Preprocessed IgG Fc glycomics data in four Croatian cohorts (LC-ESI-MS)

<p>The file contains preprocessed IgG glycan concentrations in four large scale Croatian cohorts. Glycan abundances were measured via LC-ESI-MS and preprocessed as described in the first sheet of the file. For confidentiality reasons, age and gender data could not be shared publicly; glycan values corrected for those variables are therefore additionally provided. A GGM inferred on this corrected data matrix will be substantially the same as the one presented in the original paper.</p><p></p><p>The Croatian cohorts received ethical approval of the ethics committee of the University of Split School of Medicine, as well as the South East Scotland Research. Written informed consent was obtained from each participant.</p><div><div><div> </div> </div> </div

An analysis of pleiotropy between loci associated with IgG glycans and previously reported disease/trait susceptibility loci, with linkage disequilibrium computed between the most significantly associated SNPs.

<p>Associations are those found in the GWAS Catalog track of USCS Genome browser (accessed 04/07/2012) and LD has been calculated using SNAP (<a href="http://www.broadinstitute.org/mpg/snap/Johnson" target="_blank">http://www.broadinstitute.org/mpg/snap/Johnson</a>, A. D., Handsaker, R. E., Pulit, S., Nizzari, M. M., O'Donnell, C. J., de Bakker, P. I. W. SNAP: A web-based tool for identification and annotation of proxy SNPs using HapMap <i>Bioinformatics, 2008 24(24):2938–2939</i>).</p

Groups of IgG N-glycans from Table 3 that showed statistically significant difference in observed values (corrected by sex, age, and African admixture) between 101 Afro-Caribbean cases with SLE and 183 controls.

*<p>t-test for equality of means (2-tailed).</p

Structures of glycans separated by HILIC-UPLC analysis of the IgG glycome.

<p>Structures of glycans separated by HILIC-UPLC analysis of the IgG glycome.</p

Twelve groups of IgG N-glycans (of 77 measured) that showed nominally significant difference (p<0.05) in observed values between 5 mice that were heterozygous <i>Ikzf1</i> knock-outs (Neo) and 5 wild-type controls (wt).

<p>The global difference test was significant (p = 0.03). ^*t-test for equality of means (2-tailed).</p

Validation of biomarker potential of IGP48 IgG N-glycan percentage in prediction of Systemic Lupus Erythematosus (SLE) in 101 Afro-Caribbean cases and 183 matched controls.

<p>As shown in the graph, age and sex do not have any predictive power for this disease, but addition of IGP48 substantially increases sensitivity and specificity of prediction, with area under receiver-operator curve increased to 0.828.</p

A complete list of genetic markers that showed genome-wide significant (P<2.27E-9) or strongly suggestive (P≤5E-08) association with glycosylation of Immunoglobulin G analysed by UPLC in the discovery meta-analysis.

<p>Interval: size (kb) of the genomic interval containing SNPs with R²> = 0.6 with top associated SNP; nHits: number of SNPs with GW-significant association; nTraits: number of IgG glycosylation traits associated with the region at GW-significant level;</p>*<p>effect size is in z-score units after adjustment for sex, age and first 3 principal components.</p>+<p>Description of the traits provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003225#pgen.1003225.s002" target="_blank">Table S1</a>;</p>$<p>the SNP effect in opposite direction to most significant trait.</p