Validation array coverage.

<p>Validation array coverage.</p

Comparison of hematopoietic potential of iPSCs to mouse ESCs.

<p>Fractions of Lin⁻ cells (A), KLS cells (B), Kit+Lin-Sca-1- Progenitors (C), GMPs (D), CMPs (E), and MEPs (F) from iPSCs relative to mouse ESCs after 7 days of OP9 coculture (unsorted).</p

Sequencing of iPSC clones.

<p><b>A.</b> Number of variants identified per iPSC clone. <b>B.</b> Variant allele frequencies of all validated mutations for each clone. Samples are ranked by the number of variants in decreasing order. No mutations were identified in Ax2-11, thus it is not listed in panel B.</p

Generation of iPSC clones from a single mouse C57BL/6 male mouse.

<p><b>A.</b> Schematic of experimental approach (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120585#sec002" target="_blank">Material and Methods</a> for full protocol). <b>B.</b> Representative bright-field images (left) and alkaline-phosphastase stains (right) of B6/BLU ESCs (top) and a representative iPSC (bottom, Ax1-10). All images at 100x magnification. <b>C.</b> Images from the teratoma derived from Ax1-10 demonstrating ectoderm (neural tissue), mesoderm (cartilage) and endoderm (ciliated respiratory epithelium).</p

Hematopoietic differentiation potential of the 24 iPSC clones.

<p>100,000 cells from OP9 cocultured mESCs (B6/BLU) or iPSCs were plated in methylcellulose media containing hematopoietic cytokines (SCF, IL-3, IL-6, and Epo). <b>A.</b> CFUs were counted after 7 additional days of culture. The relative number of CFUs per 100,000 cells plated from Day7 iPSC-derived progenitors vs. Day7 ESC (B6/BLU)-derived progenitors are shown. iPSC clones are ranked from the highest to the lowest average of two independent experiments. Error bars represent the means +/− one standard deviation. <b>B.</b> Morphology of day 7 OP9 cocultured ESC-derived cells after 7–8 days of additional culture in MethoCult media containing hematopoietic cytokines (SCF, IL-3, IL-6, and Epo). A scale bar of 20 μm is shown. <b>(C-E)</b>. Fractions of CD11b⁺ (<b>C</b>), CD34⁺Kit⁺ (<b>D</b>), and Ter119⁺ (<b>E</b>) cells obtained after 7 days of methylcellulose culture containing hematopoietic cytokines (SCF, IL-3, IL-6, and Epo), comparing iPSC-derived progenitors relative to ESC-derived progenitors, in the same order as panel A. <b>F.</b> Lack of correlation between the number of mutations and the hematopoietic differentiation potential of the iPSC clones (r² = 0.0006065).</p

Hematopoietic differentiation from murine ESCs.

<p><b>A.</b> Morphology of wild type ESC-derived cells after 7 days of OP9 coculture (unsorted) by Wright-Giemsa staining. A scale bar of 20 μm is shown. (B-D). Immunophenotyping of hematopoietic progenitor cells from wild-type mouse bone marrow cells (panel B), murine ESCs after 7 days of OP9 coculture (panel C), and iPSC clone Ax1-14 after 7 days of OP9 coculture (panel D). Lineage⁻ (Lin⁻), KLS (Lin⁻Kit⁺Sca-1⁺), progenitors (Lin⁻Kit⁺Sca-1⁻), CMPs (Lin⁻Kit⁺Sca-1⁻CD34⁺FCγ⁻), GMPs (Lin⁻Kit⁺Sca-1⁻CD34⁺FCγ⁺), and MEPs (Lin⁻Kit⁺Sca-1⁻CD34⁻FCγ-).</p

Whole exome sequencing coverage.

<p>Whole exome sequencing coverage.</p

Schematic of rare (MAF<1%) non-synonymous variants used in the gene-level test HDL-C in gene <i>CETP</i>.

<p>The x-axis scale (AA) is in amino acid positions. Numbers in parenthesis are the number of copies of the rare variant in persons with phenotype data. The mean HDL-C level in persons possessing variants with bold naming is increased relative to persons without the variant, for all other variants the mean HDL-C level in persons possessing variant alleles is decreased relative to persons without the variant.</p

Loci with multiple independent single-variant association signals to SNPs with MAF>0.1%.

1<p>FG and TG were LN transformed prior to analysis; the regression coefficient is on the LN scale.</p>2<p>Beta is the estimate of the regression coefficient, and provides the amount and direction the phenotype changes for each copy of the indicated allele.</p>3<p>The p-values come from separate multivariate models for each locus that include all variants listed below, and the first five PCs. P-values shown here represent the independent evidence for the specified variant, after conditioning on the array SNP.</p>4<p>The percent variance in the phenotype accounted for by just the array SNP.</p>5<p>The percent variance in the phenotype accounted for by the array SNP and the independent sequence variants.</p

Overview of quantitative trait loci investigated in this study.

1<p>The loci are named according to the first gene in the region of interest, starting at the 5′ end of the region.</p>2<p>ROI = region of interest. Number of kb sequenced for the locus.</p>3<p>Total Genes is the number of genes in the locus; Targeted Genes is the number of genes investigated in this study.</p>4<p>Please see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004147#pgen.1004147.s009" target="_blank">Table S3</a> for a complete listing of all variant sites, along with their MAF and annotation.</p>5<p>Phenotype abbreviations: TC = total cholesterol, LDL-C = low density lipoprotein cholesterol, HDL-C = high density lipoprotein cholesterol, TG = triglycerides, FG = Fasting Glucose, FI = Fasting Insulin. Previous association evidence for lipid traits is from Kathiresan <i>et al.</i> 2008, Willer <i>et al.</i> 2008 and Teslovich <i>et al.</i> 2010; for glucose Dupuis <i>et al.</i> 2010, and for insulin Sabatti <i>et al.</i> 2009. The “array SNP” is the GWAS array-genotyped SNP (not sequence variant) with the smallest p-value to indicated traits in this study and is not necessarily the same SNP highlighted in previous studies.</p>6<p>Array SNP MAF and p-values are taken from the current study.</p