Table I.

Overview of Group 3 contributions

Contribution	Phenotype	Replicates	External information	Statistical methods	Knowledge of the simulation model
Chen [2011]	Q1, Q2	All	Predicted functions of SNPs: synonymous/nonsynonymous	Bayesian hierarchical model	Yes
Fan et al. [2011]	Q1, Q2, Affected, dichotomized Q1 and Q2	All	Predicted functions of SNPs: synonymous/nonsynonymous; VEGF pathway	Combined multivariate and collapsing, weighted sum, replication-based method	Yes
Massanet-Villa [personal communication, 2010]	Affected	1	Protein interactions	Hypergeometric distribution	No
Ngwa et al. [2011]	Q1, Q4	All	Gene sets: MSigDB, canonical pathways in IPA	Linear regression-based association test, GSEA, empirical enrichment, Fisher’s exact test	Yes
Turkmen and Lin [2011]	Q1, Q2	All	SNPs within a gene	Gene-based partial least-squares method	Yes
Wei et al. [2011]	Affected	1	Predicted functions of SNPs: synonymous/nonsynonymous, PolyPhen-2, SIFT	Variable threshold association test, normal mixture model	No
Yip et al. [2011]a	Q1	All	SNPs within a gene	Nonparametric linkage analysis, modified FBAT	Yes
Zhou [personal communication, 2010]	Q1, Q2	All	SNPs within a gene	LASSO regression with gene-specific L2 norm penalties	Yes

^aFamily-based data were used.