The MAP (and SBP) Amerindian admixture mapping region on chromosome 6.

<p>The left panel provides the admixture mapping results as two lines, with the blue line that crosses the genome-wide significance threshold (horizontal grey dashed line) representing results from the primary analysis and the other, green line, representing the results from the conditional analysis, and the association results in the same region as circles. Lines and points are given as -log(<i>p</i>-value, 10) against genomic positions. Filled triangles correspond to the SNPs used in the conditional analysis. The right panel provides the ancestry-specific effect allele frequencies (EAF) for each of the SNPs used in the conditional analysis, as estimated by ASAFE applied on the HCHS/SOL data set [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188400#pone.0188400.ref030" target="_blank">30</a>].</p

Top admixture association results in significant association regions.

<p>The lead LAI provides the coordinates of the most significant local ancestry interval in the region. Ancestry freq provides the proportion of intervals inferred as inherited from the tested ancestry across the 12,116 individuals (24,232 chromosome). Effect size, SE and <i>p</i>-values were estimated based on the linear model for the effect of the local ancestry count on the trait.</p

Additional file 1 of Ancestry-driven metabolite variation provides insights into disease states in admixed populations

Additional file 1: Table S1. Descriptive statistics of 3,887 HCHS / SOL participants at visit 1. Table S2. Significant metabolites from admixture mapping. Table S3. All-ancestries and ancestry-specific admixture mapping results. Table S4. Regions whose significance was explained by adding all COJO SNVs to model

The MAP Amerindian admixture mapping region on chromosome 11.

<p>The left provides the admixture mapping results as two lines, with the blue line that crosses the genome-wide significance threshold (horizontal grey dashed line) representing results from the primary analysis and the other, green line, representing the results from the conditional analysis, and the association results in the same region as circles. Lines and points are given as -log(<i>p</i>-value, 10) against genomic positions. Filled triangles correspond to the SNPs used in the conditional analysis. The right panel provides the ancestry-specific effect allele frequencies (EAF) for each of the SNPs used in the conditional analysis, as estimated by ASAFE applied on the HCHS/SOL data set [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188400#pone.0188400.ref030" target="_blank">30</a>].</p

Selected variants in top admixture mapping association regions, and their association testing results in stratified BP GWAS (stratified by genetic analysis groups and followed by a step of meta-analysis across the groups).

<p>All admixture mapping hits here were in the analysis of Amerindian ancestry versus other ancestries. We provide the effect estimate (Effect) from both the admixture mapping (Ancestry effect), and association mapping, the frequency of the ancestry (Ancestry freq), and the frequencies of the variant in the Mexican (high Amerindian ancestry) and Cuban (low Amerindian ancestry) genetic analysis groups. Genomic positions are in human build 37. A1 is the effect (tested) allele, A2 is the other allele. Type refers to imputation: ‘g’ is genotyped, ‘i’ imputed. Info is a measure of imputation quality. ^<i>a</i> For SNP rs118163160, the association analysis results when restricted to the Mainland groups were effect = −2.85, SE = 0.69, <i>p</i>-value = 3.84E-05. <i>P</i>-value for heterogeneity of the effect across the genetic analysis groups was 0.001.</p

The PP Amerindian admixture mapping region on chromosome 17.

<p>The left panel provides the admixture mapping results as two lines, with the blue line that crosses the genome-wide significance threshold (horizontal grey dashed line) representing results from the primary analysis and the other, green line, representing the results from the conditional analysis, and the association results in the same region as circles. Lines and points are given as -log(<i>p</i>-value, 10) against genomic positions. Filled triangles correspond to the SNPs used in the conditional analysis. The right panel provides the ancestry-specific effect allele frequencies (EAF) for each of the SNPs used in the conditional analysis, as estimated by ASAFE applied on the HCHS/SOL data set [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188400#pone.0188400.ref030" target="_blank">30</a>].</p

Additional file 2 of Ancestry-driven metabolite variation provides insights into disease states in admixed populations

Additional file 2: Fig. S1. Global ancestry proportions of African, European, and Native American ancestries for participants based on their country of origin: Mainland (Mexico, Central and South America) or Caribbean (Cuba, Dominican Republic, and Puerto Rico). Note that participants from Mainland had a higher proportion of Native American ancestry, while those from Caribbean had a higher proportion of African ancestry. Fig. S2. Volcano plots showing relationship between the direction of association and driving ancestry in the three chromosomes with the largest numbers of associated metabolites. The driving ancestry was the ancestry with the smallest p-value in ancestry-specific testing. In chromosome 2, most of the associations with African ancestry were positive. In chromosome 11, most of the associations with Native American ancestry were negative

Additional file 3 of Ancestry-driven metabolite variation provides insights into disease states in admixed populations

Additional file 3: Extended Data Table S1. Significant independent local ancestry regions from admixture mapping. Extended Data Table S2. Genetic variants that do not explain association between local ancestry regions and metabolites. Extended Data Table S3. Replication of significant independent local ancestry regions from admixture mapping for 64 metabolites avaialble in the replication dataset

Results from replication testing of SNPs in significant admixture association regions in 2,347 Pima Indians.

<p>Genomic positions are in human build 37. A1 is the effect (tested) allele, A2 is the other allele. For each of HCHS/SOL and the replication study, we provide allele frequencies, estimated effect sizes, and <i>p</i>-values. For the replication study, <i>p</i>-values are one-sided as determined by the direction of association observed in the HCHS/SOL. For the HCHS/SOL frequencies we report “Amer freq”: the estimated allele frequency in the Amerindian ancestry in the HCHS/SOL, as estimated using ASAFE [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188400#pone.0188400.ref030" target="_blank">30</a>].</p

Proportion of individuals self-reporting as being “definitely a morning person”, average L5 timing, and average of sleep-midpoint across all nights for each genotype group of variants previously reported to be causal for familial advanced sleep phase in the UK Biobank (UKB), Finnish and MESA studies.

Accelerometer-based estimates of sleep timing unavailable in the Finnish studies. Self-reported “morningness” and accelerometer estimates of L5-timing unavailable in MESA.</p