Purpose: Few studies have systematically analyzed the structure and content of laboratory exome sequencing reports from the same patient.Methods: We merged 8 variants from patients into "normal"... Show morePurpose: Few studies have systematically analyzed the structure and content of laboratory exome sequencing reports from the same patient.Methods: We merged 8 variants from patients into "normal" exomes to create virtual patient-parent trios. We provided laboratories worldwide with the data and patient phenotype information (developmental delay, dysmorphic features, and cardiac hypertrophy). Laboratories analyzed the data and issued a diagnostic exome report. Reports were scored using a coding matrix developed from existing guidelines.Results: In total, 41 laboratories representing 17 countries issued reports. Reporting of quality control statistics and technical information was poor (46.3%). Although 75.6% of the reports clearly stated the classification of all reported variants, few reports listed extensive evidence supporting variant classification. Only 53.1% of laboratories that reported unsolicited or secondary findings gave advice regarding health-related follow-up and 20.5% gave advice regarding cascade testing for relatives. Of the 147 variants reported, 105 (71.4%) were classified in agreement with classifications based on American College of Medical Genetics and Genomics/Association for Molecular Pathology and Association for Clinical Genomic Science guidelines. Concordance was higher for known pathogenic variants (86.3%) than for novel unpublished variants (56.8%).Conclusion: The considerable variability identified in the components that laboratories included in their reports and their classification of variants suggests that existing guidelines are not being used consistently with significant implications for patient care. (C) 2022 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved. Show less
This thesis focusses on the further unravelling of one of the mechanisms involved in developing Parkinson's disease: the GBA1 gene, encoding the lysosomal enzyme GCase. Several questions are... Show moreThis thesis focusses on the further unravelling of one of the mechanisms involved in developing Parkinson's disease: the GBA1 gene, encoding the lysosomal enzyme GCase. Several questions are addressed: How prevalent are mutations in this gene in the Netherlands and does it affect disease onset (chapter 2 and 5)? What methodological challenges accompany the sequencing of this gene (chapter 3 and 4)? What biomarkers may be used in clinical trials targeting GCase (chapter 6)? And what are the effects of the novel GCase activator LTI-291, when first administered to healthy volunteers (chapter 7) and to GBA-PD patients (chapter 8)? Show less
The research described in this thesis aimed to evaluate several new diagnostic approaches to viral respiratory infections. In addition, relevant patient cohorts were specifically tested for... Show moreThe research described in this thesis aimed to evaluate several new diagnostic approaches to viral respiratory infections. In addition, relevant patient cohorts were specifically tested for rhinovirus, including subtyping, to increase our insight in the clinical implications of rhinovirus infections, the most prevalent respiratory pathogens. Show less
Objectives: Targeted therapies in the management of patients with lung cancer provide significantly better outcome compared to chemotherapy. Detection of the anaplastic lymphoma kinase (ALK) gene... Show moreObjectives: Targeted therapies in the management of patients with lung cancer provide significantly better outcome compared to chemotherapy. Detection of the anaplastic lymphoma kinase (ALK) gene rearrangement has great predictive value for treatment with small molecule tyrosine kinase inhibitor (crizotinib and alectinib commonly). Fluorescent in situ hybridisation (FISH) assay is a basic diagnostic test designed for detecting ALK gene rearrangements. Although being considered as gold standard method by IASLC's guideline, it is often regarded as difficult and error prone. Our aim was to examine a unique atypical ALK FISH pattern, revealed during a systematic large-scale monitoring, which carries the great risk of misinterpretation, hence may result in loss of patients eligible for targeted therapy.Materials and Methods: Tissue and cytology samples from nearly one thousand patients with advanced stage non-small cell lung cancer (NSCLC, n = 996) were routinely examined by ALK FISH and immunohistochemistry (Ventana ALK-D5F3-CDx assay). Anchored Multiplex PCR based Next Generation Sequencing (AMP-NGS) was used to detect fusion gene transcripts in ambiguous cases.Results: Fifty-nine (5,9%) of the cases were positive with ALK FISH test. Three cases