Rapid Detection of Rare Deleterious Variants by Next Generation Sequencing with Optional Microarray SNP Genotype Data

Autozygosity mapping is a powerful technique for the identification of rare, autosomal recessive, disease‐causing genes. The ease with which this category of disease gene can be identified has greatly increased through the availability of genome‐wide SNP genotyping microarrays and subsequently of exome sequencing. Although these methods have simplified the generation of experimental data, its analysis, particularly when disparate data types must be integrated, remains time consuming. Moreover, the huge volume of sequence variant data generated from next generation sequencing experiments opens up the possibility of using these data instead of microarray genotype data to identify disease loci. To allow these two types of data to be used in an integrated fashion, we have developed AgileVCFMapper, a program that performs both the mapping of disease loci by SNP genotyping and the analysis of potentially deleterious variants using exome sequence variant data, in a single step. This method does not require microarray SNP genotype data, although analysis with a combination of microarray and exome genotype data enables more precise delineation of disease loci, due to superior marker density and distribution.     

<Emphasis Type="Italic">FAM13A</Emphasis> and <Emphasis Type="Italic">POM121C</Emphasis> are candidate genes for fasting insulin: functional follow-up analysis of a genome-wide association study

Aims/hypothesis

By genome-wide association meta-analysis, 17 genetic loci associated with fasting serum insulin (FSI), a marker of systemic insulin resistance, have been identified. To define potential culprit genes in these loci, in a cross-sectional study we analysed white adipose tissue (WAT) expression of 120 genes in these loci in relation to systemic and adipose tissue variables, and functionally evaluated genes demonstrating genotype-specific expression in WAT (eQTLs).

Methods

Abdominal subcutaneous adipose tissue biopsies were obtained from 114 women. Basal lipolytic activity was measured as glycerol release from adipose tissue explants. Adipocytes were isolated and insulin-stimulated incorporation of radiolabelled glucose into lipids was used to quantify adipocyte insulin sensitivity. Small interfering RNA-mediated knockout in human mesenchymal stem cells was used for functional evaluation of genes.

Results

Adipose expression of 48 of the studied candidate genes associated significantly with FSI, whereas expression of 24, 17 and 2 genes, respectively, associated with adipocyte insulin sensitivity, lipolysis and/or WAT morphology (i.e. fat cell size relative to total body fat mass). Four genetic loci contained eQTLs. In one chromosome 4 locus (rs3822072), the FSI-increasing allele associated with lower FAM13A expression and FAM13A expression associated with a beneficial metabolic profile including decreased WAT lipolysis (regression coefficient, R?=??0.50, p?=?5.6?×?10^?7). Knockdown of FAM13A increased lipolysis by ~1.5-fold and the expression of LIPE (encoding hormone-sensitive lipase, a rate-limiting enzyme in lipolysis). At the chromosome 7 locus (rs1167800), the FSI-increasing allele associated with lower POM121C expression. Consistent with an insulin-sensitising function, POM121C expression associated with systemic insulin sensitivity (R?=??0.22, p?=?2.0?×?10^?2), adipocyte insulin sensitivity (R?=?0.28, p?=?3.4?×?10^?3) and adipose hyperplasia (R?=??0.29, p?=?2.6?×?10^?2). POM121C knockdown decreased expression of all adipocyte-specific markers by 25–50%, suggesting that POM121C is necessary for adipogenesis.

Conclusions/interpretation

Gene expression and adipocyte functional studies support the notion that FAM13A and POM121C control adipocyte lipolysis and adipogenesis, respectively, and might thereby be involved in genetic control of systemic insulin sensitivity.

     

C-type natriuretic peptide (CNP) is a bifurcation factor for sensory neurons

Neuronal circuits are shaped during development by the coordinated action of guidance factors and signals that regulate axonal branching. Unlike guidance cues, the molecules and signaling cascades that underlie axonal branching remain to be resolved. Here we show that the secreted molecule C-type natriuretic peptide (CNP) induces a cGMP signaling cascade via its receptor particulate guanylyl cyclase Npr2 which is essential for sensory axon bifurcation at the dorsal root entry zone (DREZ) of the spinal cord. In contrast, another form of sensory axon branching—collateral formation—is not affected by this pathway. We also demonstrate that cGMP signaling via the nitric oxide-stimulated soluble guanylyl cyclase system (NO-GC) is dispensable for sensory axon branching. Functionally, the bifurcation error in CNP mutant mice is maintained at mature stages and results in a reduced input on secondary neurons as detected by patch-clamp recordings.     

