Figure 1
From: Across-cohort QC analyses of GWAS summary statistics from complex traits
Recovery of cohort-level genetic background and inference of their geographic locations for GIANT BMI Metabochip cohorts and GIANT GWAS height cohorts using the Fst-derived genetic distance measure. (a) Genetic distance spectrum for all Metabochip cohorts to CEU, CHB, and YRI. The origins of the cohorts are denoted on the horizontal axis. (b) Projection for the Metabochip cohorts into FPC space defined by YRI, CHB, and CEU reference populations. The x and y axis represent relative distances derived from the genetic distance spectrum. Three dashed lines, blue for CEU, green for CHB, and red for YRI, partitioned the whole FPC space to three genealogical subspaces. (c) The genetic distance spectrum for the Metabochip European cohorts to CEU – northwest Europeans, FIN – northeast European, and TSI – southern Europeans. The nationality of the cohorts is denoted on the horizontal axis. (d) The projection for the Metabochip European cohorts to the FPC space defined by CEU, FIN, and TSI reference populations. The whole space is further partitioned into three subspaces, CEU-TSI genealogical subspace (red and blue dashed lines), FIN-TSI genealogical subspace (green-blue dashed lines), and CEU-FIN genealogical subspace (red-green dashed lines), respectively. (e) Each cohort has three Fst values by comparing with CEU, FIN, and TSI reference samples. The height of each bar represents its relative genetic distance to these three reference populations. The nationalities of the cohorts are denoted along the horizontal axis. The grey triangles along the x axis indicate MIGEN cohorts. (f) Given the three Fst values, the location of each cohort can be mapped. The whole space was partitioned into three subspaces, CEU-TSI genealogical subspace (red and blue dashed lines), FIN-TSI genealogical subspace (green and blue dashed lines), and CEU-FIN genealogical subspace (red and green dashed lines). DGI (in the blue box) had samples from the Botnia study. Across the MIGEN cohorts (denoted as red triangles in the red box), the same allele frequencies (likely calculated from a South European cohort) were presented for each cohort. The open circles represent the mean of inferred geographic locations for the cohorts from the same country. Cohort/country codes: AF, African; AU, Australia; CA, Canada; CH, Switzerland; DE, Germany; DK, Denmark; EE, Estonia; ES, Iberian Population in Spain in 1KG; EU, European Nations; FI, Finland; FIN, Fins in 1000 Genomes Project (1KG); FR, France; GBR, British in 1KG; GIB, Gujarati Indian in 1KG; GR, Greece; Hawaii, Hawaii in USA; IBS, Iberian Population in Spain in 1KG; IT, Italy; IS, Iceland; JM, Jamaica; JPT, Japanese in 1KG; LWK, Luhya in 1KG; NL, Netherlands; NO, Norway; PH, the Philippines; PK, Pakistan; SC, Seychelles; SCT, Scotland; SE, Sweden; TSI, Tuscany in 1KG; UK, United Kingdom; US, United States of America.