showed atypical pattern with a significantly reduced sized red (3') signal and complete loss of green signals. Digital signal measurement confirmed this finding, showing consistent attenuation of 3' signals throughout the tumours. In all three cases AMP-NGS and ALK IHC verified the presence of a fusion gene and expressed oncoprotein, respectively.Conclusion: Approximately 5% of the 59 ALK positive cases exhibited atypical attenuated isolated 3' signal pattern. The immunohistochemistry and AMP-NGS examinations helped to clarify the presence of oncoprotein and the fusion gene, respectively. Our results emphasize the importance of extensive exploration of the genetic background of any unexpected FISH finding to avoid false diagnosis. This enables clinicians to indicate the adequate therapy with higher efficiency for patients suffering from NSCLC. Show less
Patients presenting with ovarian tumors may pose diagnostic challenges. Primary ovarian tumors should be distinguished from metastases to the ovaries from other primary tumors. Treatment choices... Show morePatients presenting with ovarian tumors may pose diagnostic challenges. Primary ovarian tumors should be distinguished from metastases to the ovaries from other primary tumors. Treatment choices and statements about prognosis are different for localised or metastatic disease. Diagnostic workup including imaging and histologic examination of tumors is not always successful in deciphering the origin of tumors.Therefore, additional characterisation of tumors at a molecular level might be helpful. Show less
Overwater, E.; Floor, K.; Beek, D. van; Boer, K. de; Dijk, T. van; Hilhorst-Hofstee, Y.; ... ; Maugeri, A. 2017
Duchenne muscular dystrophy (DMD) is a severe progressive muscle wasting disorder. DMD is caused by reading frame disrupting mutations in the DMD gene resulting is an absence of the dystrophin... Show moreDuchenne muscular dystrophy (DMD) is a severe progressive muscle wasting disorder. DMD is caused by reading frame disrupting mutations in the DMD gene resulting is an absence of the dystrophin protein. Dystrophin is an important muscle protein as it provide stability upon muscle fiber contraction. Currently there is no therapy for the majority of the DMD patients. As part of the standard of care patient receive symptomatic treatment e.g. corticosteroids, respiratory and cardiac support. Various therapeutic approached are currently under development. Most advanced therapeutic approach is aimed to restore dystrophin production by using antisense oligonucleotides (AON): exon skipping. This thesis focusses on delivery of AON to skeletal and cardiac muscle for DMD. With the help of phage display technology combined with next generation sequencing analyses, muscle homing peptides have been identified. In this thesis is described how for the first time these homing peptides upon conjugation to a 2OMePS AON resulted in increased delivery and exon skipping in a mouse model for DMD. In Conclusion, muscle homing peptides have the potential to facilitate delivery of AONs and perhaps other compounds to skeletal and cardiac muscle. Show less
Hoogenboom, J.; Gaag, K.J. van der; Leeuw, R.H. de; Sijen, T.; Knijff, P. de; Laros, J.F.J. 2017
Analysis of the transcriptome, the total of all expressed RNA transcripts in a cell or an organism, contributes to our understanding of gene regulation during development and disease processes and... Show moreAnalysis of the transcriptome, the total of all expressed RNA transcripts in a cell or an organism, contributes to our understanding of gene regulation during development and disease processes and is therefore of great importance in the field of genomic research. This thesis focuses on the analysis of transcriptome complexity during infectious disease and cancer. The zebrafish was applied as an immunological model organism, due to the remarkable similarities of its immune system to that of human. The studies took advantage of novel opportunities for transcriptome profiling provided by recent developments in microarray and next generation sequencing technology that have made an enormous impact on biology. In addition to studying expression of protein coding genes, the work addressed regulatory functions of microRNAs, small non-coding RNAs playing important roles in the function of the immune system and other processes. The transcriptome data provide a valuable reference set of infection-responsive genes and microRNAs in zebrafish models and have identified microRNAs conserved between human and zebrafish liver cancer. These genomic data sets provide a strong basis for future applications of zebrafish as an infection and cancer model and contribute to the understanding of pathogenesis and the development of novel strategies for disease treatment. Show less
