its role in ovarian cancer survival. Our objective was to determine relationships between intake of folate, related one-carbon nutrients, single nucleotide polymorphisms (SNPs) in folate-metabolising genes and survival following ovarian cancer diagnosis. MethodsThis analysis included 1270 women with invasive epithelial ovarian cancer diagnosed in 2002–2006. Pre-diagnostic and some post-diagnostic lifestyle, dietary, and sociodemographic information was collected via self-administered questionnaires. DNA samples were genotyped for SNPs in methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR) and methionine synthase reductase (MTRR) genes. Adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated using Cox regression. ResultsMultivariate analyses did not identify associations between higher pre-diagnostic intake of folate, folic acid, vitamins B2, B6, and B12, methionine, betaine or choline and survival overall. In stratified analyses, higher folic acid and folate intake was associated with significantly worse survival among women with mucinous tumours (HRs per 100μg 1.30 and 1.43, respectively) and smokers (HRs per 100μg 1.23 and 1.16 respectively). There was also a suggestion that higher supplemental folic acid use post-diagnosis was associated with worse survival (HR per 100μg 1.03, 95%CI 1.00–1.05). MTHFR SNP rs2066470 was significantly associated with survival (per allele HR 0.81, 95%CI 0.67–0.98). ConclusionsOur data provide little evidence that folate intake affects ovarian cancer survival. However, combined effects with smoking, and findings within the mucinous subtype and for post-diagnosis folic acid, warrant further investigation.

Abstract 2629: Common genetic variants in the vitamin D pathway including genome-wide associated variants in relation to glioma risk and outcome

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&amp;gt;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&amp;gt;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&amp;gt;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

Abstract 875: Genetic variation in the natural killer cell activating receptor NKG2D and its ligands in relation to glioma risk and outcome

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

Abstract 870: Candidate SNPs in angiogenesis and lymphangiogenesis and risk of cutaneous melanoma

Abstract Background: Currently, a combination of clinical and pathologic features are used to predict patient outcome in localized melanoma including age, sex, and tumor location, ulceration and Breslow depth. The presence or absence of metastasis in the local draining (sentinel) lymph node (SLN) as determined by SLN biopsy is considered the most accurate method for staging localized melanoma and is the most important predictor of recurrence and survival in patients with clinically node-negative melanoma. Additional biomarkers are needed to improve prediction models and target therapies to individual patients. Among the most promising candidate biomarkers are genes affecting lymph/angiogenesis which are thought to play a critical role in the development and progression of melanoma. We investigated whether single nucleotide polymorphisms (SNPs) in the lymph/angiogenesis pathway are associated with risk of SLN metastasis and mortality in patients with invasive melanoma of the skin. Methods: We examined risk of SLN metastasis and melanoma-related death in relation to 290 candidate and tagging SNPs in 26 lymph/angiogenesis genes in patients referred to the Moffitt Cancer Center between 1999 and 2008 for wide local excision and SLN staging of a primary invasive melanoma of the skin. Genotypes by the Illumina Goldengates in lymph/angiogenesis pathway genes were compared in a total of 177 patients with pathologically documented SLN metastasis and 375 patients negative for nodal metastasis, of whom a total of 41 (23%) and 19 (5%) patients, respectively, died from systemic disease. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) for the risk of SLN metastasis in relation to examined genotypes adjusting for age and gender. Proportional hazards regression was used to estimate age and gender-adjusted hazard ratios (HR) for melanoma-related death. Results: A total of 17 variant alleles in 8 lymph/angiogenesis genes including COL18A1, ELAVL1, FLT1, HSPG2, PDGFD, PIK3CA, NFRSF1b and VEGFA were associated with presence of SLN metastasis. An additional 17 SNPs in 10 genes including 4 genes associated with SLN metastasis (COL18A1, ELAVL1, PDGFD, PIK3CA), CXCL12, EGFR, FGFR4, IL10, NOS3, and PDPN were associated with survival. Carriers of the variant allele in COL18A1 rs728142 (minor allele frequency: 25%) were at increased risk of SLN metastasis (per allele OR: 1.33; 95% CI: 1.00-1.77; p trend =0.05) and melanoma-related death (per allele HR: 1.57; 95% CI: 1.06-2.33; p trend =0.03). Conclusion: Results from this exploratory analysis suggest that genetic variation in the lymphangiogenesis pathway may influence melanoma aggressiveness and patient outcome. 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 870. doi:10.1158/1538-7445.AM2011-870

