Top SNPs from the Raine cohort GWAS that were genotyped in our GWAS of COME/ROM.

<p>We report our OR and allele frequency using the Risk Allele corresponding to the Risk Allele listed in the Raine cohort GWAS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104212#pone.0104212-Rye1" target="_blank">[9]</a>.</p><p>*Indicates SNP is intergenic and therefore reports the nearest gene.</p>∧<p>Indicates the SNP was a top genotyped SNP from a subset of Raine study participants with full covariate data.</p

Power was computed using TDT Power Calculator [15] varying SNP minor allele frequency (MAF) and genetic relative risk (GRR).

<p>Power was computed using TDT Power Calculator <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104212#pone.0104212-Chen1" target="_blank">[15]</a> varying SNP minor allele frequency (MAF) and genetic relative risk (GRR).</p

Scatter plots of –log₁₀(p-value) from 550K GWAS and GWAS using incorporated genotype data.

<p>Scatter plots of –log₁₀(p-value) from 550K GWAS and GWAS using incorporated genotype data.</p

Sample characteristics of Alzheimer disease, fibrinogen, HDL and uric acid data in the genotyped and imputed sample.

<p>For continuous variables, mean value and standard deviation (in parenthesis) are presented, while for binary variables, the number of cases and its proportion (in parenthesis) are presented.</p

Number of genome-wide significant SNPs (p-value <1.25E-7) with improved statistical significance (smaller p-value) from GWAS of Alzheimer disease, fibrinogen, HDL and uric acid using incorporated genotype data (new GWAS).

<p>Number of genome-wide significant SNPs (p-value <1.25E-7) with improved statistical significance (smaller p-value) from GWAS of Alzheimer disease, fibrinogen, HDL and uric acid using incorporated genotype data (new GWAS).</p

Scatter plot of MAF in well-genotyped sample and filtered (person_specific imputation certainty greater than 50%) imputed sample.

<p>Scatter plot of MAF in well-genotyped sample and filtered (person_specific imputation certainty greater than 50%) imputed sample.</p

Mean imputation certainty of the top SNPs in the entire 3121 imputed sample and in the person-specific certainty >0.5, SNP-specific certainty >0.6 and phenotyped sample.

†<p><b><i>N</i></b>: the number of phenotyped and imputed individuals with person-specific certainty >0.5 and SNP-specific certainty >0.6.</p

Results of top SNPs (p-value <1.25E-7) from GWAS of Alzheimer disease, fibrinogen, HDL and uric acid using 550K genotype data and incorporated genotype data.

<p>Results of top SNPs (p-value <1.25E-7) from GWAS of Alzheimer disease, fibrinogen, HDL and uric acid using 550K genotype data and incorporated genotype data.</p

Example for pedigree splitting and trimming.

<p>Example for pedigree splitting and trimming.</p

Haplotype risk analysis of WTCCC type 1 diabetes data.

<p>We assessed the risk of haplotypes spanning <i>HLA-DRB1</i>, <i>HLA-DQA1</i> and <i>HLA-DQB1</i>, and compared these to the published risk estimates from an independent study <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064683#pone.0064683-Cucca1" target="_blank">[20]</a>. The published odds ratios were based on transmission/non-transmission of alleles from familial data, while our odds ratios were estimated from case/control data. We used the same classification scheme by dividing haplotypes into three risk groups. The odds ratios are computed with respect to the DRB1*01-DQA1*0101-DQB1*0501 haplotype.</p