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Genomic profiling of iPSC lines from African Somatic and Stem Cell Bank. A, Workflow. B–I, Genetic analyses of iPSC. B, PCA of common genetic variants measured in unique iPSC lines (gray, cohort) compared to 1000 Genomes reference: AFR, AMR, EAS, EUR, SAS. C, Frequency of APOE genotypes among iPSC lines. D–I, PRS. D–E, Distribution of PRS represented using reference (salmon, REF) and iPSC samples (cyan, TRG). G–H, Distribution of PRS represented based on Nigerian ethnic group. D, G, PRS for AD including the APOE gene locus. E, H, PRS for AD excluding the APOE gene locus. F, I, PRS for PD. J, PCA of transcriptomic data generated from iPSCs (500 most variable gene transcripts). K, XIST, expressed on the inactivated X‐chromosome, in iPSC lines. Graphs represent CPM mean ± SEM. ****, p < 0.0001. Blue, female. Red, male. AD, Alzheimer's disease; AFR, Africans; AMR, admixed Americans; APOE , apolipoprotein E; CPM, counts per million; EAS, East Asians; EUR, Europeans; <t>GWAS,</t> <t>genome‐wide</t> <t>association</t> <t>study;</t> iPSC, induced pluripotent stem cell; PCA, principal component analysis; PD, Parkinson's disease; PRS, polygenic risk score; REF, reference; SAS, South Asian; SEM, standard error of the mean.
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Genomic profiling of iPSC lines from African Somatic and Stem Cell Bank. A, Workflow. B–I, Genetic analyses of iPSC. B, PCA of common genetic variants measured in unique iPSC lines (gray, cohort) compared to 1000 Genomes reference: AFR, AMR, EAS, EUR, SAS. C, Frequency of APOE genotypes among iPSC lines. D–I, PRS. D–E, Distribution of PRS represented using reference (salmon, REF) and iPSC samples (cyan, TRG). G–H, Distribution of PRS represented based on Nigerian ethnic group. D, G, PRS for AD including the APOE gene locus. E, H, PRS for AD excluding the APOE gene locus. F, I, PRS for PD. J, PCA of transcriptomic data generated from iPSCs (500 most variable gene transcripts). K, XIST, expressed on the inactivated X‐chromosome, in iPSC lines. Graphs represent CPM mean ± SEM. ****, p < 0.0001. Blue, female. Red, male. AD, Alzheimer's disease; AFR, Africans; AMR, admixed Americans; APOE , apolipoprotein E; CPM, counts per million; EAS, East Asians; EUR, Europeans; <t>GWAS,</t> <t>genome‐wide</t> <t>association</t> <t>study;</t> iPSC, induced pluripotent stem cell; PCA, principal component analysis; PD, Parkinson's disease; PRS, polygenic risk score; REF, reference; SAS, South Asian; SEM, standard error of the mean.
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Genomic profiling of iPSC lines from African Somatic and Stem Cell Bank. A, Workflow. B–I, Genetic analyses of iPSC. B, PCA of common genetic variants measured in unique iPSC lines (gray, cohort) compared to 1000 Genomes reference: AFR, AMR, EAS, EUR, SAS. C, Frequency of APOE genotypes among iPSC lines. D–I, PRS. D–E, Distribution of PRS represented using reference (salmon, REF) and iPSC samples (cyan, TRG). G–H, Distribution of PRS represented based on Nigerian ethnic group. D, G, PRS for AD including the APOE gene locus. E, H, PRS for AD excluding the APOE gene locus. F, I, PRS for PD. J, PCA of transcriptomic data generated from iPSCs (500 most variable gene transcripts). K, XIST, expressed on the inactivated X‐chromosome, in iPSC lines. Graphs represent CPM mean ± SEM. ****, p < 0.0001. Blue, female. Red, male. AD, Alzheimer's disease; AFR, Africans; AMR, admixed Americans; APOE , apolipoprotein E; CPM, counts per million; EAS, East Asians; EUR, Europeans; GWAS, genome‐wide association study; iPSC, induced pluripotent stem cell; PCA, principal component analysis; PD, Parkinson's disease; PRS, polygenic risk score; REF, reference; SAS, South Asian; SEM, standard error of the mean.

Journal: Alzheimer's & Dementia

Article Title: Somatic and Stem Cell Bank to study the contribution of African ancestry to dementia: African iPSC Initiative

doi: 10.1002/alz.70145

Figure Lengend Snippet: Genomic profiling of iPSC lines from African Somatic and Stem Cell Bank. A, Workflow. B–I, Genetic analyses of iPSC. B, PCA of common genetic variants measured in unique iPSC lines (gray, cohort) compared to 1000 Genomes reference: AFR, AMR, EAS, EUR, SAS. C, Frequency of APOE genotypes among iPSC lines. D–I, PRS. D–E, Distribution of PRS represented using reference (salmon, REF) and iPSC samples (cyan, TRG). G–H, Distribution of PRS represented based on Nigerian ethnic group. D, G, PRS for AD including the APOE gene locus. E, H, PRS for AD excluding the APOE gene locus. F, I, PRS for PD. J, PCA of transcriptomic data generated from iPSCs (500 most variable gene transcripts). K, XIST, expressed on the inactivated X‐chromosome, in iPSC lines. Graphs represent CPM mean ± SEM. ****, p < 0.0001. Blue, female. Red, male. AD, Alzheimer's disease; AFR, Africans; AMR, admixed Americans; APOE , apolipoprotein E; CPM, counts per million; EAS, East Asians; EUR, Europeans; GWAS, genome‐wide association study; iPSC, induced pluripotent stem cell; PCA, principal component analysis; PD, Parkinson's disease; PRS, polygenic risk score; REF, reference; SAS, South Asian; SEM, standard error of the mean.

Article Snippet: Samples were analyzed by an Infinium Global Screening Array‐24 v.30 GWAS Chip.

Techniques: Generated, GWAS