Abstract 877: Genetic variation in podoplanin in relation to glioma risk and outcome

Abstract Gliomas are highly invasive tumors that invariably disseminate throughout the brain. The mechanisms of glioma cell migration are still poorly understood. Human PDPN (eg. podoplanin) is a novel transmembrane glycoprotein and a lymphatic endothelial marker thought to play a role in wound healing and frequently upregulated in human neoplasia. Although its physiologic function is still unknown, the recent observation of restricted expression at the leading invasive edge of solid tumors in experimental systems has raised the possibility that PDPN plays a role in tumor cell migration and invasion. Microarray-based gene expression analysis has recently identified PDPN as a novel candidate gene in glioma pathogenesis (Clin Cancer Res. 2009 15:6541-50). In this study, we examined whether polymorphisms in the gene encoding PDPN (located at 1p36.21) are associated with glioma risk and outcome in a clinic-based case-control study encompassing 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 cancer. DNA was isolated from saliva samples. A total of 22 candidate and haplotype tagging SNPs in PDPN including the 5’ and 3’ UTR region of PDPN were genotyped using the Illumina Goldengate assay. 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) according to PDPN genotypes. No consistent associations were observed for any examined PDPN variant with glioma risk, overall, or according to glioma histological subtype. In contrast, 3 intronic SNPs (rs92406, rs2487643 and rs4391657) in moderately high linkage disequilibrium (r2: 0.57-0.96) residing in a haplotype block spanning 8kb were significantly associated with GBM mortality with the strongest signal observed in rs4391657 (NT_004610.19:g.617369T&amp;gt;C) (per variant “T” allele HR: 1.62; 95% CI: 1.28-2.05; P=0.00006; allele frequency: 0.20). The magnitude of association was similar for deaths occurring within 12 months (per variant allele HR: 1.51; 95% CI: 1.13-2.02; P=0.005) and greater than 12 months (per variant allele HR: 1.84; 95% CI: 1.21-2.80; P=0.004) following GBM diagnosis. The median survival times were 14.4, 11.4 and 8.9 months in those carrying 0, 1, or 2 at-risk “T” alleles in PDPN rs4391657 (log rank P value 0.0018), irrespective of therapy. To our knowledge this is the first report of an association of a PDPN genetic variant predicting survival times in malignancy. Further studies are needed to confirm this observation and to identify the putative causal variant. 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 877. doi:10.1158/1538-7445.AM2011-877

Abstract 876: Genetic variation in the voltage-gated chloride channel family members CLCN2 and CLCN3 in relation to glioma risk and outcome

