One of the questions that arise from

One of the questions that arise from the study is: What is the underlying cause for the rest of cases? As authors address in the paper, WES may not detect those variants in non-coding regions neither deletions nor gene rearrangements. Indeed, next-generation sequencing techniques using densely placed probes throughout the entire genes including non-coding regions or multiplex ligation-dependent probe amplification (MLPA) would be required to detect gross MM-102 and duplication variants. Those mutations in genes responsible for transcriptional and translational regulation are also not detected. For instance, variations in long non-coding RNAs and miRNAs could be responsible for the abnormal transcription of the mRNA or the aberrant translation of the protein (). Antithrombin, protein C, and protein S are glycoproteins. WES cannot detect variants that affect the final glycosylation of the protein. In fact, it has been recently described that congenital disorders of glycosylation may influence the glycosylation of antithrombin and, therefore, its final secretion in antithrombin-deficient patients in which has no mutations (). Glycosylation may have great relevance to the function as has been reported for antithrombin and protein C (). As a consequence, all those alterations in the glycosylation of natural anticoagulants may result in a functional deficiency. Additionally, Halvorsen and coworkers detect new variants in and genes that should be studied and characterized to understand the effect of the mutation and to determine the frequency in the population or in selected cohorts. Among the mutations identified in , antithrombin Cambridge II variant was not detected, even though it is considered the most common mutation among antithrombin deficiencies. This is explained by the fact that this mutation is an ethnic-specific variant, rare in Africans and Asians. In addition, the analysis pipeline removes any variants with allele frequency higher than 0.1%. There are other variants detected in , , and whose effect is described by other studies in which the same residue is affected although the change is not the same (). All these mutants should also be further characterized to better know the effect or the mechanism by which they provoke the deficiency.
In , Kemna et al. hypothesized that glycosylation status of IgG antibodies can predict relapse in PR3-ANCA associated vasculitis (AAV) (). AAV constitute a group of inflammatory diseases affecting small and medium sized vessels and are characterized by anti-neutrophil cytoplasmic antibodies (ANCA) directed towards proteinase 3 (PR3) and myeloperoxidase (MPO) (). AAV are severe diseases that can cause kidney failure due to necrotizing glomerulonephritis (NCGN), but can quite often be successfully treated with aggressive immunosuppressive therapy. ANCAs of IgG isotype are most likely involved in driving the disease (), and sometimes rise in ANCA titers precede relapses. However, the titers alone seem to be a poor predictor of relapse, and therefore Kemna et al. hypothesized that glycosylation status of the ANCAs could more accurately predict relapse. The rationale for this is that the glycosylation status in the Fc-portion of IgG has proven to influence qualitative aspects of effector functions such as Fc-receptor biding and complement activation (). It has also been shown in animal models of AAV that deglycosylation of MPO-ANCA attenuates disease (), and in patients with severe AAV total IgG Fc glycans have lower levels of galactosylation, sialylation, and bisecting -acetylglucosamine (GlcNAc) (). However, glycosylation status of antigen specific IgG has not previously been investigated in AAV patients. In this study, a cohort of 75 patients in remission with a subtype of AAV, called granulomatosis with polyangiitis (GPA) was studied. They all had rising PR3-ANCA titers and 43 patients relapsed within 2–16months. Affinity purified antibodies from these patients at the time of ANCA rise and relapse were analyzed using an advanced mass spectrometry based methodology that can identify and quantitate specific glycopeptides that represent specific IgG glycoforms in total IgG and PR3-ANCA. This revealed that patients with low galactosylation or sialylation of total IgG1 were highly prone to relapse after an ANCA rise. In relapsing patients, there was a significant decrease of total IgG1 sialylation, galactosylation and bisection and increase of fucosylation from the time of ANCA rise to relapse, while in non-relapsing patients the glycosylation profiles did not change. Somewhat surprising, PR3-ANCA galactosylation, sialylation, and fucosylation decreased in both relapsing and non-relapsing patients.