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Table 1 Contribution of the “Genetics of Gene Expression” subgroup

From: Gene expression in large pedigrees: analytic approaches

    Real data    
Paper Sample size Relatedness correction Phenotype Genotype Simulated data Analytic approach Results
Cantor [21] 653 R SOLAR-MGA and FaST-LMM for expression and simulated traits TIMM10 and LR8 expression probes 6 MAP4 SNPs 47 and 180 in TIMM10, LR8 200 replicates of SBP. DBP and Q1 Type 1 error and power estimated. Single SNPs and Sequential conditioning with SOLAR-MGA and FaST-LMM Software results similar. Multiple independent SNPs associated with eQTL, supporting complexity
Howey [23] 954 R GEMMA for expression, FaST-LMM for BP 11 expression probes, SBP DBP, HTN, PP and MAP 44 candidate HTN SNPs 14 SNP-SNP inter-actions Not used FaST-LMM for HTN related phenotypes, GEMMA for SNP–SNP interactions. Linear regression using PLINK SNPs not significant. 2 SNP–SNP interactions with expression
1946 U
Peralta [22] 959 R variance components within SOLAR 20527 gene expression values 10552 potential allele specific DNase hypersensitivity sites Simulated 10,000 heritable quantitative phenotypes Covariance kernels (weighted and nonweighted for DHS likelihood) using 10,552 SNPs, as predictors of gene expression 10 transcripts associated with weighted DHS kernel, 8 associated with nonweighted kernel
  1. DBP diastolic blood pressure; DHS DNase hypersensitivity site; eQTL expression quantitative trait locus; HTN hypertension; MAP mean arterial pressure; PP pulse pressure; R related individuals; SBP systolic blood pressure; SNP single nucleotide polymorphism; SNV single nucleotide variant; U unrelated individuals