Abstract Gliomas account for the majority of primary brain neoplasias and are among the most lethal human tumors. Tumor cells diffusely infiltrate surrounding brain tissue. The invasion of glioma cells into normal brain is thought to be facilitated by ion channels which dynamically regulate cell volume and the ability of tumor cells to shrink and invade through tortuous extracellular spaces in the brain. To shrink, glioma cells release K+ and Cl- through ion channels, which induce water to leave the cells through aquaporins. Recent evidence suggests that CL- transport in glioma cells is mediated primarily by the voltage-gated chloride channel family members, CLCN2 and CLCN3, making them attractive candidate genes in glioma pathogenesis. In the present study, we tested whether single nucleotide polymorphisms (SNPs) in CLCN2 (3q27) and CLCN3 (4q33) are associated with glioma risk or patient outcome in a clinic-based case-control study conducted at medical centers in the southeastern US. A total of 15 candidate and haplotype tagging SNPs (4 SNPs in CLCN2 and 11 SNPs in CLCN3) 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. DNA was isolated from saliva samples. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) for glioma risk in relation to individual genotypes 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 SNP. No consistent associations were observed for any examined variant in CLCN2. In contrast, 6 of the examined SNPs in CLCN3, all in moderate linkage disequilibrium (r2: 0.30-0.80), were significantly associated with glioma risk. Among them, the strongest signal was observed in rs3797040 (NT_016354.19:g.95088578C&amp;gt;T), a SNP located in a putative transcription binding site (per variant “T” allele OR: 1.25; 95% CI:1.05-1.47; p=0.0095; allele frequency: 0.49); the observed excess risk associated with the variant rs3797040 allele was consistent in GBM (per allele OR: 1.23; 95% CI: 1.01-1.51; p=0.042), astrocytomas (per allele OR: 1.15; 95% CI: 0.88-1.49; p=0.312) and oligodendrogliomas (per allele OR: 1.75; 95% CI: 1.23-2.44; p=0.001). The ancestral “C” allele in CLCN3 rs3797040 was associated with increased mortality rates among the patients with GBM (per allele HR: 1.31; 95% CI: 1.06-1.62; p=0.011). To our knowledge this is the first report suggesting that genetic variation in plasma membrane ion channels may be a determinant of glioma risk. Further studies are needed to confirm these observations and identify the putative causal variant. 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 876. doi:10.1158/1538-7445.AM2011-876

Common genetic variants and modification of penetrance of BRCA2-associated breast cancer.

The considerable uncertainty regarding cancer risks associated with inherited mutations of BRCA2 is due to unknown factors. To investigate whether common genetic variants modify penetrance for BRCA2 mutation carriers, we undertook a two-staged genome-wide association study in BRCA2 mutation carriers. In stage 1 using the Affymetrix 6.0 platform, 592,163 filtered SNPs genotyped were available on 899 young (<40 years) affected and 804 unaffected carriers of European ancestry. Associations were evaluated using a survival-based score test adjusted for familial correlations and stratified by country of the study and BRCA2*6174delT mutation status. The genomic inflation factor (λ) was 1.011. The stage 1 association analysis revealed multiple variants associated with breast cancer risk: 3 SNPs had p-values<10−5 and 39 SNPs had p-values<10−4. These variants included several previously associated with sporadic breast cancer risk and two novel loci on chromosome 20 (rs311499) and chromosome 10 (rs16917302). The chromosome 10 locus was in ZNF365, which contains another variant that has recently been associated with breast cancer in an independent study of unselected cases. In stage 2, the top 85 loci from stage 1 were genotyped in 1,264 cases and 1,222 controls. Hazard ratios (HR) and 95% confidence intervals (CI) for stage 1 and 2 were combined and estimated using a retrospective likelihood approach, stratified by country of residence and the most common mutation, BRCA2*6174delT. The combined per allele HR of the minor allele for the novel loci rs16917302 was 0.75 (95% CI 0.66–0.86, ) and for rs311499 was 0.72 (95% CI 0.61–0.85, ). FGFR2 rs2981575 had the strongest association with breast cancer risk (per allele HR = 1.28, 95% CI 1.18–1.39, ). These results indicate that SNPs that modify BRCA2 penetrance identified by an agnostic approach thus far are limited to variants that also modify risk of sporadic BRCA2 wild-type breast cancer.

Association Between a Germline OCA2 Polymorphism at Chromosome 15q13.1 and Estrogen Receptor–Negative Breast Cancer Survival

