Research Topics
Genomes and Genes | Johan T den DunnenSummaryAffiliation: Leiden University Medical Center Country: The Netherlands Publications
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Publications
Mutation nomenclature extensions and suggestions to describe complex mutations: a discussionJ T den Dunnen
MGC Department of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands corrected
Hum Mutat 15:7-12. 2000..In this article, suggestions are presented for reporting just such complex mutations...
Calling on a million minds for community annotation in WikiProteinsBarend Mons
Erasmus Medical Centre, Department of Medical Informatics, Rotterdam, The Netherlands
Genome Biol 9:R89. 2008..We call on a 'million minds' to annotate a 'million concepts' and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org...- High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropodMuriel E de Boer
VU University Amsterdam, Department of Ecological Science, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
BMC Mol Biol 12:11. 2011..We investigated the affected molecular responses resulting from either treatment and developed and validated 44 qPCR assays for their responses using a high throughput nano-liter RT-qPCR platform for the analysis of the samples... - Gene expression variation between mouse inbred strainsRolf Turk
Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
BMC Genomics 5:57. 2004..In this study, we investigated the effect of genetic background on expression profiles. We analysed the transcriptome of mouse hindlimb muscle of five frequently used mouse inbred strains using spotted oligonucleotide microarrays... - Can subtle changes in gene expression be consistently detected with different microarray platforms?Paola Pedotti
Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
BMC Genomics 9:124. 2008..Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle... - Literature-aided meta-analysis of microarray data: a compendium study on muscle development and diseaseRob Jelier
Department of Medical Informatics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
BMC Bioinformatics 9:291. 2008.... - Therapeutic exon skipping for dysferlinopathies?Annemieke Aartsma-Rus
Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Eur J Hum Genet 18:889-94. 2010..We also show that DYSF exon skipping seems to be as straightforward as DMD exon skipping, as AONs to induce efficient skipping of four DYSF exons were readily identified... 
Fine-tiling array CGH to improve diagnostics for α- and β-thalassemia rearrangementsMarion Phylipsen
Hemoglobinopathies Laboratory, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Hum Mutat 33:272-80. 2012....- Dual exon skipping in myostatin and dystrophin for Duchenne muscular dystrophyDwi U Kemaladewi
Center for Human and Clinical Genetics, Leiden University Medical Center, Postzone S4 P, PO Box 9600, Leiden, 2300RC, The Netherlands
BMC Med Genomics 4:36. 2011..In this study, we aim to knockdown myostatin by means of exon skipping, a technique which has been successfully applied to reframe the genetic defect of dystrophin gene in DMD patients... - Leiden Open Variation Database of the MUTYH geneAstrid A Out
Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Hum Mutat 31:1205-15. 2010..This open-access repository allows all involved to quickly share all variants encountered and communicate potential consequences, which will be especially useful to classify variants of uncertain significance... - mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundancePeter A C 't Hoen
Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Nucleic Acids Res 39:556-66. 2011..In conclusion, control of stability and degradation emerge as important determinants for differential expression of mRNA transcripts and splice variants... - Accurate quantification of dystrophin mRNA and exon skipping levels in duchenne muscular dystrophyPietro Spitali
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
Lab Invest 90:1396-402. 2010..The use of the same technique allows comparison between different groups working on exon skipping in the mdx mouse model... - Curating gene variant databases (LSDBs): toward a universal standardJacopo Celli
Human and Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
Hum Mutat 33:291-7. 2012..Our overview is a first step toward establishing overall guidelines for database curation and ultimately covers one aspect of establishing quality-assured gene variant databases... - Deep sequencing to reveal new variants in pooled DNA samplesAstrid A Out
Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Hum Mutat 30:1703-12. 2009..We describe custom bioinformatics and statistics to optimize detection of rare variants and to estimate required sequencing depth. Our results provide directions for designing high-throughput analyses of candidate genes... - High-throughput genotyping of mannose-binding lectin variants using high-resolution DNA-melting analysisRolf H A M Vossen
Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
Hum Mutat 31:E1286-93. 2010..The present study thereby facilitates further clinical studies into the role of MBL in inflammatory and infectious disease... - Experiences with array-based sequence capture; toward clinical applicationsRowida Almomani
Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Eur J Hum Genet 19:50-5. 2011..Future arrays should contain probes from both DNA strands, and to obtain a more even coverage, one could add fewer probes from densely and more probes from sparsely covered regions... - Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNAAnastasios Mastrokolias
Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC, Leiden, The Netherlands
BMC Genomics 13:28. 2012..We have removed globin transcripts from 6 human whole blood RNA samples with a human globin reduction kit and compared them with the same non-reduced samples using deep Serial Analysis of Gene Expression... - The effects of low levels of dystrophin on mouse muscle function and pathologyMaaike van Putten
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
PLoS ONE 7:e31937. 2012..Based on these findings, we conclude that while even dystrophin levels below 15% can improve pathology and performance, levels of >20% are needed to fully protect muscle fibers from exercise-induced damage... - A formalized description of the standard human variant nomenclature in Extended Backus-Naur FormJeroen F J Laros
Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
