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Fig. 1 | Infectious Agents and Cancer

Fig. 1

From: HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study

Fig. 1

QC Array super-population assignments. A Super-population clusters of select 1000 Genomes reference samples and ICC samples with QC Array call rates > 85%, projected onto the first three principal components (PC1–3). 1000 Genomes individuals from AFR populations and QC Array samples from patients expected to have African ancestry were most clearly distinguished by the first two principal components. 1000 Genomes individuals from current EUR and EAS populations were separated along the third and, to a lesser extent, second principal components. B Similar to (A) but with the third principal component plotted against the fourth (PC4), demonstrating that AMR individuals become more distinct along the fourth principal component. No QC Array samples were predicted to have SAS ancestry. These principal components were not the primary method for assigning ethnicities but provide an effective way to visualize variation among samples. C Frequencies of reported race per archive type, as well as supervised AMR/EUR predictions for archived DNA and frozen tissues from reported “White/Caucasian” individuals. Counts are among HPV + tumor samples, counted once per patient per archive type. If race was not reported (or reported to be “Other”) or QC Array data were not available, the corresponding samples were not included in this plot

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