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Fig. 1 | Genome Medicine

Fig. 1

From: Global genetic analyses reveal strong inter-ethnic variability in the loss of activity of the organic cation transporter OCT1

Fig. 1

Schematic representation of the DNA samples and the genetic variants that were analyzed in this study. a A flowchart illustrating which analyses were performed using the enriched HGDP-CEPH panel only and which using both the enriched HGDP-CEPH panel and the 1000 Genomes panel. In the analyses that required unambiguous identification of the geographical origin of the populations (the global frequency analyses, the global loss-of-function, and the population genetic analyses) only the nine non-admixed populations of the 1000 Genomes Project were used together with the 53 populations of the enriched HGDP-CEPH panel. The highly admixed 1000 Genomes populations CLM-1 K, MXL-1 K, PRU-1 K, CEU-1 K, and ASW-1 K were omitted in these analyses. b A flowchart illustrating the process of selection of the 21 genetic variants that were analyzed in detail in this study. The 21 variants were selected from the variants identified by high-throughput sequencing and the variants previously suggested in the literature to cause loss of OCT1 function. In the context of the analysis pipeline presented in panel a, this diagram can be placed between the steps of ‘NextGen sequencing’ and ‘Conventional genotyping’. A detailed list of the non-coding, the synonymous, and the predicted non-deleterious variants is available in Additional file 5. We regarded variants as potentially deleterious if they were previously reported to cause a more than 50 % decrease in OCT1 activity for at least one substrate; or if they were predicted to be deleterious by at least five of eight software prediction packages used in this study. Details about the prediction software used and the prediction results are given in the text and in Additional files 3 and 6. The variants Gln97Lys and Gly220Val were not identified by sequencing of the enriched HGDP-CEPH panel, but were included in the detailed analyses as they were previously reported in the literature (Gln97Lys, [17]) or in the 1000 Genomes project (Gly220Val) and fulfilled the criteria for deleterious variants

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