senegambia_genotype_data

Plasmodium falciparum isolates from Senegal and The Gambia, some DNA directly drawn and some from culture-adapted parasites; only single infections included. SNP calling was as described in (Van Tyne, et al. 2011): Parasite DNA was hybridized to a P. falciparum Affymetrix array containing 74,656 SNP markers and genotypes called using the BRLMM-P algorithm. SNPs were validated by comparing array genotypes with Sanger sequencing genotypes for 17 reference strains (Van Tyne, et al. 2011); perfect concordance was required, as was a minimum 80% call rate. Genomic positions and translations are based on the PlasmoDB v5.0 assembly and annotation

The 42-SNP barcode detects population divergence.

<p><b>(A)</b> 95% confidence intervals for F_ST values. All F_ST values reflect statistically significant population divergence (p < 10^-5). <b>(B)</b> Population pairs separate in PCA with the first two principal components.</p

The 42-SNP barcode is distributed across the genome.

<p>The location of the 42 SNPs is illustrated on the 14 chromosomes of the <i>P. vivax</i> genome. SNPs are colored by their average minor allele frequency (AMAF) among the populations tested; 17 SNPs had AMAF ≥ 0.3, 18 SNPs had 0.3 > AMAF ≥ 0.2, and 7 SNPs had 0.2 > AMAF > 0.1 (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003539#pntd.0003539.s009" target="_blank">S7 Table</a>). Putative centromere locations are indicated by the pinched location on the perimeter of each chromosome [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003539#pntd.0003539.ref016" target="_blank">16</a>].</p

Barcodes with a reduced number of SNPs lose the ability to classify samples by geographic origin.

<p>PCA analysis of the global sample set, with samples colored by collection site. <b>(A)</b> The 42-SNP barcode shows separation by continent in PCA, and the three continental clusters are circled. Samples from South America appear to show substructure, with Brazil samples dividing into two distinct clusters, one of which overlaps the single cluster of samples from French Guiana. <b>(B)</b> A 28-SNP and <b>(C)</b> a 14-SNP barcode selected for maximal population diversity were unable to distinguish populations.</p

WGA does not affect results in HRM analysis.

<p>The derivative melt graphs show the comparison of T_m profiles of a representative assay (14) tested with mixtures of monogenomic clinical samples processed with and without WGA prior to PCR. The ratios of reference (T) allele to alternate (C) allele in the mixtures were: <b>(A)</b> 1:2 and 1:4 and <b>(B)</b> 4:1 and 2:1.</p

qPCR-HRM assays quantify alleles within DNA mixtures.

<p>The derivative melt graphs show the T_m profiles of a representative assay (12) tested with mixtures of clinical samples known to contain only one allele at this assay position. The ratios of genomic DNA from samples containing reference (C) allele to alternate (T) allele in the mixtures were: <b>(A)</b> 1:10, 1:4, 1:2, 1:1 and <b>(B)</b> 10:1, 4:1, 2:1 1:1. The other 41 assays not shown were tested similarly and all performed comparably to detect mixed allelic samples.</p

Association of rs2046210 and rs12662670 with breast cancer.

<p>Results are presented overall and separately for Europeans and Asians. Pooled analyses adjusted for study only as well as adjusted for rs12662670 or rs2046210, respectively, in addition to study were performed.</p>a<p>P-value derived from the log-additive model.</p>b<p>Odds ratio per minor allele (A allele for rs2046210, G allele for rs12662670).</p>c<p>Odds ratio relative to the major allele homozygous (GT) genotype.</p

Association of rs12662670 with breast cancer in European ER

<p>−<b>*versus ER+**cases and controls.</b> *Estrogen receptor negative; **Estrogen receptor positive.</p

Association of rs2046210 with breast cancer in European ER

<p>−<b>*versus ER+*cases and controls.</b> *Estrogen receptor negative; **Estrogen receptor positive.</p