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

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

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Manhattan plot of genome-wide associations with PQ activities from 35 parasite isolates.

<p>Horizontal axis is genome position, and vertical axis is –log₁₀(p-value). Chromosomes alternate yellow and red, starting from chromosome 1 on the left. Yellow spire on chromosome 7 is in the region of <i>pfcrt</i>.</p

Haplotype plot for <i>pfcrt</i> (MAL7P1.27), sorted by CQ and PQ activities.

<p>Left panel is sorted top to bottom by increasing CQ IC₅₀, and the right panel is sorted by PQ IC₅₀. Each row represents a sample, and each column a potential SNP. Drug activity is shown as increasing green intensity in the far left column of each plot. Blue cells indicate positions matching the reference genome, and red the alternate allele. Mixed infections are represented by blending of red and blue, proportional to the within-sample allele frequencies. White cells indicate missing data. Nonsynonymous SNPs are labeled with the amino acid substitution along the bottom, and with a dot if synonymous.</p

SNPs achieving significance (q-value<0.05) after correcting p-values for multiple hypothesis tests.

1<p>Amino Acid Change. Synonymous substitutions indicated with a dot. Allele associated with drug tolerance in bold.</p>2<p>Meets genome-wide significance without principal components in model (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096486#s3" target="_blank">Results</a>).</p

Manhattan plot of genome-wide associations with CQ activities from 35 parasite isolates.

<p>Horizontal axis is genome position, and vertical axis is –log₁₀(p-value). Chromosomes alternate yellow and red, starting from chromosome 1 on the left. Yellow spire on chromosome 7 is in the region of <i>pfcrt</i>.</p