Johan T den Dunnen

Johan T den Dunnen

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Johan T den Dunnen

Publications by authors named "Johan T den Dunnen"

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Phenotype predictions for exon deletions/duplications: A user guide for professionals and clinicians using Becker and Duchenne muscular dystrophy as examples.

Hum Mutat 2019 10 29;40(10):1630-1633. Epub 2019 Jul 29.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1002/humu.23850DOI Listing
October 2019

Templated Insertions: A Smoking Gun for Polymerase Theta-Mediated End Joining.

Trends Genet 2019 Sep 8;35(9):632-644. Epub 2019 Jul 8.

Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2019.06.001DOI Listing
September 2019

Recommendations for a nomenclature system for reporting methylation aberrations in imprinted domains.

Epigenetics 2018 25;13(2):117-121. Epub 2018 Jan 25.

i Applied Human Molecular Genetics, Kennedy Centre, Copenhagen University Hospital, Rigshospitalet , Glostrup , Denmark.

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http://dx.doi.org/10.1080/15592294.2016.1264561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5873357PMC
December 2018

Short hypervariable microhaplotypes: A novel set of very short high discriminating power loci without stutter artefacts.

Forensic Sci Int Genet 2018 07 22;35:169-175. Epub 2018 May 22.

Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333, ZC, Leiden, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.fsigen.2018.05.008DOI Listing
July 2018

Yet another database?

Hum Mutat 2018 06;39(6):755

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http://dx.doi.org/10.1002/humu.23429DOI Listing
June 2018

Describing Sequence Variants Using HGVS Nomenclature.

Methods Mol Biol 2017 ;1492:243-251

Department of Human Genetics, Leiden University Medical Center, 9600, 2300RC, Leiden, The Netherlands.

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http://dx.doi.org/10.1007/978-1-4939-6442-0_17DOI Listing
January 2018

Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing.

Hum Mutat 2017 07 29;38(7):870-879. Epub 2017 May 29.

Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.

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http://dx.doi.org/10.1002/humu.23223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5488171PMC
July 2017

The UCL low-density lipoprotein receptor gene variant database: pathogenicity update.

J Med Genet 2017 04 7;54(4):217-223. Epub 2016 Nov 7.

Centre for Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK.

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http://dx.doi.org/10.1136/jmedgenet-2016-104054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502305PMC
April 2017

In Silico Functional Meta-Analysis of 5,962 ABCA4 Variants in 3,928 Retinal Dystrophy Cases.

Hum Mutat 2017 04 3;38(4):400-408. Epub 2017 Feb 3.

Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1002/humu.23165DOI Listing
April 2017

Flexible and Scalable Full-Length CYP2D6 Long Amplicon PacBio Sequencing.

Hum Mutat 2017 03 18;38(3):310-316. Epub 2017 Jan 18.

Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, 2333ZA, The Netherlands.

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http://dx.doi.org/10.1002/humu.23166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324676PMC
March 2017

Hypomorphic MKS1 mutation in a Pakistani family with mild Joubert syndrome and atypical features: Expanding the phenotypic spectrum of MKS1-related ciliopathies.

Am J Med Genet A 2016 12 29;170(12):3289-3293. Epub 2016 Aug 29.

Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.

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http://dx.doi.org/10.1002/ajmg.a.37934DOI Listing
December 2016

Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer.

Curr Protoc Hum Genet 2016 07 1;90:7.13.1-7.13.19. Epub 2016 Jul 1.

Clinical Genetics & Human Genetics, Leiden University Medical Center, on behalf of the HGVS/HVP/HUGO Sequence Variant Description Working Group (SVD-WG), Leiden, The Netherlands.

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http://dx.doi.org/10.1002/cphg.2DOI Listing
July 2016

HGVS Nomenclature in Practice: An Example from the United Kingdom National External Quality Assessment Scheme.

Hum Mutat 2016 06 18;37(6):576-8. Epub 2016 Mar 18.

Department of Molecular Genetics, Medical Genetics, Polwarth Building, Aberdeen, UK.

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http://dx.doi.org/10.1002/humu.22978DOI Listing
June 2016

HGVS Recommendations for the Description of Sequence Variants: 2016 Update.

Hum Mutat 2016 06 25;37(6):564-9. Epub 2016 Mar 25.

Generade Centre of Expertise Genomics and University of Applied Sciences Leiden, Leiden, The Netherlands.

