Johan T den Dunnen

Summary

Affiliation: Leiden University Medical Center
Country: The Netherlands

Publications

  1. ncbi Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion
    J T den Dunnen
    MGC Department of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands corrected
    Hum Mutat 15:7-12. 2000
  2. pmc Calling on a million minds for community annotation in WikiProteins
    Barend Mons
    Erasmus Medical Centre, Department of Medical Informatics, Rotterdam, The Netherlands
    Genome Biol 9:R89. 2008
  3. pmc High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropod
    Muriel E de Boer
    VU University Amsterdam, Department of Ecological Science, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
    BMC Mol Biol 12:11. 2011
  4. pmc Gene expression variation between mouse inbred strains
    Rolf Turk
    Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
    BMC Genomics 5:57. 2004
  5. pmc 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
  6. pmc Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease
    Rob Jelier
    Department of Medical Informatics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
    BMC Bioinformatics 9:291. 2008
  7. pmc 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
  8. ncbi Exome sequencing identifies a branch point variant in Aarskog-Scott syndrome
    Emmelien Aten
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Hum Mutat 34:430-4. 2013
  9. doi Fine-tiling array CGH to improve diagnostics for α- and β-thalassemia rearrangements
    Marion Phylipsen
    Hemoglobinopathies Laboratory, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Hum Mutat 33:272-80. 2012
  10. doi Leiden Open Variation Database of the MUTYH gene
    Astrid A Out
    Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Hum Mutat 31:1205-15. 2010

Detail Information

Publications44

  1. ncbi Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion
    J 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...
  2. pmc Calling on a million minds for community annotation in WikiProteins
    Barend 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...
  3. pmc High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropod
    Muriel 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...
  4. pmc Gene expression variation between mouse inbred strains
    Rolf 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...
  5. pmc 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...
  6. pmc Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease
    Rob Jelier
    Department of Medical Informatics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
    BMC Bioinformatics 9:291. 2008
    ....
  7. pmc 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...
  8. ncbi Exome sequencing identifies a branch point variant in Aarskog-Scott syndrome
    Emmelien Aten
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Hum Mutat 34:430-4. 2013
    ..Our results show that besides digging deeper to reveal nonobvious variants, isolation and analysis of RNA provides a valuable but under-appreciated tool to resolve cases with unknown genetic defects...
  9. doi Fine-tiling array CGH to improve diagnostics for α- and β-thalassemia rearrangements
    Marion Phylipsen
    Hemoglobinopathies Laboratory, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Hum Mutat 33:272-80. 2012
    ....
  10. doi Leiden Open Variation Database of the MUTYH gene
    Astrid 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...
  11. pmc Dual exon skipping in myostatin and dystrophin for Duchenne muscular dystrophy
    Dwi 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...
  12. doi GPSM2 and Chudley-McCullough syndrome: a Dutch founder variant brought to North America
    Rowida Almomani
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Am J Med Genet A 161:973-6. 2013
    ..Since the c.1473delG variant was found in Mennonite settlers, it likely originated in Europe. To support DNA diagnostics, we established an LOVD database for GPSM2 containing all variants thus far described...
  13. doi Accurate quantification of dystrophin mRNA and exon skipping levels in duchenne muscular dystrophy
    Pietro 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...
  14. doi Curating gene variant databases (LSDBs): toward a universal standard
    Jacopo 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...
  15. pmc mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance
    Peter 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...
  16. doi High-throughput genotyping of mannose-binding lectin variants using high-resolution DNA-melting analysis
    Rolf 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...
  17. doi Deep sequencing to reveal new variants in pooled DNA samples
    Astrid 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...
  18. pmc Targeting several CAG expansion diseases by a single antisense oligonucleotide
    Melvin M Evers
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    PLoS ONE 6:e24308. 2011
    ....
  19. doi LOVD v.2.0: the next generation in gene variant databases
    Ivo 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...
  20. pmc Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA
    Anastasios 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...
  21. doi Single molecule sequencing of free DNA from maternal plasma for noninvasive trisomy 21 detection
    Jessica 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...
  22. pmc The effects of low levels of dystrophin on mouse muscle function and pathology
    Maaike 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...
  23. pmc Experiences with array-based sequence capture; toward clinical applications
    Rowida 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...
  24. pmc Novel protein-protein interactions inferred from literature context
    Herman 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...
  25. pmc A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
    Jeroen 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...
  26. doi Autosomal recessive spinocerebellar ataxia 7 (SCAR7) is caused by variants in TPP1, the gene involved in classic late-infantile neuronal ceroid lipofuscinosis 2 disease (CLN2 disease)
    Yu Sun
    Center for Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
    Hum Mutat 34:706-13. 2013
    ....
  27. doi Mutation nomenclature
    Johan 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...
  28. pmc Cost-effective HRMA pre-sequence typing of clone libraries; application to phage display selection
    Barry 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...
  29. doi Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome
    Gijs W E Santen
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Nat Genet 44:379-80. 2012
    ....
  30. doi Keratosis Follicularis Spinulosa Decalvans is caused by mutations in MBTPS2
    Emmelien 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...
  31. doi Literature-aided interpretation of gene expression data with the weighted global test
    Rob 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...
  32. ncbi Theoretic applicability of antisense-mediated exon skipping for Duchenne muscular dystrophy mutations
    Annemieke 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...
  33. doi New insights in gene-derived therapy: the example of Duchenne muscular dystrophy
    Annemieke 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...
  34. ncbi TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes
    Seyed Yahya Anvar
    Department of Human Genetic, Leiden Genome Technology Center, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands and Netherlands Bioinformatics Centre, Leiden, The NetherlandsDepartment of Human Genetic, Leiden Genome Technology Center, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands and Netherlands Bioinformatics Centre, Leiden, The Netherlands
    Bioinformatics 30:1651-9. 2014
    ..Based on its design, requiring only two short flanking sequences, TSSV can work without the use of a complete reference sequence to reliably profile highly polymorphic, repetitive or uncharacterized regions...
  35. pmc Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2
    Richard 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...
  36. doi Sharing data between LSDBs and central repositories
    Johan 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...
  37. doi Describing structural changes by extending HGVS sequence variation nomenclature
    Peter 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...
  38. doi Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
    Peter A C 't Hoen
    1 Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands 2 Netherlands Bioinformatics Centre, Leiden, The Netherlands
    Nat Biotechnol 31:1015-22. 2013
    ..We provide a set of quality measures and guidelines for assessing technical biases in RNA-seq data. ..
  39. pmc Loss-of-function mutations in IGSF1 cause an X-linked syndrome of central hypothyroidism and testicular enlargement
    Yu Sun
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Nat Genet 44:1375-81. 2012
    ..Collectively, our observations delineate a new X-linked disorder in which loss-of-function mutations in IGSF1 cause central hypothyroidism, likely secondary to an associated impairment in pituitary TRH signaling...
  40. doi High-resolution melting analysis (HRMA): more than just sequence variant screening
    Rolf 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...
  41. doi Multiplex PCR for identifying DMD gene deletions
    Johan 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...
  42. pmc Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    Peter 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...
  43. doi Protein truncation test
    Rolf 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...
  44. doi The value of data
    Barend Mons
    Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Nat Genet 43:281-3. 2011
    ....