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Table 2 Contributions toward phenotype imputation and empirical kinship application from the GWAS group

From: Methods and results from the genome-wide association group at GAW20

Contribution Genotypes Phenotypes Evaluation Quality Control
Chen et al. [11] Restricted simulated SNP genotypes.
1. Null scenario: 19,763 SNPs on chromosomes 21 and 22
2. Alternative scenario: 5 known causal SNPs (rs9661059, rs736004, rs1012116, rs10828412 and rs4399565)
Simulated TG levels
(a) Average difference between pretreatment (visits 1 and 2) and posttreatment (visits 3 and 4) or (b) single difference between visits 1 and 3 of log-transformed TG levels
1. Type I error rate evaluation in “null scenario”
2. Power evaluation in “alternative scenario”
No quality control (QC) conducted on restricted simulated data
Blackburn et al. [12] Genome-wide (autosome) SNP data from 822 subjects in 173 pedigrees TG and HDL-C levels were averaged for pre-treatment (visits 1 and 2) and post-treatment (visits 3 and 4) and regressed on age, sex, their interactions (age × sex, age2, age2 × sex), study center, smoking, and principal components 1–4; resulting residuals were inverse normalized Under 3 different kinship models:
1. Heritability analyses
2. Single variant association testing
Exclusion of 6 individuals with unexpected relationships
Variants were uplifted to hg19 mapping coordinates, excluding 135 conversion failures
Porto et al. [14] Genome-wide (autosome) SNP data from 822 subjects in 173 pedigrees Averaged TG levels of pre- (visits 1 and 2) and post-treatment (visits 3 and 4) Genomic best linear unbiased prediction (G-BLUP) under 3 different kinship models Exclusion of 6 individuals with unexpected relationships; variants were uplifted to hg19 mapping coordinates, excluding 135 conversion failures
Peralta et al. [13] Genome-wide (autosome) SNP data from 822 subjects in 173 pedigrees Averaged and log-transformed TG levels pre-treatment (visits 1 and 2) and post-treatment and corresponding empirical genetic values (EGVs) from Porto et al. [14]
Simulated traits with zero mean, unit variance and a 35% heritability, but not linked to any real loci
Multipoint variance component linkage analyses under the pedigree-based kinship model Exclusion of 2 individuals with unexpected relationships and 1 monozygotic twin to guard against the artificial inflation of heritability estimates.
Variants were uplifted to hg19 mapping coordinates, excluding 135 conversion failures; LD based pruning of r2 ≥ 0.9 and exclusion of variants of minor allele count (MAC) > 5 left 375,632 variants for analysis
  1. HDL-C high-density lipoprotein cholesterol, LD linkage disequilibrium, SNP single-nucleotide polymorphism, TG triglyceride
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