Additional file 3: of A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

Table S2. GWAS Catalog detailed descriptions with ancestry category assignments. (XLSX 77 kb

Additional file 2: of A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

Table S1. GWAS Catalog countries of recruitment for which no ancestry information was provided. (XLSX 77 kb

Additional file 1: of A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

Figure S1. Detailed sample description displayed in the internal GWAS Catalog curation interface. Figure S2. a Structured ancestry and recruitment information displayed in the internal GWAS Catalog curation interface. b GWAS Catalog ancestry and recruitment data entry page of internal curation interface. Supplementary Box 1. Genomic methods of ancestry determination. Figure S3. Distribution of studies by ancestry category focused on Catalog traits with highest number of studies in the Catalog. Figure S4. Methods of ancestry ascertainment used in a subset of publications included in the GWAS Catalog. Supplementary References. (DOCX 893 kb

Additional file 5: of A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

Table S4. HapMap Project and 1000 Genomes Project populations with assigned ancestry category. (XLSX 27 kb

Additional file 4: of A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

Table S3. Specific examples to illustrate the application of the framework to the GWAS Catalog. (XLSX 70 kb

Association between cancer GWAS SNPs and melanoma.

<p>2a) SNPs showing a statistically significant association with melanoma at a Bonferroni-corrected threshold of 0.05/181 = 2.8x10^-4.</p><p>2b) SNPs showing a marginal association with melanoma at p<0.05.</p><p>Association between cancer GWAS SNPs and melanoma.</p

List of Prioritized Genes by Trait.

<p>List of Prioritized Genes by Trait.</p

Association between SNPs in the <i>TPCN2/MYEOV</i> region and melanoma.

<p>3a) Association between SNP rs12418451 melanoma, both overall and stratified by sex.</p><p>3b) Four additional SNPs within the same locus as rs12418451, shown for comparison (r² with rs12418451 < 0.13 in 1000G CEU).</p><p>Association between SNPs in the <i>TPCN2/MYEOV</i> region and melanoma.</p

Enhanced Imputation Accuracy with Custom Content Addition.

<p>Enhanced Imputation Accuracy with Custom Content Addition.</p

Enrichment of rarer variation in custom content.

<p>Comparison of minor allele frequency distribution between the MEGA GWAS backbone and the custom content stratified by race. Allele frequencies were calculated in PAGE II study populations.</p