Novel loci associated with eGFRcrea.

<p>SNPs are listed in the stratum where the smallest <i>P</i> value in the discovery analysis was observed. Sample size/number of studies in the discovery phase: 74,354/26 (overall, direction test), 66,931/24 (No Diabetes), 46,435/23 (age ≤65 years); replication phase: 56,246/19 (overall, direction test), 41,218/17 (No Diabetes), 28,631/16 (age ≤65 years); combined analysis: 130,600/45 (overall, direction test), 108,149/41 (No Diabetes), 75,066/39 (age ≤65 years).</p><p>Chr.: chromosome; bp: base-pairs; Ref./Non-Ref. All.: reference/non-reference alleles; RAF: reference allele frequency; SE: standard error.</p>‡<p>Genes nearby were based on RefSeq genes (build 36). The gene closest to the SNP is listed first and is in boldface if the SNP is located within the gene.</p>§<p>Effects on log(eGFRcrea); post GWAS meta-analysis genomic control correction applied to <i>P</i> values and SEs.</p>*<p>While being uncovered in the younger samples, this locus showed consistent results in the non-diabetic group (combined-analysis <i>P</i> value 5.7×10⁻¹⁶) and in the overall population (<i>P</i> value 9.5×10⁻²²) - see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002584#pgen.1002584.s028" target="_blank">Tables S16</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002584#pgen.1002584.s022" target="_blank">S10</a> for additional details.</p>**<p>The direction test was performed in the overall dataset; the genomic control corrected <i>P</i> value from the direction test for the SNP rs2928148 was 4.0×10⁻⁷. In the combined analysis, the largest effect size (0.0054 on log eGFR in ml/min/1.73 m²) and the smallest <i>P</i> value (3.7×10⁻⁸) were observed in the non-diabetic group.</p>†<p>All results were confirmed by random-effect meta-analysis.</p

Genetic association and LD distribution of the <i>MPPED2</i> gene locus in European and African ancestry populations.

<p>Regional association plots in the CKDGen European ancestry discovery analysis (N = 74,354) (A) and in the CARe African ancestry discovery analysis (N = 8,110) (B). LD structure: comparison between the HapMap release II – CEU and YRI samples in the region included within +/−100 kb from the target SNP rs3925584 identified in the CKDGen GWAS. The green circle highlights a stream of high LD connecting the two blocks, indicating the presence of common haplotypes (C).</p

Interrogation of the six novel loci uncovered in the European ancestry (EA) individuals (CKDGen consortium) in individuals of African ancestry (AA) from the CARe consortium for the trait eGFRcrea.

<p>Ref./Non-Ref. All.: reference/non-reference alleles; RAF: reference allele frequency; SE: standard error.</p>*<p>Characteristics of the six lead SNPs in the EA individuals from the CKDGen consortium can be found in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002584#pgen-1002584-t001" target="_blank">Table 1</a>.</p>§<p>The gene closest to the SNP is listed first and is in boldface if the SNP is located within the gene.</p>**<p>S = number of independent, typed SNPs interrogated.</p>†<p>No LD information available in the HapMap database between the target SNP and the best SNP in the DDX1 region.</p>‡<p>The SNP rs11078903 was not present in the CARe consortium database.</p

<i>Mpped2</i> and <i>casp9</i> knockdowns result in defective kidney development.

<p>(A–E) Whole mount <i>in situ</i> hybridization in control embryos demonstrates normal expression of the global kidney marker <i>pax2a</i> (A: lateral view; B: dorsal view), the glomerular marker <i>nephrin</i> (C), and the tubular markers <i>slc20a1a</i> (proximal tubule, D), and <i>slc12a3</i> (distal tubule, E) at 48 hours post fertilization (hpf). (F–J) <i>Mpped2</i> morpholino (MO) knockdown embryos develop glomerular gene expression defects (F–H, arrowheads), but tubular marker expression is normal (I, J). (K–O) <i>Casp9</i> MO knockdown embryos demonstrate reduced glomerular gene expression (K–M, arrowheads) and shortened distal tubules (O). (P) Quantification of observed abnormalities per number of embryos reveal significant differences in expression of <i>pax2a</i> and <i>nephrin</i> in response to knockdown of both <i>mpped2</i> and <i>casp9</i> (Fisher's exact test). (Q–V) Embryos were injected with control, <i>mpped2</i>, <i>or casp9</i> MO at the one-cell stage and subsequently injected with 70,000 MW fluorescent rhodamine dextran at 80 hpf. Dextran fluorescence was monitored over the next 48 hours. All dextran-injected embryos show equal loading into the cardiac sinus venosus at 2 hours post-injection (2 hpi/82 hpf; Q, S, U). Compared to control MO-injected embryos (R) and <i>mpped2</i> knockdown embryos (T), knockdown of <i>casp9</i> resulted in reduced dextran clearance at 48 hpi as shown by increased trunk fluorescence (V). (W) <i>Casp9</i> knockdown results in increased susceptibility to edema formation both spontaneously (−dex) (<i>P</i> value = 0.0234, Fisher's exact test) and after dextran challenge (+dex) (<i>P</i> value<0.0001). Embryos injected with both MO and dextran did not survive to 6 dpf (N/A). (X) Edema develops earlier and with higher frequency in <i>casp9</i> morphants following injection of the nephrotoxin gentamicin.</p