Usefulness of pretransplant aortic arch calcification evaluation for kidney transplant outcome prediction in one year follow-up

Vascular calcification (VC) is linked to post-transplant cardiovascular events and hypercalcemia which may influence kidney graft function in the long term. We aimed to evaluate whether pretransplant aortic arch calcification (AoAC) can predict post-transplant cardiovascular or cerebrovascular events (CVEs), and to assess its association with post-transplant plasma calcium levels and renal function in one-year follow-up. Our single-center observational prospective study enrolled 37 kidney transplant recipients (KTR) without previous history of vascular events. Two radiologists evaluated pretransplant AoAC on chest X-ray as suggested by Ogawa et al. in 2009. Cohen’s kappa coefficient was 0.71. The mismatching results were repeatedly reviewed and resulted in consensus. Carotid-femoral (cfPWV) and carotid-radial pulse wave velocity (crPWV) was measured using applanation tonometry before and one year after transplantation. Patient clinical, biochemical data, and cardiovascular/CVE rate were monitored within 1 year. We found out that eGFR_1year correlated with eGFR_discharge and calcium based on hospital discharge data (β?=?0.563, p?=?.004 and β?=?51.360, p?=?.026, respectively). Multivariate linear regression revealed that donor age, donor gender, and recipient eGFR_discharge (R-squared 0.65, p?=?.002) better predict eGFR_1year than AoAC combined with recipient eGFR_discharge (R-squared 0.35, p?=?.006). During 1-year follow-up, four (10.81%) patients experienced cardiovascular events, which were predicted by PWV ratio (HR 7.549, p?=?.045), but not related to AoAC score (HR 1.044, p?=?.158). In conclusion, KTR without previous vascular events have quite low cardiovascular/CVE rate within 1-year follow-up. VC evaluated as AoAC on pretransplant chest X-ray together with recipient eGFR_discharge could be related to kidney function in one-year follow-up.     

The dynamic cardiac biosimulator: A method for training physicians in beating-heart mitral valve repair procedures

Objective

Previously, cardiac surgeons and cardiologists learned to operate new clinical devices for the first time in the operating room or catheterization laboratory. We describe a biosimulator that recapitulates normal heart valve physiology with associated real-time hemodynamic performance.

Perceptions of assertive community treatment in the UK and Lithuania

BACKGROUND: There is current uncertainty over the future of assertive community and outreach teams in view of recent evidence suggesting that they no longer reduce hospital admissions. Despite this, assertive teams remain popular among practitioners. AIMS: To examine the views of assertive community team members and other mental health professionals in London (UK) and Vilnius (Lithuania) to determine important differences in attitudes. METHOD: A questionnaire, involving the assessment of statements giving common opinions on assertive community teams, was given to 62 staff in Vilnius, Lithuania and West London, UK, 33 from assertive community or outreach teams and 29 from other mental health professionals. RESULTS: The results of the questionnaire showed that personnel in experienced assertive outreach teams in London believed that they gave more intensive care (p < 0.001), felt it of greater value to see patients in the community (p < 0.001) and were not just well-resourced community teams with low caseloads (p < 0.01) than did other groups, but they placed lower value on assertiveness (p = 0.04) and comprehensive care (p < 0.04). These differences were less marked in Lithuania where staff regarded home treatment as similar to clinic treatment and were more supportive of comprehensive care. CONCLUSION: The results suggest that in experienced community teams the notion of assertiveness has become less important in planned intensive community care and so the term ACT may be outmoded. However, for countries such as Lithuania, somewhat similar to the United States in 1972 when ACT began, the original principles are still appropriate and 'assertive' is a major component of their effectiveness.