Gene-trait association testing

Descriptions and Benchmarks for RNAseq tools

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Gene-trait association testing

  • Summary-data-based Mendelian Randomization (SMR)(Zhu, Z., Zhang, F., Hu, H., Bakshi, A., Robinson, M. R., Powell, J. E., et al. (2016). Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nature Genetics, 48(5), 481–487)
  • Transcriptome-Wide Association Study (TWAS) (Gusev, A., Ko, A., Shi, H., Bhatia, G., Chung, W., Penninx, B. W. J. H., et al. (2016). Integrative approaches for large-scale transcriptome-wide association studies. Nature Genetics, 48(3), 245–252)
  • PrediXcan (Gamazon, E. R., Wheeler, H. E., Shah, K. P., Mozaffari, S. V., Aquino-Michaels, K., Carroll, R. J., et al. (2015). A gene-based association method for mapping traits using reference transcriptome data. Nature Genetics, 47(9), 1091–1098)
  • Sherlock (He, X., Fuller, C. K., Song, Y., Meng, Q., Bin Zhang, Yang, X., & Li, H. (2013). Sherlock: Detecting Gene-Disease Associations by Matching Patterns of Expression QTL and GWAS. American Journal of Human Genetics, 92(5), 667–680)
  • enloc (Wen, X., Pique-Regi, R., & Luca, F. (2017). Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization. PLoS Genetics, 13(3), e1006646–25)
  • coloc (Giambartolomei, C., Vukcevic, D., Schadt, E. E., Franke, L., Hingorani, A. D., Wallace, C., & Plagnol, V. (2014). Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics. PLoS Genetics, 10(5), e1004383–15)
  • QTLMatch (Plagnol, V., Smyth, D. J., Todd, J. A., & Clayton, D. G. (2008). Statistical independence of the colocalized association signals for type 1 diabetes and RPS26 gene expression on chromosome 12q13. Biostatistics, 10(2), 327–334)

  • eCAVIAR (Hormozdiari, F., van de Bunt, M., Segrè, A. V., Li, X., Joo, J. W. J., Bilow, M., et al. (2016). Colocalization of GWAS and eQTL Signals Detects Target Genes. American Journal of Human Genetics, 99(6), 1245–1260)

  • See here and here for discussion of the limits of these approaches for inference of causality