Drug sensitivity testing on patient-derived sarcoma cells predicts patient response to treatment and identifies c-Sarc inhibitors as active drugs for translocation sarcomas.

Background: Heterogeneity and low incidence comprise the biggest challenge in sarcoma diagnosis and treatment. Chemotherapy, although efficient for some sarcoma subtypes, generally results in poor clinical responses and is mostly recommended for advanced disease. Specific genomic aberrations have been identified in some sarcoma subtypes but few of them can be targeted with approved drugs.

Susceptibility to infections, without concomitant hyper-IgE, reported in 1976, is caused by hypomorphic mutation in the phosphoglucomutase 3 (PGM3) gene.

Phosphoglucomutase 3 (PGM3) is an enzyme converting N-acetyl-glucosamine-6-phosphate to N-acetyl-glucosamine-1-phosphate, a precursor important for glycosylation. Mutations in the PGM3 gene have recently been identified as the cause of novel primary immunodeficiency with a hyper-IgE like syndrome. Here we report the occurrence of a homozygous mutation in the PGM3 gene in a family with immunodeficient children, described already in 1976.

HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples.

In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomolecular analyses.

Diagnostics of primary immunodeficiency diseases: a sequencing capture approach.

Primary Immunodeficiencies (PID) are genetically inherited disorders characterized by defects of the immune system, leading to increased susceptibility to infection. Due to the variety of clinical symptoms and the complexity of current diagnostic procedures, accurate diagnosis of PID is often difficult in daily clinical practice. Thanks to the advent of "next generation" sequencing technologies and target enrichment methods, the development of multiplex diagnostic assays is now possible.

Hypomorphic homozygous mutations in phosphoglucomutase 3 (PGM3) impair immunity and increase serum IgE levels.

Background: Recurrent bacterial and fungal infections, eczema, and increased serum IgE levels characterize patients with the hyper-IgE syndrome (HIES). Known genetic causes for HIES are mutations in signal transducer and activator of transcription 3 (STAT3) and dedicator of cytokinesis 8 (DOCK8), which are involved in signal transduction pathways. However, glycosylation defects have not been described in patients with HIES.

PCM1 and schizophrenia: a replication study in the Northern Swedish population.

Previous studies implicated centrosomal dysfunction as a source of various neuropsychiatric disorders, including schizophrenia (SZ). Two recent reports [Gurling et al., 2006; Datta et al.

Support for NRG1 as a susceptibility factor for schizophrenia in a northern Swedish isolated population.

Context: Neuregulin 1 (NRG1), a growth factor involved in neurodevelopment, myelination, neurotransmitter receptor expression, and synaptic plasticity, first joined the list of candidate genes for schizophrenia when a 7-marker haplotype at the 5' end of the gene (Hap(ICE)) was shown to be associated with the disorder in the Icelandic population. Since then, more genetic and functional evidence has emerged, which supports a role for NRG1 in the development of schizophrenia.

Objective: To determine the contribution of NRG1 to susceptibility for schizophrenia in a northern Swedish isolated population.

Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing.

We evaluated multiplex PCR amplification as a front-end for high-throughput sequencing, to widen the applicability of massive parallel sequencers for the detailed analysis of complex genomes. Using multiplex PCR reactions, we sequenced the complete coding regions of seven genes implicated in peripheral neuropathies in 40 individuals on a GS-FLX genome sequencer (Roche). The resulting dataset showed highly specific and uniform amplification.

Detailed analysis of the serotonin transporter gene (SLC6A4) shows no association with bipolar disorder in the Northern Swedish population.

Through active reuptake of serotonin into presynaptic neurons, the serotonin transporter (5-HTT) plays an important role in regulating serotonin concentrations in the brain, and it is the site of binding for tricyclic antidepressants and selective serotonin reuptake inhibitors (SSRIs). Therefore it has been hypothesized that this transporter is involved in the etiology of bipolar (BP) disorder. Inconsistent association study results for the SLC6A4 gene encoding 5-HTT reported in literature emphasize the need for more systematic and detailed analyses of this candidate gene.

Gene expression analysis of estrogenic compounds in the liver of common carp (Cyprinus carpio) using a custom cDNA microarray.

