16 research outputs found
Association analysis results and locations of seven index SNPs identified by grouping analysis of the xMHC.
<p>Recombination rates were estimated from HapMap data and are indicated by vertical bars.</p
Binary tree computed by conditional recursive partitioning on HLA-DQA1 and HLA-DQB1 genotypes.
<p>Binary tree computed by conditional recursive partitioning on HLA-DQA1 and HLA-DQB1 genotypes.</p
Association Results for Seven Index SNPs Representing Independent Loci.
*<p>Either the gene that the SNP occurs in, or the nearest gene within the same LD haplotype block as the index SNP.</p>#<p>Indicates adjustment for known common high-risk alleles by inclusion of the five-level variable computed by recursive partitioning.</p
Results of sensitivity analysis for SNP grouping analysis showing the relationship between the group linkage disequilibrium parameter (<i>r</i><sup>2</sup>) and the number of index SNPs identified, with <i>r</i><sup>2</sup> ranging from (a) 0.05 to 0.95, and focused on the range from (b) 0.01 to 0.15.
<p>Results (c) show the relationship between the minimum statistical significance parameter for the association between the disease and the index SNP and the number of index SNPs identified.</p
Characteristics of Five-Level Variable for Known HLA High-Risk Alleles Computed by Conditional Recursive Partitioning.
<p>Characteristics of Five-Level Variable for Known HLA High-Risk Alleles Computed by Conditional Recursive Partitioning.</p
Association results for 1898 SNPs across xMHC, without accounting for the known HLA high-risk genotypes in the statistical analysis.
<p>Vertical bars indicate recombination rates generated from HapMap database. All pairwise linkage disequilibrium coefficients (<i>r</i><sup>2</sup>) included the most significantly associated SNP, rs2647044.</p
Association results for 17 SNPs from the current GWAS and the GWAS reported by Dubois et al. (REF) within the FRMD4B gene on 3p14.1.
<p>Association results for 17 SNPs from the current GWAS and the GWAS reported by Dubois et al. (REF) within the FRMD4B gene on 3p14.1.</p
Results of association analysis of microscopic colitis and dermatitis herpetiformis across celiac associated regions.
<p>Results of association analysis of microscopic colitis and dermatitis herpetiformis across celiac associated regions.</p
p-values of association (−log10 scale) with breast cancer risk in <i>BRCA2</i> carriers for genotyped and imputed SNPs in the <i>NEIL2</i> gene.
<p>SNP rs1466785 is indicated with a purple arrow and the best causal imputed SNPs, rs804276 and rs804271 are indicated with a red arrow. Colors represent the pariwise r<sup>2</sup>. Plot generated with LocusZoom <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004256#pgen.1004256-Pruim1" target="_blank">[42]</a> (<a href="http://csg.sph.umich.edu/locuszoom/" target="_blank">http://csg.sph.umich.edu/locuszoom/</a>).</p
Associations with breast and ovarian cancer risk for SNPs observed at p-trend<0.05 in stage II of the experiment.
a<p>Hazard Ratio per allele (1 df) estimated from the retrospective likelihood analysis.</p>b<p>Hazard Ratio under the genotype specific models (2df) estimated from the retrospective likelihood analysis.</p>c<p>p-values were based on the score test.</p>d<p>HR per allele of 1.69 and p-trend of 1×10<sup>−4</sup> for <i>BRCA2</i> mutation carriers in stage I of the study.</p>e<p>HR per allele of 1.43 and p-trend of 0.01 for <i>BRCA1</i> mutation carriers in stage I of the study.</p>f<p>HR per allele of 1.30 and p-trend of 0.03 for <i>BRCA1</i> mutation carriers in stage I of the study.</p>g<p>HR per allele of 0.64 and p-trend of 0.057 for <i>BRCA2</i> mutation carriers in stage I of the study.</p>h<p>HR per allele of 1.25 and p-trend of 0.04 for <i>BRCA1</i> mutation carriers in stage I of the study.</p>i<p>HR per allele of 1.25 and p-trend of 0.058 for <i>BRCA2</i> mutation carriers in stage I of the study.</p>j<p>rs3093926 did not yield results under the genotype specific model due to the low minor allele frequency.</p><p>Complete description of results from stage I are included in Supplementary <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004256#pgen.1004256.s002" target="_blank">Table S1</a>.</p><p>Highlighted in bold are those SNPs showing strongest associations with breast or ovarian cancer risk (p<0.01).</p