Traditional prognostic factors for survival and treatment response of patients with breast cancer do not fully account for observed survival variation. We used available genotype data from a previously conducted two-stage, breast cancer susceptibility genome-wide association study (ie, Studies of Epidemiology and Risk factors in Cancer Heredity [SEARCH]) to investigate associations between variation in germline DNA and overall survival. We evaluated possible associations between overall survival after a breast cancer diagnosis and 10 621 germline single-nucleotide polymorphisms (SNPs) from up to 3761 patients with invasive breast cancer (including 647 deaths and 26 978 person-years at risk) that were genotyped previously in the SEARCH study with high-density oligonucleotide microarrays (ie, hypothesis-generating set). Associations with all-cause mortality were assessed for each SNP by use of Cox regression analysis, generating a per rare allele hazard ratio (HR). To validate putative associations, we used patient genotype information that had been obtained with 5' nuclease assay or mass spectrometry and overall survival information for up to 14 096 patients with invasive breast cancer (including 2303 deaths and 70 019 person-years at risk) from 15 international case-control studies (ie, validation set). Fixed-effects meta-analysis was used to generate an overall effect estimate in the validation dataset and in combined SEARCH and validation datasets. All statistical tests were two-sided. In the hypothesis-generating dataset, SNP rs4778137 (C>G) of the OCA2 gene at 15q13.1 was statistically significantly associated with overall survival among patients with estrogen receptor-negative tumors, with the rare G allele being associated with increased overall survival (HR of death per rare allele carried = 0.56, 95% confidence interval [CI] = 0.41 to 0.75, P = 9.2 x 10(-5)). This association was also observed in the validation dataset (HR of death per rare allele carried = 0.88, 95% CI = 0.78 to 0.99, P = .03) and in the combined dataset (HR of death per rare allele carried = 0.82, 95% CI = 0.73 to 0.92, P = 5 x 10(-4)). The rare G allele of the OCA2 polymorphism, rs4778137, may be associated with improved overall survival among patients with estrogen receptor-negative breast cancer.

Genetic variation in SIPA1 in relation to breast cancer risk and survival after breast cancer diagnosis

Genetic variation in SIPA1, signal-induced proliferation-associated gene 1, has been proposed to be associated with aggressive breast tumor characteristics related to metastasis and worse prognosis in humans and rodents. To test this hypothesis, we genotyped 3 single nucleotide polymorphisms (SNP) located at -3092 (A<G, rs931127), exon 3-135 (C>T, rs3741378), and exon 14 + 14 (C>T, rs746429), and examined them in relation to breast cancer risk and overall survival, stratified by tumor characteristics in 2 independent case-control studies conducted in Poland (1,995 cases, 2,296 controls) and in Britain (2,142 cases, 2,257 controls). Vital status (n = 396 deaths) was available for 911 Polish and 1,919 British breast cancer cases with an average follow-up time of 5.5 years. Overall, we found no significant associations between genetic variants of SIPA1 SNPs and breast cancer risk (per allele odds ratios, 95% confidence intervals (CI): rs931127-0.99, 0.93-1.06; rs3741378-1.03, 0.94-1.13; and, rs74642-0.98, 0.92-1.04). In both studies, SIPA1 polymorphisms were not related to overall mortality (per allele hazard ratios, 95% CI: 1.02, 0.88-1.17; 0.90, 0.72-1.11; 1.04, 0.90-1.21, respectively). Our results do not support a relationship between SIPA1 polymorphisms and breast cancer risk or subsequent survival.

The Effects of Common Genetic Variants in Oncogenes on Ovarian Cancer Survival

The 5-year survival rate for invasive epithelial ovarian cancer is <35%. It has been suggested that common, germline genetic variation may influence survival after cancer diagnoses, which might enable the prediction of response to treatment and survival in the clinical setting. The aim of this study was to evaluate associations between common germline genetic variants in the oncogenes BRAF, ERBB2, KRAS, NMI, and PIK3CA, and survival after a diagnosis of epithelial ovarian cancer. We evaluated the association between 34 tagging single nucleotide polymorphisms and survival in 1,480 cases of invasive epithelial ovarian cancer cases from three different studies. Cox regression analysis, stratified by study, was used to estimate per rare allele hazard ratios (HR). The minor allele rs6944385 in BRAF was significantly associated with poor survival [HR, 1.19; 95% confidence intervals (95% CI), 1.02-1.39; P = 0.024]. The association remained after adjusting for prognostic factors (adjusted HR, 1.20; 95 CI, 1.03-1.40; P = 0.018). A haplotype of BRAF was also associated with poor survival (HR, 1.24; 95% CI, 1.02-1.51; P = 0.029) and was more significant after adjustment (HR, 1.44; 95% CI, 1.15-1.81; P = 0.001). We also found evidence of an association between a KRAS haplotype and poor survival in serous subtype (HR, 1.69; 95% CI, 1.21-2.38; P = 0.002), but this was no longer significant after adjustment. Finally, when analyses were restricted to the serous histologic subtype, the rare allele rs10842513 in KRAS, was associated with poor survival (HR, 1.40; 95% CI, 1.10-1.78; P = 0.007). Common genetic variants in the BRAF and KRAS oncogenes may be important in the prediction of survival in patients with invasive epithelial ovarian cancer.