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http://dx.doi.org/10.1002/humu.22981DOI Listing
June 2016

The Complete Genome Sequence of the Murine Pathobiont Helicobacter typhlonius.

Front Microbiol 2015 8;6:1549. Epub 2016 Jan 8.

Leiden Genome Technology Center, Leiden University Medical CenterLeiden, Netherlands; Department of Human Genetics, Leiden University Medical CenterLeiden, Netherlands.

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http://dx.doi.org/10.3389/fmicb.2015.01549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705304PMC
January 2016

The Human Variome Project: ensuring the quality of DNA variant databases in inherited renal disease.

Pediatr Nephrol 2015 Nov 11;30(11):1893-901. Epub 2014 Nov 11.

Research Department of Genetics, Evolution and Environment, University College London, London, UK.

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http://dx.doi.org/10.1007/s00467-014-2994-1DOI Listing
November 2015

Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice.

Carcinogenesis 2015 Nov 29;36(11):1388-96. Epub 2015 Aug 29.

Laboratory of Microbiology, Wageningen University 6703 HB, Wageningen, The Netherlands, Department of Veterinary Biosciences, University of Helsinki 00014, Helsinki, Finland.

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http://carcin.oxfordjournals.org/content/early/2015/09/09/ca
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http://www.carcin.oxfordjournals.org/lookup/doi/10.1093/carc
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http://dx.doi.org/10.1093/carcin/bgv120DOI Listing
November 2015

SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing.

Nucleic Acids Res 2015 Jul 23;43(12):e80. Epub 2015 Mar 23.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499118PMC
July 2015

Next-generation diagnostics: gene panel, exome, or whole genome?

Hum Mutat 2015 Jun 17;36(6):648-55. Epub 2015 Apr 17.

Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1002/humu.22783DOI Listing
June 2015

Assessing the translational landscape of myogenic differentiation by ribosome profiling.

Nucleic Acids Res 2015 May 14;43(9):4408-28. Epub 2015 Apr 14.

Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands

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http://dx.doi.org/10.1093/nar/gkv281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482065PMC
May 2015

Selection and characterization of llama single domain antibodies against N-terminal huntingtin.

Neurol Sci 2015 Mar 8;36(3):429-34. Epub 2014 Oct 8.

Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.

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http://dx.doi.org/10.1007/s10072-014-1971-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341019PMC
March 2015

Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing.

Mol Ecol Resour 2015 Jan 17;15(1):8-16. Epub 2014 Jun 17.

Human and Clinical Genetics, Leiden Genome Technology Center, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands; Bioinformatics, University of Applied Sciences Leiden, Zernikedreef 11, 2333CK, Leiden, The Netherlands.

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http://dx.doi.org/10.1111/1755-0998.12288DOI Listing
January 2015

The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV.

BMC Genomics 2014 Oct 20;15:914. Epub 2014 Oct 20.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-15-914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210602PMC
October 2014

RNA sequencing: from tag-based profiling to resolving complete transcript structure.

Cell Mol Life Sci 2014 Sep 15;71(18):3537-51. Epub 2014 May 15.

Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.

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http://dx.doi.org/10.1007/s00018-014-1637-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143603PMC
September 2014

TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes.

Bioinformatics 2014 Jun 13;30(12):1651-9. Epub 2014 Feb 13.

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 NetherlandsDepartment of Human Genetic, Leiden Genome Technology Center, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands and Netherlands Bioinformatics Centre, Leiden, The Netherlands.

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http://bioinformatics.oxfordjournals.org/content/early/2014/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btu068DOI Listing
June 2014

Pathogenic: light or dark skin?

Hum Mutat 2014 May 7;35(5):520. Epub 2014 Apr 7.

Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://doi.wiley.com/10.1002/humu.22543
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http://dx.doi.org/10.1002/humu.22543DOI Listing
May 2014

A 3-base pair deletion, c.9711_9713del, in DMD results in intellectual disability without muscular dystrophy.

Eur J Hum Genet 2014 Apr 31;22(4):480-5. Epub 2013 Jul 31.

1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands [2] Institute of Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands [3] Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/ejhg.2013.169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953899PMC
April 2014

DMD transcript imbalance determines dystrophin levels.

FASEB J 2013 Dec 23;27(12):4909-16. Epub 2013 Aug 23.

1Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.

