Genome-Wide Association Study of Serum Minerals Levels in Children of Different Ethnic Background

<div><p>Calcium, magnesium, potassium, sodium, chloride and phosphorus are the major dietary minerals involved in various biological functions and are commonly measured in the blood serum. Sufficient mineral intake is especially important for children due to their rapid growth. Currently, the genetic mechanisms influencing serum mineral levels are poorly understood, especially for children. We carried out a genome-wide association (GWA) study on 5,602 European-American children and 4,706 African-American children who had mineral measures available in their electronic medical records (EMR). While no locus met the criteria for genome-wide significant association, our results demonstrated a nominal association of total serum calcium levels with a missense variant in the calcium –sensing receptor (<i>CASR</i>) gene on 3q13 (rs1801725, <i>P</i> = 1.96 × 10^-3) in the African-American pediatric cohort, a locus previously reported in Caucasians. We also confirmed the association result in our pediatric European-American cohort (<i>P</i> = 1.38 × 10^-4). We further replicated two other loci associated with serum calcium levels in the European-American cohort (rs780094, <i>GCKR</i>, <i>P</i> = 4.26 × 10^-3; rs10491003, <i>GATA3</i>, <i>P</i> = 0.02). In addition, we replicated a previously reported locus on 1q21, demonstrating association of serum magnesium levels with <i>MUC1</i> (rs4072037, <i>P</i> = 2.04 × 10^-6). Moreover, in an extended gene-based association analysis we uncovered evidence for association of calcium levels with the previously reported gene locus <i>DGKD</i> in both European-American children and African-American children. Taken together, our results support a role for <i>CASR</i> and <i>DGKD</i> mediated calcium regulation in both African-American and European-American children, and corroborate the association of calcium levels with <i>GCKR</i> and <i>GATA3</i>, and the association of magnesium levels with <i>MUC1</i> in the European-American children.</p></div

Additional file 1: Table S1. of Association of a rare NOTCH4 coding variant with systemic sclerosis: a family-based whole exome sequencing study

Table of rare coding variants segregating with the SSc/scleroderma phenotype. (XLS 27 kb

rs6441201 risk allele at 3q25 correlates with increased <i>MLF1</i> expression and <i>MLF1</i> silencing results in decreased cell growth in neuroblastoma cells.

<p><b>(a)</b><i>MLF1</i> mRNA expression is significantly higher in neuroblastoma cell lines harboring one or more copies of the rs6441201 risk allele (A) compared to neuroblastoma cell lines homozygous for the protective allele (GG). <b>(b)</b> Silencing of RSRC1 or MLF1 expression using pooled siRNAs resulted in 50–90% reduced mRNA levels by real-time quantitative PCR in neuroblastoma cell lines. <b>(c)</b> Confirmation by Western blot of knockdown at the protein level for RSRC1 and MLF1 after siRNA mediated silencing in neuroblastoma cell lines. <b>(d-g)</b> siRNA mediated silencing of MLF1 results in significant growth inhibition of neuroblastoma cells compared to non-targeting control siRNA; no effect was observed upon silencing of RSRC1. Cell growth measured by real-time cell sensing system (RT-ces).</p

Statistically significant and replicated SNP associations at 3q25 and 4p16.

<p>Statistically significant and replicated SNP associations at 3q25 and 4p16.</p

Discovery of neuroblastoma susceptibility loci at chromosome 3q25 and 4p16.

<p>Regional association plots of genotyped and imputed SNPs novel susceptibility loci. Plots were generated using LocusZoom. Y-axes represent the significance of association (-log10 transformed P values) and the recombination rate. SNPs are color-coded based on pair-wise linkage disequilibrium (r²) with indicated SNPs <b>(a)</b> 3q25 locus: rs6441201 shown in purple (3.01 x 10⁻⁷; Odds Ratio: 1.21, 95% C.I.: 1.12–1.30). <b>(b)</b> 4p16 locus: rs3796727 shown in purple (p = 5.25 x 10⁻⁹; Odds Ratio: 1.26, 95% C.I.: 1.16–1.36).</p

Additional file 1: of Variants in CXCR4 associate with juvenile idiopathic arthritis susceptibility

Supplemental Data: Table S1. The clinical characteristics of samples in each JIA cohort. Table S2. Genome-wide significant associations at the HLA locus (p < 5×10-8 in the discovery cohort).Table S3. Association results for top SNPs in known JIA associated genes PTPN22, IL2RA, ANTXR2. TableS4. The most significantly associated SNPs at CXCR4 locus on chromosome 2q22.1. Table S5 . Genomewideassociation results for imputed SNPs (p < 1×10-4 in combined analysis) in the vicinity of CXCR4 in our JIA cohort. Table S6. Primers used in Sanger sequencing validation of rare variants at CXCR4 locus. Figure S1. Genome-wide association results for JIA. Figure S2. Regional association plot for the 2q22.1 region. Figure S3. CXCR4 tissue-specific gene expression levels. Figure S4. CXCR4 expression levels stratified by SNP genotype. (DOC 466 kb

Additional file 1: Table S1. of Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

Tagging and coverage of MHC region markers. Table S2: Tagging and coverage of Tx-specific genes. Table S3: Untranslated regions (UTRs) considered in the TxArray design. Table S4: Loss-of-function variants included in the TxArray. Table S5: Copy number polymorphisms (CNPs) and variations (CNVs) included in the TxArray. (DOCX 54 kb