Genetic Logistic Regression Research Articles

Abstract 4173: Previously identified common glioma risk SNPs are associated with familial glioma

Abstract BACKGROUND: Approximately 5% of gliomas occur in individuals with a family history of glioma, and first-degree relatives of brain tumor cases have a two-fold increase in risk of brain tumor. Recent somatic characterization has shown that tumors from familial cases are indistinguishable from sporadic cases, suggesting that familial cases may arise through similar mechanisms of gliomagenesis, and therefore may be associated with common variants as well as rare mutations. In this analysis, we assessed whether previously identified common risk variants are associated with familial glioma. METHODS: Data were obtained from the Glioma International Case Control (GICC) and Gliogene studies for 448 cases with reported family history, 4,405 cases without reported family history, and 3,288 controls. We assessed 25 risk loci previously identified by glioma GWAS, and odds ratios (OR) and 95% confidence intervals (95%CI) were calculated using an additive genetic logistic regression model adjusted for age, sex, and the first two principal components for familial cases versus unaffected controls, and non-familial cases versus controls. Results were considered significant at p<0.002 (Bonferroni correction for 25 tests). RESULTS: Significant associations were detected at 5/25 loci, including TERT, EGFR, CCDC26, CDKN2B, and RTEL1. The strongest association was at rs55705857 (CCDC26, OR=2.7, p=7.49x10-17). For GBM (222 familial cases), significant associations were detected at 6/26 loci (TERT, EGFR, CDKN2B, TP53 and RTEL1), while in non-GBM (205 familial cases) significant associations were detected at 3/25 loci (LRIG1, CCDC26, PHLDB1). These SNPs were further examined using a case-only approach comparing familial to non-familial cases, and there was no significant difference in allele frequencies by family history status. There was a strong correlation between log(OR) for familial cases only versus non-familial cases (adjusted R2=0.88). CONCLUSIONS: In this analysis we identified a significant association between familial glioma and five common risk loci previously identified by glioma GWAS. This provides further evidence of shared pathways of genetic risk and gliomagenesis between familial and non-familial glioma. Further exploration is necessary to determine the overall contribution of common genetic variation to risk of familial glioma. Citation Format: Quinn T. Ostrom, Georgina Armstrong, Christopher I. Amos, Jonine L. Bernstein, Elizabeth B. Claus, Jeanette E. Eckel-Passow, Dora Il'yasova, Christoffer Johansen, Daniel H. Lachance, Rose K. Lai, Ryan T. Merrell, Sara H. Olson, Joellen H. Schildkraut, Sanjay S. Shete, Richard S. Houlston, Robert B. Jenkins, Margaret R. Wrensch, Beatrice Melin, Jill S. Barnholtz-Sloan, Melissa L. Bondy. Previously identified common glioma risk SNPs are associated with familial glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4173.

Differential seed germination responses to the ratio of red to far-red light in temperate and tropical species

Variation in vegetation density creates a range of red to far-red ratios of irradiance (R:FR) potentially permitting fine-scale discrimination of light conditions for seed germination. However, remarkably few studies have explored whether R:FR responses of germination vary among species that differ in distribution and life-history traits. In this study, we explored the relationships between R:FR requirements and four species characteristics: seed mass, latitudinal distribution (tropical vs. temperate), seed dormancy (dormant vs. nondormant), and plant growth form (woody vs. nonwoody). We obtained data on germination response to R:FR of 62 species from published literature and added new data for ten species from aseasonal tropical forests in Borneo. First, we analyzed whether species characteristics influenced overall light dependency of germination using phylo- genetic logistic regression. We found that seed mass had a strong negative effect on light dependency, but that the seed mass at which tropical taxa had a 50 % probability of light dependency was 40 times that of temperate taxa. For light-dependent species, we found that the threshold R:FR that stimulates 50 % of maximum germination (R:FR50) was also related to seed mass and latitudinal distribution. In agreement with an earlier study, we found that for temperate taxa, the R:FR50 was significantly negatively correlated with seed mass. In contrast, for 22 tropical taxa, we found a significant positive correlation. These oppos- ing relationships suggest contrasting selection pres- sures on germination responses of tropical taxa (mostly trees) and temperate herbaceous plants, and which are likely related to differences in seed longev- ity, seed burial rates, and reproductive output.