Summary statistics for Regional Heritability Mapping

Summary statistics for Regional Heritability Mapping method for blood lipid traits (high-density lipoprotein (HDL), low-density lipoprotein (LDL), plasma concentrations of total cholesterol (TC) and triglycerides (TG) in R Data file

Summary statistics for Single SNP GWAS

Summary statistics for Single SNP GWAS for for blood lipid traits (high-density lipoprotein (HDL), low-density lipoprotein (LDL), plasma concentrations of total cholesterol (TC) and triglycerides (TG) in R Data file

Power of GWAS and Regional Genomic Relationship Mapping in simulated data.

<p>Data were simulated based on real data by random selection of 1, 5 or 10 genotyped SNPs at either high or low MAF from a region of 50 SNPs. In each case the total simulated effects of the SNPs in a region contributed 2.5% to the heritability. The background trait heritability was either moderate at <i>circa</i> 30% as for serum uric acid concentration or high at <i>circa</i> 80% as for height. Power is the number of significant tests at the Bonferroni corrected threshold for either a GWAS of 275 k markers or a regional heritability analysis <i>circa</i> 11000 overlapping 50 SNP windows. Lines of the same colour represent results from the same simulated data produced by regional heritability analysis (solid) or by single marker analysis (dashed).</p

Regional heritability using single and multiple regional relationship matrices (100 SNPs) for Height.

<p>(LRT from all windows were significant at suggestive level).</p>1<p>Likelihood ratio test for regional heritability >0;</p>2<p>Estimated regional heritability in model with that single region and genomic effects;</p>3<p>Minimum heritability for that region from models with sets of 5 regional effects and genomic effect;</p>4<p>Maximum heritability for that region from models with sets of 5 regional effects and genomic effect;</p>5<p>Average heritability for that region over models with sets of 5 regional effects and genomic effect.</p

Comparison of single marker analysis and regional heritability analyses of serum uric acid concentration in a population from Orkney.

<p>-log P values are plotted against position in the genome. Points represent individual markers and circles results from regional heritability analysis with 100 marker windows. Genome-wide significance thresholds are represented by dashed lines (red for single marker analysis, blue for regional heritability analysis). Alternating shades represent the separate chromosomes. Results surpassing the genome-wide significance threshold are solid red for single marker analysis and solid blue for regional heritability analysis.</p

Results from genome-wide analyses of two traits.

<p>Plots show the likelihood ratio test (LRT) and regional, genomic and total heritabilities across the genome from analyses of data from Croatian and Italian populations: a) serum uric acid concentration and b) height. Vertical axis is the LRT and heritability (%) and horizontal axis is window number across the genome. RG h2, WG h2 and total h2 are regional heritability, residual whole genome heritability and total (sum of genomic and regional) heritability, respectively.</p

Q-Q plot of distribution of observed against expected –log₁₀ P values from permuted data.

<p>Observed values are calculated assuming the LRT is distributed as 1/2χ²(0)+1/2χ²(1). The dotted line shows the slope of unity.</p

Comparisons of regional heritability and GWAS results for two most significant windows for uric acid concentration.

<p>Comparisons shown on –log₁₀ P basis by conversion of likelihood ratio test (LRT) statistic assuming is distribution is a mixture of half χ₁² and half zero. Lines indicate results for regional heritability for three window sizes (100 SNP = green; 20 SNP = red; 10 SNP = blue). Crosses show results for individual SNPs in GWAS with grey line showing moving average of 10 adjacent SNPs. <b>a</b>) Results for chromosome 4, window 21 (SLC2A9 region). Additional dashed green line is result for 100 SNP window with relationships estimated omitting 14 most significant individual SNPs (in red). <b>b</b>) Results for chromosome 5, window 277. Additional dashed green line is result for 100 SNP window with relationships estimated omitting 3 most significant individual SNPs (indicated by red crosses).</p

Regional heritabilities for uric acid concentration for three most significant windows.

<p>Heritabilities are estimated in a model with both regional and genomic genetic effects using all 100 SNPs in the window to derive regional relationships and fitting 0, 1 or 3 SNPs with the highest –Log₁₀ P value from the GWAS in that window as covariates in the analysis.</p

Additional file 13: of Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants

GS_HRC_imputed_Waist_Hip_Ratio_significant_SNPS. (XLSX 8 kb