Investigation of FANCA mutations in greek patients

Background: Fanconi anemia (FA) is a rare genetic disease characterized by considerable heterogeneity. Fifteen subtypes are currently recognised and deletions of the Fanconi anemia complementation group A (FANCA) gene account for more than 65% of FA cases. We report on the results from a cohort of 166 patients referred to the Department of Medical Genetics of Athens University for genetic investigation after the clinical suspicion of FA. Materials and Methods: For clastogen-induced chromosome damage, cultures were set up with the addition of mitomycin C (MMC) and diepoxybutane (DEB), respectively. Following a positive cytogenetic result, molecular analysis was performed to allow identification of causative mutations in the FANCA gene. Results: A total of 13/166 patients were diagnosed with FA and 8/13 belonged to the FA-A subtype. A novel point mutation was identified in exon 26 of FANCA gene. Conclusion: In our study 62% of FA patients were classified in the FA-A subtype and a point mutation in exon 26 was noted for the first time

Identification of a Novel Intragenic Deletion of the PHKED1 Gene in a Patient with Autosomal Recessive Polycystic Kidney Disease

Background Autosomal recessive polycystic kidney disease (ARPKD) is caused by mutations in the PKHD1 gene. In the present study, we describe a severe case of ARPKD carrying a point mutation and a novel four-exon deletion of PKHD1 gene. Materials and Methods The PKHD1, PKD1 and PKD2 genes were analyzed using next-generation sequencing, whereas the PKHD1 gene exon deletions/duplications were screened using multiplex ligation-dependent probe amplification. Results The c.2279G>A (p.Arg760His) mutation and a deletion encompassing exons 24-27 of PKHD1 gene were detected in compound heterozygosity in the affected neonate. The complete documentation of the genetic basis of the disease offered the possibility of a targeted prenatal diagnosis in the following pregnancy of the couple. Conclusion Given that the molecular analysis of ARPKD is mainly based on sequencing techniques, the PKHD1 gene exon deletion/duplication screening should be performed as a complementary assay in patients suspected to have ARPKD in the absence of two pathogenic mutations

Cell-free plasma DNA as a novel marker of aseptic inflammation severity related to exercise overtraining

Background: Circulating free plasma DNA is implicated in conditions associated with tissue injury, including exercise-induced inflammation, and thus is a potential marker for athletic overtraining. Methods: We measured free plasma DNA along with C-reactive protein (CRP), creatine kinase (CK), and uric acid (UA) in 17 recreationally trained men participating in a 12-week resistance training regimen (8 resistance multi-joint exercises selected to stress the entire musculature: bench press, squat, leg press, snatch, hang clean, dead lifts, barbell arm curls, and rowing), consisting of 4 training periods (t1, t2, t3, and t4). Results: Plasma DNA concentrations increased markedly after t1, t2, and t3 and returned to baseline after t4. There were substantial differences between t2 and t1 and between t3 and t2 plasma DNA concentrations. CRP increased by 300% after t2 and by 400% after t3 (there was no difference between t2 and t3 CRP values) compared with baseline (t0). CK increased only after t3. UA increased after t2 and t3, with a greater increase after t3. Conclusions: This study demonstrates that, after chronic excessive resistance exercise, plasma DNA concentrations increase in proportion to training load, suggesting that plasma DNA may be a sensitive marker for overtraining-induced inflammation. (c) 2006 American Association for Clinical Chemistry

SURVEYOR on the Spot: Strengths and Weaknesses in Molecular Diagnostics

This correspondence addresses J Mol Diagn 2009, 11:311–318, on the advantages and disadvantages of using SURVEYOR in molecular diagnostic mutation detection

Time of sampling is crucial for measurement of cell-free plasma DNA following acute aseptic inflammation induced by exercise

Objectives: To determine the time-course changes of cell-free plasma DNA (cfDNA) following heavy exercise. Methods: cfDNA concentration, C-reactive protein levels (hs-CRP), uric acid concentration (UA), creatine kinase activity (CK) were measured before and post-exercise (immediately post, 0.5 h, 1 h, 2 h, 3 h, 4 h, 5 h, 6 h, 8 h, 10 h, 24 h). Results: cfDNA increased (15-fold) 30-min post-exercise and normalized thereafter. hs-CRP increased (56%, p<0.001) 1 h post-exercise, remained elevated throughout recovery (52-142%, p<0.0001), and peaked (200% rise, p<0.0001) at 24 h post-exercise. UA and CK increased (p<0.05), immediately post-exercise, remained elevated throughout recovery (p<0.0001), and peaked (p<0.0001) at 24 h of post-exercise recovery. Conclusions: cfDNA sampling timing is crucial and a potential source of error following aseptic inflammation. (C) 2010 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved

Impaired degradation and aberrant phagocytosis of necrotic cell debris in the peripheral blood of patients with primary Sjogren's syndrome

