Table_1_A rapid turnaround gene panel for severe autoinflammation: Genetic results within 48 hours.docx

There is an important unmet clinical need for fast turnaround next generation sequencing (NGS) to aid genetic diagnosis of patients with acute and sometimes catastrophic inflammatory presentations. This is imperative for patients who require precise and targeted treatment to prevent irreparable organ damage or even death. Acute and severe hyper- inflammation may be caused by primary immunodeficiency (PID) with immune dysregulation, or more typical autoinflammatory diseases in the absence of obvious immunodeficiency. Infectious triggers may be present in either immunodeficiency or autoinflammation. We compiled a list of 25 genes causing monogenetic immunological diseases that are notorious for their acute first presentation with fulminant inflammation and which may be amenable to specific treatment, including hemophagocytic lymphohistiocytosis (HLH); and autoinflammatory diseases that can present with early-onset stroke or other irreversible neurological inflammatory complications. We designed and validated a pipeline that enabled return of clinically actionable results in hours rather than weeks: the Rapid Autoinflammation Panel (RAP). We demonstrated accuracy of this new pipeline, with 100% sensitivity and 100% specificity. Return of results to clinicians was achieved within 48-hours from receiving the patient’s blood or saliva sample. This approach demonstrates the potential significant diagnostic impact of NGS in acute medicine to facilitate precision medicine and save “life or limb” in these critical situations.</p

Regions through time and space: Problem of regionalization

The thesis is rooted in the new regional geography paradigm that gained strength in geographical thought since the 1980s. This approach is characterized by emphasizing the socially constructed nature of regions; thus, regions are scrutinized as a historically contingent process. A region is formed, reproduced and eventually disappears in time. The thesis works with the assumption that a plurality of regions, that exists in changing time- space contexts of different mechanisms and meanings, can be experienced de facto in any particular area. In simpler terms, it can be understood as a plurality of regional images produced on the one side by regional actors to fulfil their particular goals and on the other regional images produced by inhabitants in and outside the region in order to understand the outside world and position themselves within it. Motivation for the production of images can vary, from a simple manifestation of one position in the regional system, through the attempt to attract attention towards the region to exploitation of the regional potential in order to fulfil particular power-oriented aims. The general idea of a region can be sought throughout the synthesis of the many regional images that can be understood as somewhat layers of a region. The thesis contributes to the discussion..

Additional file 5: of Mitochondrial and oxidative stress genes are differentially expressed in neutrophils of sJIA patients treated with tocilizumab: a pilot microarray study

File contains the enriched genes for KEGG_Oxidative Phosphorylation pathway obtained from GSEA. (XLS 13 kb

Table_1.DOCX

<p>Cutaneous leukocytoclastic vasculitis arises from immune complex deposition and dysregulated complement activation in small blood vessels. There are many causes, including dysregulated host response to infection, drug reactions, and various autoimmune conditions. It is increasingly recognised that some monogenic autoinflammatory diseases cause vasculitis, although genetic causes of vasculitis are extremely rare. We describe a child of consanguineous parents who presented with chronic cutaneous leukocytoclastic vasculitis, recurrent upper respiratory tract infection, and hypocomplementaemia. A homozygous p.His380Arg mutation in the complement factor I (CFI) gene CFI was identified as the cause, resulting in complete absence of alternative complement pathway activity, decreased classical complement activity, and low levels of serum factor I, C3, and factor H. C4 and C2 levels were normal. The same homozygous mutation and immunological defects were also identified in an asymptomatic sibling. CFI deficiency is thus now added to the growing list of monogenic causes of vasculitis and should always be considered in vasculitis patients found to have persistently low levels of C3 with normal C4.</p

Table_2.docx

<p>Cutaneous leukocytoclastic vasculitis arises from immune complex deposition and dysregulated complement activation in small blood vessels. There are many causes, including dysregulated host response to infection, drug reactions, and various autoimmune conditions. It is increasingly recognised that some monogenic autoinflammatory diseases cause vasculitis, although genetic causes of vasculitis are extremely rare. We describe a child of consanguineous parents who presented with chronic cutaneous leukocytoclastic vasculitis, recurrent upper respiratory tract infection, and hypocomplementaemia. A homozygous p.His380Arg mutation in the complement factor I (CFI) gene CFI was identified as the cause, resulting in complete absence of alternative complement pathway activity, decreased classical complement activity, and low levels of serum factor I, C3, and factor H. C4 and C2 levels were normal. The same homozygous mutation and immunological defects were also identified in an asymptomatic sibling. CFI deficiency is thus now added to the growing list of monogenic causes of vasculitis and should always be considered in vasculitis patients found to have persistently low levels of C3 with normal C4.</p

Imputation analysis for sJIA, pOJIA, and eOJIA, showing nominal (p = 0.05) and region-wide significance at p = 00016.

<p>For imputed SNPs a cut-off of Rsq >0.3 was used (see text).</p

Results of single point analysis for JIA subtypes and 5723 WTCCC2 controls, showing tSNPs associated at p<0.05. MAF = minor allele frequency.

<p>Significant evidence of association was detected at rs1400986 for sJIA.</p>*<p>Allele frequencies of the first allele (minor allele) is indicated.</p>∧<p>rs2981572 is from PGA.</p>†<p>tSNPs examined for correlation between lymphoblastoid mRNA expression and HapMap genotypes.</p

Odds ratios for each haplotype in the best-fitting model for each JIA subtypes, with 95% CI (grey band, with width proportional to haplotype frequency in controls).

<p>Odds ratios for each haplotype in the best-fitting model for each JIA subtypes, with 95% CI (grey band, with width proportional to haplotype frequency in controls).</p

Conditional analysis on the most significant SNPs for each JIA subtype.

<p>For each SNP, the square represents the p-value after adjusting for the effect of the conditioned SNP, while the other end of the line shows the p-value of a single-locus analysis, prior to conditioning. Colours show the range of r² between the conditioned SNP and the tested SNP as indicated in the insert. Location of the conditioned SNPs is indicated by a black square. Thresholds are indicated for nominal (p = 0.05), suggestive (p = 0.0189) thresholds, with tSNPs above suggestive threshold indicated in bold.</p

Conditional analysis, conditioning on the SNP with the strongest evidence of association, and adding additional SNPs into the model.

<p>For each JIA subtype, the most significant SNP from single point analysis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047673#pone-0047673-t001" target="_blank">Table 1</a>) was used to start the conditional analysis, and then the most significant SNP achieving at least suggestive significance (p<0.0189) was added into the conditional model until no further SNPs were identified. In parentheses are reported the empirical p-values obtained by running 100,000 permutations.</p