Mismatch repair gene polymorphisms and survival in invasive ovarian cancer patients

Aims Inherited genetic factors may help partially explain variability of survival length amongst ovarian cancer patients. Of particular interest are genes involved in DNA repair, specifically those involved in mismatch repair (MMR). The aim of this study was to investigate the possible association between the common variants in MMR genes and invasive ovarian cancer overall survival. Method/results We examined associations between 44 variants that tag the known common variants (minor allele frequency ⩾0.05) in seven MMR genes ( MLH1, MLH3, MSH2, MSH3, MSH6, PMS1 and PMS2) and survival of invasive ovarian cancer patients in three case–control studies from United Kingdom (UK), Denmark and California of United States of America (USA). DNA from up to 1495 women were genotyped. The genotypes of each polymorphism were tested for association with survival using Cox regression analysis stratified by study. A nominally significant association ( P = 0.04) between genotype and ovarian cancer survival was observed for rs2228006 in PMS2. The per-rare allele hazard ratio (HR 95%CI) was 0.84 (0.71–0.99), however, it was not significant after adjusting for multiple covariants ( P = 0.47). When the analyses were restricted to serous type ovarian cancer, two SNPs showed marginal significant associations; the per-rare allele HR was 1.3 (1.05–1.6) ( P = 0.02) for rs1799977 in MLH1 and 1.4 (1.03–1.9) ( P = 0.04) for rs6151662 in MSH3. Neither was significant after adjusting for multiple covariants. Conclusion It is unlikely that common variants in the MMR pathways examined have moderate effects on survival after diagnosis with ovarian cancer. Much larger studies would be needed to exclude common variants with small effects.

Epigenetic modification of epithelial and hematopoietic neoplasia due to DNA methylation

Inherited genetic factors may help partially explain variability of survival length amongst ovarian cancer patients. Of particular interest are genes involved in DNA repair, specifically those involved in mismatch repair (MMR). The aim of this study was to investigate the possible association between the common variants in MMR genes and invasive ovarian cancer overall survival.We examined associations between 44 variants that tag the known common variants (minor allele frequency ⩾0.05) in seven MMR genes (MLH1, MLH3, MSH2, MSH3, MSH6, PMS1 and PMS2) and survival of invasive ovarian cancer patients in three case–control studies from United Kingdom (UK), Denmark and California of United States of America (USA). DNA from up to 1495 women were genotyped. The genotypes of each polymorphism were tested for association with survival using Cox regression analysis stratified by study. A nominally significant association (P = 0.04) between genotype and ovarian cancer survival was observed for rs2228006 in PMS2. The per-rare allele hazard ratio (HR 95%CI) was 0.84 (0.71–0.99), however, it was not significant after adjusting for multiple covariants (P = 0.47). When the analyses were restricted to serous type ovarian cancer, two SNPs showed marginal significant associations; the per-rare allele HR was 1.3 (1.05–1.6) (P = 0.02) for rs1799977 in MLH1 and 1.4 (1.03–1.9) (P = 0.04) for rs6151662 in MSH3. Neither was significant after adjusting for multiple covariants.It is unlikely that common variants in the MMR pathways examined have moderate effects on survival after diagnosis with ovarian cancer. Much larger studies would be needed to exclude common variants with small effects.