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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