13 research outputs found
Genotype distribution at <i>CAPN10</i> UCSNP44, -43, -19 and -63 sites and analysis of Hardy-Weinberg equilibrium (HWE).
<p>Allele nomenclature according to Horikawa <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002953#pone.0002953-Horikawa1" target="_blank">[1]</a> and Evans <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002953#pone.0002953-Evans1" target="_blank">[34]</a></p
Haplogenotypic association analysis.
<p>Results are given as p-values. Numbers in brackets represents the percentages of increase or decrease of the phenotypic mean with respect to the remaining haplotypes. All values are adjusted by age, sex, alcohol consumption, smoking, physical activity and BMI.</p
Haplotypic frequencies and association analysis with OGTT values in Spanish population
<p>F: population frequency.</p
Baseline characteristics of study subjects.
<p>Baseline characteristics of study subjects.</p
Analysis of Hardy-Weinberg equilibrium (HWE) at UCSNP63 locus in different populations.
<p>FA: familial antecedents of T2DM.</p
Genotypic association analysis.
<p>Only the association studies which obtained a p value under 0.05 are shown. SE: standard error; Ns: Not significant. All values are adjusted by age, sex, alcohol consumption, smoking, physical activity and BMI.</p
A Colorectal Cancer Susceptibility New Variant at 4q26 in the Spanish Population Identified by Genome-Wide Association Analysis
<div><p>Background</p><p>Non-hereditary colorectal cancer (CRC) is a complex disorder resulting from the combination of genetic and non-genetic factors. Genome–wide association studies (GWAS) are useful for identifying such genetic susceptibility factors. However, the single loci so far associated with CRC only represent a fraction of the genetic risk for CRC development in the general population. Therefore, many other genetic risk variants alone and in combination must still remain to be discovered. The aim of this work was to search for genetic risk factors for CRC, by performing single-locus and two-locus GWAS in the Spanish population.</p><p>Results</p><p>A total of 801 controls and 500 CRC cases were included in the discovery GWAS dataset. 77 single nucleotide polymorphisms (SNP)s from single-locus and 243 SNPs from two-locus association analyses were selected for replication in 423 additional CRC cases and 1382 controls. In the meta-analysis, one SNP, rs3987 at 4q26, reached GWAS significant p-value (p = 4.02×10<sup>−8</sup>), and one SNP pair, rs1100508 CG and rs8111948 AA, showed a trend for two-locus association (p = 4.35×10<sup>−11</sup>). Additionally, our GWAS confirmed the previously reported association with CRC of five SNPs located at 3q36.2 (rs10936599), 8q24 (rs10505477), 8q24.21(rs6983267), 11q13.4 (rs3824999) and 14q22.2 (rs4444235).</p><p>Conclusions</p><p>Our GWAS for CRC patients from Spain confirmed some previously reported associations for CRC and yielded a novel candidate risk SNP, located at 4q26. Epistasis analyses also yielded several novel candidate susceptibility pairs that need to be validated in independent analyses.</p></div
Best SNP×SNP interactions validated in the phase II and meta-analysis results.
<p>SNP: Single Nucleotide Polymorphism; OR: HFCC Odds Ratio; P: value associated with HFCC OR (1 df).</p>†<p>The nearest gene or the gene where the SNP is located.</p
SNPs validated in the phase II.
<p>CHR: Chromosome; SNP: Single Nucleotide Polymorphism; BP: Base pair position; A1: Reference allele (minor allele). The last eight columns show the minor allele frequency in cases (MAF A), the minor allele frecuency in controls (MAF U) and, the p and the Odds Ratio (OR) values obtained in each analyzed sample.</p><p>*SNPs selected by two-locus association analyses in the NXC-GWAS sample.</p>†<p>The nearest gene or the gene where the SNP is located.</p>‡<p>According to UCSC genome browser (NCBI36/hg18) and dbSNP build 130.</p
Meta-analysis of SNPs validated in the phase II.
<p>CHR: Chromosome; SNP: Single Nucleotide Polymorphism; BP: Base pair position; A1: Reference allele (minor allele); P: Fixed-effects p-value; P(R): Random-effects p-value; OR: Fixed-effects Odds Ratio; OR(R): Random-effects Odds Ratio; Q: p-value for heterogeneity of OR; I: effect size for heterogeneity of OR.</p><p>*SNPs selected by two-locus association analyses in the NXC-GWAS sample.</p>†<p>The nearest gene or the gene where the SNP is located.</p>‡<p>According to UCSC genome browser (NCBI36/hg18) and dbSNP build 130.</p