Exposure to a variety of compounds with estrogenic activity has been shown to interfere with normal developmental and reproductive processes in various vertebrate species. The aim of this study was to determine the transcriptional profile of the natural estrogen, 17 beta-estradiol, and three synthetic estrogenic compounds (4-nonylphenol, bisphenol A, ethinylestradiol) in the liver of common carp, using a custom cDNA microarray. For that purpose, fish were aqueously exposed to three concentrations of each chemical for 24 or 96 h.

Use of suppression subtractive hybridization PCR for the development of cDNA arrays for the detection of endocrine disruption in carp (Cyprinus carpio).

The potential of a variety of xenobiotic compounds to modulate or disrupt the endocrine system of humans and wildlife is now widely recognized. In the present study, we developed a molecular tool for the evaluation of endocrine disruption in common carp (Cyprinus carpio). Suppression Subtractive Hybridization PCR was applied for the isolation of a relevant gene set, consisting of gender- and hormone-responsive gene fragments.

Effluent impact assessment using microarray-based analysis in common carp: a systems toxicology approach.

Effluents are a main source of direct and continuous input of pollutants to the aquatic environment, and can cause ecotoxicological effects at different levels of biological organization. Since gene expression responses represent the primary interaction site between environmental contaminants and biota, they provide essential clues to understand how chemical exposure can affect organismal health. The aim of the present study was to investigate the applicability of a microarray approach for unraveling modes of action of whole effluent toxicity and impact assessment.

Daphnia magna and ecotoxicogenomics: gene expression profiles of the anti-ecdysteroidal fungicide fenarimol using energy-, molting- and life stage-related cDNA libraries.

In the present study, the existing life stage-specific cDNA library was extended with energy- and molting-related genes using Suppression Subtractive Hybridization PCR and a microarray for the aquatic test organism Daphnia magna was created. A gene set of 2455 fragments was produced belonging to different pathways such as carbohydrate and lipid metabolism, O2 transport and heme metabolism, immune response, embryo development, cuticula metabolism and visual perception pathways. Using this custom microarray, gene expression profiles were generated from neonates exposed to three concentrations of the anti-ecdysteroidal fungicide fenarimol (0.

Patterns of gene expression in carp liver after exposure to a mixture of waterborne and dietary cadmium using a custom-made microarray.

Gene expression changes in carp liver tissue were studied after acute (3 and 24h) and subchronic (7 and 28 days) exposure to a mixture of waterborne (9, 105 and 480 microg/l) and dietary (9.5, 122 and 144 microg/g) cadmium, using a custom-made microarray. Suppression subtractive hybridization-PCR (SSH-PCR) was applied to isolate a set of 643 liver genes, involved in multiple biological pathways, such as energy metabolism (e.

Neuropharmaceuticals in the environment: mianserin-induced neuroendocrine disruption in zebrafish (Danio rerio) using cDNA microarrays.

Because of their environmental occurrence and high biological activity, human pharmaceuticals have received increasing attention from environmental and health agencies. A major bottleneck in their risk assessment is the lack of relevant and specific effect data. We developed an approach using gene expression analysis in quantifying adverse effects of neuroendocrine pharmaceuticals in the environment.

Expression profiling of endocrine-disrupting compounds using a customized Cyprinus carpio cDNA microarray.

Exposure to a variety of anthropogenic compounds has been shown to interfere with normal development, physiology, and reproduction in a wide range of organisms, both in laboratory studies and wildlife. We have developed a Cyprinus carpio cDNA microarray consisting of endocrine-related genes. In the current study, we investigated the applicability of this microarray (1) to study the molecular effects induced by exposure to a variety of endocrine-disrupting compounds (EDCs) in fish and (2) to discriminate the specific transcriptional profiles associated with these compounds.

Effects of the antidepressant mianserin in zebrafish: molecular markers of endocrine disruption.

Due to their environmental occurrence and intrinsic biological activity, human pharmaceuticals have received increasing attention from environmental and health agencies. Of particular, ecotoxicological concern are drugs that affect nervous- and endocrine-systems. Zebrafish genome-wide oligo arrays are used to collect mechanistic information on mianserin-induced changes in gene expression in zebrafish.

Molecular impact of propiconazole on Daphnia magna using a reproduction-related cDNA array.

We have developed a first version cDNA microarray of the cladoceran Daphnia magna. Through Suppression Subtractive Hybridisation PCR (SSH-PCR) 855 life stage-specific cDNAs were collected and used to document the toxicological mode of action of the pesticide propiconazole. DNA sequencing analysis revealed gene fragments related to important functional classes such as embryo development, energy metabolism, molting and cell cycle.