Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector

Herein we present Gene-Collector, a method for multiplex amplification of nucleic acids. The procedure has been employed to successfully amplify the coding sequence of 10 human cancer genes in one assay with uniform abundance of the final products. Amplification is initiated by a multiplex PCR in this case with 170 primer pairs. Each PCR product is then specifically circularized by ligation on a Collector probe capable of juxtapositioning only the perfectly matched cognate primer pairs. Any amplification artifacts typically associated with multiplex PCR derived from the use of many primer pairs such as false amplicons, primer-dimers etc. are not circularized and degraded by exonuclease treatment. Circular DNA molecules are then further enriched by randomly primed rolling circle replication. Amplification was successful for 90% of the targeted amplicons as seen by hybridization to a custom resequencing DNA micro-array. Real-time quantitative PCR revealed that 96% of the amplification products were all within 4-fold of the average abundance. Gene-Collector has utility for numerous applications such as high throughput resequencing, SNP analyses, and pathogen detection

Increasing Prevalence and High Risk of Associated Anomalies in Congenital Vertebral Defects : A Population-based Study

Background: Congenital vertebral anomalies are a heterogeneous group of diagnoses, and studies on their epidemiology are sparse. Our aim was to investigate the national prevalence and mortality of these anomalies, and to identify associated anomalies. Methods: We conducted a population-based nationwide register study and identified all cases with congenital vertebral anomalies in the Finnish Register of Congenital Malformations from 1997 to 2016 including live births, stillbirths, and elective terminations of pregnancy because of major fetal anomalies. Cases were categorized based on the recorded diagnoses, associated major anomalies were analyzed, and prevalence and infant mortality were calculated. Results: We identified 255 cases of congenital vertebral anomalies. Of these, 92 (36%) were diagnosed with formation defects, 18 (7.1%) with segmentation defects, and 145 (57%) had mixed vertebral anomalies. Live birth prevalence was 1.89 per 10,000, and total prevalence was 2.20/10,000, with a significantly increasing trend over time (P < 0.001). Overall infant mortality was 8.2% (18/219); 3.5% (3/86) in patients with formation defects, 5.6% (1/18) in segmentation defects, and 12.2% (14/115) in mixed vertebral anomalies (P = 0.06). Co-occurring anomalies and syndromes were associated with increased mortality, P = 0.006. Majority of the cases (82%) were associated with other major anomalies affecting most often the heart, limbs, and digestive system. Conclusions: In conclusion, the prevalence of congenital vertebral anomalies is increasing significantly in Finnish registers. Detailed and systematic examination is warranted in this patient population to identify underlying comorbidities as the majority of cases are associated with congenital major anomalies.Peer reviewe

Prevalence and risk factors of radial ray deficiencies: A population based case-control study

Peer reviewe

CO carbonylation and first evaluation as a P-gp tracer in rats

BACKGROUND: At present, several positron emission tomography (PET) tracers are in use for imaging P-glycoprotein (P-gp) function in man. At baseline, substrate tracers such as R-[(11)C]verapamil display low brain concentrations with a distribution volume of around 1. [(11)C]phenytoin is supposed to be a weaker P-gp substrate, which may lead to higher brain concentrations at baseline. This could facilitate assessment of P-gp function when P-gp is upregulated. The purpose of this study was to synthesize [(11)C]phenytoin and to characterize its properties as a P-gp tracer. METHODS: [(11)C]CO was used to synthesize [(11)C]phenytoin by rhodium-mediated carbonylation. Metabolism and, using PET, brain pharmacokinetics of [(11)C]phenytoin were studied in rats. Effects of P-gp function on [(11)C]phenytoin uptake were assessed using predosing with tariquidar. RESULTS: [(11)C]phenytoin was synthesized via [(11)C]CO in an overall decay-corrected yield of 22 ± 4%. At 45 min after administration, 19% and 83% of radioactivity represented intact [(11)C]phenytoin in the plasma and brain, respectively. Compared with baseline, tariquidar predosing resulted in a 45% increase in the cerebral distribution volume of [(11)C]phenytoin. CONCLUSIONS: Using [(11)C]CO, the radiosynthesis of [(11)C]phenytoin could be improved. [(11)C]phenytoin appeared to be a rather weak P-gp substrate

Genetic Risk Factors in Lupus Nephritis and IgA Nephropathy - No Support of an Overlap

Background: IgA nephropathy (IgAN) and nephritis in Systemic Lupus Erythematosus (SLE) are two common forms of glomerulonephritis in which genetic findings are of importance for disease development. We have recently reported an association of IgAN with variants of TGFB1. In several autoimmune diseases, particularly in SLE, IRF5, STAT4 genes and TRAF1-C5 locus have been shown to be important candidate genes. The aim of this study was to compare genetic variants from the TGFB1, IRF5, STAT4 genes and TRAF1-C5 locus with susceptibility to IgAN and lupus nephritis in two Swedish cohorts. Patients and Methods: We genotyped 13 single nucleotide polymorphisms (SNPs) in four genetic loci in 1252 DNA samples from patients with biopsy proven IgAN or with SLE (with and without nephritis) and healthy age-and sex-matched controls from the same population in Sweden. Results: Genotype and allelic frequencies for SNPs from selected genes did not differ significantly between lupus nephritis patients and SLE patients without nephritis. In addition, haplotype analysis for seven selected SNPs did not reveal a difference for the SLE patient groups with and without nephritis. Moreover, none of these SPNs showed a significant difference between IgAN patients and healthy controls. IRF5 and STAT4 variants remained significantly different between SLE cases and healthy controls. In addition, the data did not show an association of TRAF1-C5 polymorphism with susceptibility to SLE in this Swedish population. Conclusion: Our data do not support an overlap in genetic susceptibility between patients with IgAN or SLE and reveal no specific importance of SLE associated SNPs for the presence of lupus nephritis.Original Publication: Mai Tuyet Vuong, Iva Gunnarsson, Sigrid Lundberg, Elisabet Svenungsson, Lars Wramner, Anders Fernström, Ann-Christine Syvanen, Lieu Thi Do, Stefan H. Jacobson and Leonid Padyukov, Genetic Risk Factors in Lupus Nephritis and IgA Nephropathy - No Support of an Overlap, 2010, PLOS ONE, (5), 5. http://dx.doi.org/10.1371/journal.pone.0010559 Licensee: Public Library of Science (PLoS) http://www.plos.org/</p

