Sex-specific gene and pathway modeling of inherited glioma risk

Ostrom, Q. T.; Coleman, W.; Huang, W.; Rubin, J. B.; Lathia, J. D.; Berens, M. E.; Speyer, G.; Liao, P.; Wrensch, M. R.; Eckel-Passow, J. E.; Armstrong, G.; Rice, T.; Wiencke, J. K.; McCoy, L. S.; Hansen, H. M.; Amos, C. I.; Bernstein, J. L.; Claus, E. B.; Il'yasova, D.; Johansen, C.; Lachance, D. H.; Lai, R. K.; Merrell, R. T.; Olson, S. H.; Sadetzki, S.; Schildkraut, J. M.; Shete, S.; Houlston, R. S.; Jenkins, R. B.; Andersson, U.; Rajaraman, P.; Chanock, S. J.; Linet, M. S.; Wang, Z.; Yeager, M.; Melin, B.; Bondy, M. L.; Barnholtz-Sloan, J. S.

doi:10.1101/235408

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bioRxiv · 10.1101/235408

Sex-specific gene and pathway modeling of inherited glioma risk

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Abstract

BackgroundGenome-wide association studies (GWAS) have identified 25 risk variants for glioma, which explain ~30% of heritable risk. Most glioma histologies occur with significantly higher incidence in males. A sex-stratified analysis ide7ntified sex-specific glioma risk variants, and further analyses using gene- and pathway-based approaches may further elucidate risk variation by sex.\n\nMethodsResults from the Glioma International Case-Control Study were used as a testing set, and results from three GWAS were combined via meta-analysis and used as a validation set. Using summary statistics for autosomal SNPs found to be nominally significant (p<0.01) in a previous meta-analysis and X chromosome SNPs with nominally significant association (p<0.01), three algorithms (Pascal, BimBam, and GATES) were used to generate gene-scores, and Pascal was used to generate pathway scores. Results were considered significant when p<3.3x10-6 in [2/3] algorithms.\n\nResults25 genes within five regions and 19 genes within six regions reached the set significance threshold in at least 2/3 algorithms in males and females, respectively. EGFR and RTEL1-TNFRSF6B were significantly associated with all glioma and glioblastoma in males only, and a female-specific association in TERT, all of which remained nominally significant after conditioning on known risk loci. There were nominal associations with the Telomeres, Telomerase, Cellular Aging, and Immortality pathway in both males and females.\n\nConclusionsThese results suggest that there may be biologically relevant significant differences by sex in genetic risk for glioma. Additional gene- and pathway-based analyses may further elucidate the biological processes through which this risk is conferred.

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Ostrom, Q. T., Coleman, W., Huang, W., Rubin, J. B., Lathia, J. D., Berens, M. E., Speyer, G., Liao, P., Wrensch, M. R., Eckel-Passow, J. E., Armstrong, G., Rice, T., Wiencke, J. K., McCoy, L. S., Hansen, H. M., Amos, C. I., Bernstein, J. L., Claus, E. B., Il'yasova, D., Johansen, C., Lachance, D. H., Lai, R. K., Merrell, R. T., Olson, S. H., Sadetzki, S., Schildkraut, J. M., Shete, S., Houlston, R. S., Jenkins, R. B., Andersson, U., Rajaraman, P., Chanock, S. J., Linet, M. S., Wang, Z., Yeager, M., Melin, B., Bondy, M. L., Barnholtz-Sloan, J. S.. 2017-12-18. Sex-specific gene and pathway modeling of inherited glioma risk. https://doi.org/10.1101/235408

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