BMC Bioinformatics 12:S5. 2011..Development of new tools is hampered by the complexity of the current nomenclature, which requires processing at the character level to recognize the specific syntactic constructs used in variant descriptions... - Targeting several CAG expansion diseases by a single antisense oligonucleotideMelvin M Evers
Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
PLoS ONE 6:e24308. 2011.... - LOVD v.2.0: the next generation in gene variant databasesIvo F A C Fokkema
Center of Human and Clinical Genetics, Department of Human Genetics, Leiden University Medical Center, Leiden, Nederland
Hum Mutat 32:557-63. 2011..To promote LSDB standardization and thereby database interoperability, we offer free server space and help to establish an LSDB on our Leiden server... - Novel protein-protein interactions inferred from literature contextHerman H H B M van Haagen
Biosemantics Association, Department of Human Genetics, Leiden University Medical Center, Leiden, and Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
PLoS ONE 4:e7894. 2009..Our framework can be used for prioritizing potential interaction partners, hitherto undiscovered, for follow-up studies and to aid the generation of accurate protein interaction maps... - Single molecule sequencing of free DNA from maternal plasma for noninvasive trisomy 21 detectionJessica M E van den Oever
Center for Human and Clinical Genetics, Laboratory for Diagnostic Genome Analysis, Leiden University Medical Center, Leiden, The Netherlands
Clin Chem 58:699-706. 2012..To eliminate this bias, and thereby experimental noise, we have used single molecule sequencing as an alternative method... - Literature-aided interpretation of gene expression data with the weighted global testRob Jelier
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
Brief Bioinform 12:518-29. 2011..Literature mining tools are therefore powerful additions to the toolbox for the interpretation of high-throughput genomics data... - New insights in gene-derived therapy: the example of Duchenne muscular dystrophyAnnemieke Aartsma-Rus
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
Ann N Y Acad Sci 1214:199-212. 2010..This review will explain the rationale and current state of affairs of these approaches and will then discuss how these gene-derived therapies might also be applicable to other diseases... - Mutation nomenclatureJohan T den Dunnen
Leiden University Medical Center, Leiden, The Netherlands
Curr Protoc Hum Genet . 2003..This unit summarizes these nomenclature recommendations, which stimulated a uniform and unequivocal description of sequence variants in literature... - Keratosis Follicularis Spinulosa Decalvans is caused by mutations in MBTPS2Emmelien Aten
Center of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Nederlands
Hum Mutat 31:1125-33. 2010..Other missense mutations in MBTPS2 have recently been identified in patients with IFAP syndrome. We postulate that both phenotypes are in the spectrum of one genetic disorder with a partially overlapping phenotype... - Theoretic applicability of antisense-mediated exon skipping for Duchenne muscular dystrophy mutationsAnnemieke Aartsma-Rus
Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Hum Mutat 30:293-9. 2009..Further research is needed to determine the functionality of different in-frame dystrophins and a number of hurdles has to be overcome before this approach can be applied clinically... - Cost-effective HRMA pre-sequence typing of clone libraries; application to phage display selectionBarry A Pepers
Center for Human and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
BMC Biotechnol 9:50. 2009..In the current study we show that high-resolution melt curve analysis (HRMA) is a simple, cost-saving tool to quickly study clonal variation without prior nucleotide sequence knowledge... - Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndromeGijs W E Santen
Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Nat Genet 44:379-80. 2012.... - Sharing data between LSDBs and central repositoriesJohan T den Dunnen
Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
Hum Mutat 30:493-5. 2009..The document has been circulated in the HGVS/LSDB community and was discussed extensively. Here we summarize these discussions and present the concluded recommendations for LSDB data sharing with central repositories... - Describing structural changes by extending HGVS sequence variation nomenclaturePeter E M Taschner
Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, Nederland
Hum Mutat 32:507-11. 2011..g., Mutalyzer, http://www.mutalyzer.nl/). We are extending the functionality of Mutalyzer to incorporate the latest version of the HGVS sequence variation nomenclature guidelines... - Protein truncation testRolf Vossen
Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Curr Protoc Hum Genet . 2004..The translation products are detected on immunoblots via chemiluminescence. An Alternate Protocol using coupled in vitro transcription/translation and radiolabeled proteins is also presented... - The value of dataBarend Mons
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
Nat Genet 43:281-3. 2011.... - Multiplex PCR for identifying DMD gene deletionsJohan T den Dunnen
Leiden University Medical Center, Leiden, The Netherlands
Curr Protoc Hum Genet . 2006..The Alternate Protocol is a modification of the Basic Protocol for radioactive detection of duplications in males and deletions in carrier females... - Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platformsPeter A C 't Hoen
The Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Nucleic Acids Res 36:e141. 2008..We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies... - High-resolution melting analysis (HRMA): more than just sequence variant screeningRolf H A M Vossen
Leiden Genome Technology Center LGTC, Human and Clincal Genetics, Leiden University Medical Center, Leiden, The Netherlands
Hum Mutat 30:860-6. 2009..Together, these diverse applications make HRMA a multipurpose technology and a standard tool that should be present in any laboratory studying nucleic acids... - Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2Richard J L F Lemmers
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
Nat Genet 44:1370-4. 2012..Our study identifies SMCHD1 as an epigenetic modifier of the D4Z4 metastable epiallele and as a causal genetic determinant of FSHD2 and possibly other human diseases subject to epigenetic regulation...