Multicolour interphase cytogenetics: 24 chromosome probes, 6 colours, 4 layers

From the late 1980s onwards, the use of DNA probes to visualise sequences on individual chromosomes (fluorescent in-situ hybridisation - FISH) revolutionised the study of cytogenetics. Following single colour experiments, more fluorochromes were added, culminating in a 24 colour assay that could distinguish all human chromosomes. Interphase cytogenetics (the detection of chromosome copy number in interphase nuclei) soon followed, however 24 colour experiments are hampered for this application as mixing fluorochromes to produce secondary colours produces images that are not easily distinguishable from overlapping signals. This study reports the development and use of a novel protocol, new fast hybridising FISH probes, and a bespoke image capture system for the assessment of chromosome copy number in interphase nuclei. The multicolour probe sets can be used individually or in sequential hybridisation layers to assess ploidy of all 24 human chromosomes in the same nucleus. Applications of this technique are in the investigation of chromosome copy number and the assessment of nuclear organisation for a range of different cell types including human sperm, cancer cells and preimplantation embryos

Gelatine matrix with human thrombin decreases blood loss in adolescents undergoing posterior spinal fusion for idiopathic scoliosis A MULTICENTRE, RANDOMISED CLINICAL TRIAL

Aims In a multicentre, randomised study of adolescents undergoing posterior spinal fusion for idiopathic scoliosis, we investigated the effect of adding gelatine matrix with human thrombin to the standard surgical methods of controlling blood loss. Patients and Methods Patients in the intervention group (n = 30) were randomised to receive a minimum of two and a maximum of four units of gelatine matrix with thrombin in addition to conventional surgical methods of achieving haemostasis. Only conventional surgical methods were used in the control group (n = 30). We measured the intra-operative and total blood loss (intra-operative blood loss plus post-operative drain output). Results Each additional hour of operating time increased the intra-operative blood loss by 356.9 ml (p <0.001) and the total blood loss by 430.5 ml (p <0.001). Multiple linear regression analysis showed that the intervention significantly decreased the intra-operative (-171 ml, p = 0.025) and total blood loss (-177 ml, p = 0.027). The decrease in haemoglobin concentration from the day before the operation to the second post-operative day was significantly smaller in the intervention group (-6 g/I, p = 0.013) than in the control group. Conclusion The addition of gelatine matrix with human thrombin to conventional methods of achieving haemostasis reduces both the intra-operative blood loss and the decrease in haemoglobin concentration post-operatively in adolescents undergoing posterior spinal fusion for idiopathic scoliosis. Take home message: A randomised clinical trial showed that gelatine matrix with human thrombin decreases intra-operative blood loss by 30% when added to traditional surgical haemostatic methods in adolescents undergoing posterior spinal fusion for idiopathic scoliosis.Peer reviewe

Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells

$\textbf{BACKGROUND}$: The observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene expression underlies the development of many complex traits. In order to efficiently make a comprehensive assessment of the impact of non-coding genetic variation in immune related diseases we emulated the whole-exome sequencing paradigm and developed a custom capture panel for the known DNase I hypersensitive site (DHS) in immune cells - "Immunoseq". $\textbf{RESULTS}$: We performed Immunoseq in 30 healthy individuals where we had existing transcriptome data from T cells. We identified a large number of novel non-coding variants in these samples. Relying on allele specific expression measurements, we also showed that our selected capture regions are enriched for functional variants that have an impact on differential allelic gene expression. The results from a replication set with 180 samples confirmed our observations. $\textbf{CONCLUSIONS}$: We show that Immunoseq is a powerful approach to detect novel rare variants in regulatory regions. We also demonstrate that these novel variants have a potential functional role in immune cells.This work was supported by grants from the Canadian Institute of Health Research (CIHR), the UK Medical Research Council (G1100125), the Swedish Research Council (DO283001) and Knut and Alice Wallenberg Foundation (KAW). We also acknowledge the use of subjects from the Cambridge BioResource and the support of the Cambridge NIHR Biomedical Research Centre. AM was supported by the Fond de Recherche Santé Québec Doctoral training award. TP and CL holds a Canada Research Chair

Radioiodination of sulfhydryl-sensitive proteins

A new procedure is described for the radioiodination of proteins with sulfhydryl groups essential for their biological activity. Aniline is iodinated with 125I-labeled sodium iodide in the presence of chloramine-T, the product separated by solvent extraction, diazotized and coupled to protein.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22016/1/0000432.pd