Aberrant removal of necrotic debris is considered a feature with inflammatory consequences in SLE. Herein, primary Sjogren's syndrome (SS) patients were investigated for the first time for the capacity of their sera to degrade secondary necrotic cell remnants (SNEC) and DNA (endonuclease DNase1 activity), as well as for uptake of SNEC by blood-borne phagocytes. For comparison, specimens from unselected SLE and RA patients and from healthy blood donors (HBD) were also studied. Compared to HBD, the sera from SS and SLE patients studied (but not RA) were found to exhibit significantly impaired capacity for degradation of SNEC (both for p = 0.007) and deficient DNase1 activity (both for p < 0.0001). The deficient DNase1 activity in SS and SLE sera did not owe to decreased DNase1 protein levels. It correlated inversely with increased serum levels of circulating nucleosomes and cell-free DNA (p < 0.0001), as well as with the disease activity indices of SS (r = -0.445, p = 0.0001) and SLE (r = -0.500, p = 0.013). In ex-vivo whole blood analyses, SS and SLE patients (but not RA) also manifested significantly increased SNEC-phagocytosis by monocytes and granulocytes (all for p < 0.0001) that also correlated with disease severity indices of SS (p = 0.001) and SLE (p = 0.01). In various cross-admixture experiments, such aberration was found to reside in the hyperfunctional activity of phagocytes, the impaired degrading activity of serum DNase1 and the SNEC-binding capacity of serum IgG of SS and SLE patients. The sera of SS and SLE patients (but not of RA) induced significant SNEC-phagocytosis by healthy monocytes that correlated inversely with the DNase1 activity (r = -0.634, p < 0.0001) of these sera. In line with this, the inhibition of DNase1 in HBD sera by G-actin was found to lead to significantly diminished SNEC degradation and increased SNEC uptake by healthy phagocytes (p = 0.0009), supporting the important physiologic role of serum DNase1 in the prevention of SNEC-phagocytosis. Purified serum IgG preparations from SS and SLE patients manifested increased binding to SNEC and were able to enhance significantly the engulfment of SNEC by healthy phagocytes both directly (under serum-free conditions, p <= 0.009) and via the prevention of physiologic degradation of SNEC by serum, most likely due to their "shielding" against endonuclease digestion (p = 0.0005). These data indicate that upon cell necrosis, the immune system of SS and SLE patients may be overly exposed to the necrotic debris, a fact that probably holds a key role in the pathogenesis of inflammatory and autoimmune reactions observed in these disorders. (C) 2014 Elsevier Ltd. All rights reserved

The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome

Congenital heart defect (CHD) occurs in 40% of Down syndrome (DS) cases. While carrying three copies of chromosome 21 increases the risk for CHD, trisomy 21 itself is not sufficient to cause CHD. Thus, additional genetic variation and/or environmental factors could contribute to the CHD risk. Here we report genomic variations that in concert with trisomy 21, determine the risk for CHD in DS. This case-control GWAS includes 187 DS with CHD (AVSD = 69, ASD = 53, VSD = 65) as cases, and 151 DS without CHD as controls. Chromosome 21–specific association studies revealed rs2832616 and rs1943950 as CHD risk alleles (adjusted genotypic P-values <0.05). These signals were confirmed in a replication cohort of 92 DS-CHD cases and 80 DS-without CHD (nominal P-value 0.0022). Furthermore, CNV analyses using a customized chromosome 21 aCGH of 135K probes in 55 DS-AVSD and 53 DS-without CHD revealed three CNV regions associated with AVSD risk (FDR ≤ 0.05). Two of these regions that are located within the previously identified CHD region on chromosome 21 were further confirmed in a replication study of 49 DS-AVSD and 45 DS- without CHD (FDR ≤ 0.05). One of these CNVs maps near the RIPK4 gene, and the second includes the ZBTB21 (previously ZNF295) gene, highlighting the potential role of these genes in the pathogenesis of CHD in DS. We propose that the genetic architecture of the CHD risk of DS is complex and includes trisomy 21, and SNP and CNV variations in chromosome 21. In addition, a yet-unidentified genetic variation in the rest of the genome may contribute to this complex genetic architecture.The study was supported by grants from the NCCR–Frontiers in Genetics, the European AnEuploidy project, the Fondation Child Care, the SNF 144082, the ERC 249968 to S.E.A., and the Spanish Ministry of Ecomomy and Competitivity to X.E. P.M. was supported by a grant from the Bodossaki foundation. K.P. was supported by the EMBO long-term fellowship program ALTF 527-201

Evaluation of PCR-based preimplantation genetic diagnosis applied to monogenic diseases: a collaborative ESHRE PGD consortium study

Preimplantation genetic diagnosis (PGD) for monogenic disorders currently involves polymerase chain reaction (PCR)-based methods, which must be robust, sensitive and highly accurate, precluding misdiagnosis. Twelve adverse misdiagnoses reported to the ESHRE PGD-Consortium are likely an underestimate. This retrospective study, involving six PGD centres, assessed the validity of PCR-based PGD through reanalysis of untransferred embryos from monogenic-PGD cycles. Data were collected on the genotype concordance at PGD and follow-up from 940 untransferred embryos, including details on the parameters of PGD cycles: category of monogenic disease, embryo morphology, embryo biopsy and genotype assay strategy. To determine the validity of PCR-based PGD, the sensitivity (Se), specificity (Sp) and diagnostic accuracy were calculated. Stratified analyses were also conducted to assess the influence of the parameters above on the validity of PCR-based PGD. The analysis of overall data showed that 93.7% of embryos had been correctly classified at the time of PGD, with Se of 99.2% and Sp of 80.9%. The stratified analyses found that diagnostic accuracy is statistically significantly higher when PGD is performed on two cells versus one cell (P=0.001). Se was significantly higher when multiplex protocols versus singleplex protocols were applied (P=0.005), as well as for PGD applied on cells from good compared with poor morphology embryos (P=0.032). Morphology, however, did not affect diagnostic accuracy. Multiplex PCR-based methods on one cell, are as robust as those on two cells regarding false negative rate, which is the most important criteria for clinical PGD applications. Overall, this study demonstrates the validity, robustness and high diagnostic value of PCR-based PGD