From: Gene expression in large pedigrees: analytic approaches
Real data | |||||||
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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 |