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http://dx.doi.org/10.1096/fj.13-232025DOI Listing
December 2013

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.

Nat Biotechnol 2013 Nov 15;31(11):1015-22. Epub 2013 Sep 15.

1] Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. [2] Netherlands Bioinformatics Centre, Leiden, The Netherlands.

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http://dx.doi.org/10.1038/nbt.2702DOI Listing
November 2013

Expanding the MTM1 mutational spectrum: novel variants including the first multi-exonic duplication and development of a locus-specific database.

Eur J Hum Genet 2013 May 12;21(5):540-9. Epub 2012 Sep 12.

Unidade de Investigação e Desenvolvimento, Departamento de Genética, Centro de Genética Médica Dr Jacinto Magalhães, Instituto Nacional de Saúde Dr Ricardo Jorge, IP, Porto, Portugal.

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http://www.nature.com/articles/ejhg2012201
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http://dx.doi.org/10.1038/ejhg.2012.201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641378PMC
May 2013

Transcriptional responses indicate attenuated oxidative stress in the springtail Folsomia candida exposed to mixtures of cadmium and phenanthrene.

Ecotoxicology 2013 May 13;22(4):619-31. Epub 2013 Mar 13.

Department of Ecological Science, VU University Amsterdam, De Boelelaan 1085, Amsterdam, 1081, HV, The Netherlands,

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http://dx.doi.org/10.1007/s10646-013-1053-1DOI Listing
May 2013

GPSM2 and Chudley-McCullough syndrome: a Dutch founder variant brought to North America.

Am J Med Genet A 2013 May 13;161A(5):973-6. Epub 2013 Mar 13.

Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://doi.wiley.com/10.1002/ajmg.a.35808
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http://dx.doi.org/10.1002/ajmg.a.35808DOI Listing
May 2013

Exome sequencing identifies a branch point variant in Aarskog-Scott syndrome.

Hum Mutat 2013 Mar 20;34(3):430-4. Epub 2012 Dec 20.

Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.

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http://dx.doi.org/10.1002/humu.22252DOI Listing
March 2013

Transposon proliferation in an asexual parasitoid.

Mol Ecol 2012 Aug 30;21(16):3898-906. Epub 2012 Apr 30.

Department of Human Genetics, Leiden University Medical Center S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands.

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http://www.researchgate.net/profile/Jacques_Alphen/publicati
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http://doi.wiley.com/10.1111/j.1365-294X.2012.5582.x
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http://dx.doi.org/10.1111/j.1365-294X.2012.5582.xDOI Listing
August 2012

Single molecule sequencing of free DNA from maternal plasma for noninvasive trisomy 21 detection.

Clin Chem 2012 Apr 25;58(4):699-706. Epub 2012 Jan 25.

Center for Human and Clinical Genetics, Laboratory for Diagnostic Genome Analysis, Leiden University Medical Center, Leiden, the Netherlands.

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http://dx.doi.org/10.1373/clinchem.2011.174698DOI Listing
April 2012

Curating gene variant databases (LSDBs): toward a universal standard.

Hum Mutat 2012 Feb 3;33(2):291-7. Epub 2011 Nov 3.

Human and Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands.

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http://dx.doi.org/10.1002/humu.21626DOI Listing
February 2012

Guidelines for establishing locus specific databases.

Hum Mutat 2012 Feb 9;33(2):298-305. Epub 2011 Dec 9.

Institute of Biomedical Technology, University of Tampere, Finland.

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http://dx.doi.org/10.1002/humu.21646DOI Listing
February 2012

Phage display screening without repetitious selection rounds.

Anal Biochem 2012 Feb 13;421(2):622-31. Epub 2011 Nov 13.

Center for Human and Clinical Genetics and Leiden Genome Technology Center, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.

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http://dx.doi.org/10.1016/j.ab.2011.11.005DOI Listing
February 2012

Reporting of Genetic Variants by Diagnostic Laboratories and other Centres.

Clin Biochem Rev 2012 Feb;33(1):21-4

Curator, International Society for Gastrointestinal Hereditary Tumours (InSiGHT), The Royal Melbourne Hospital, Parkville, Vic., Australia;

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284340PMC
February 2012

Fine-tiling array CGH to improve diagnostics for α- and β-thalassemia rearrangements.

Hum Mutat 2012 Jan 31;33(1):272-80. Epub 2011 Oct 31.

Hemoglobinopathies Laboratory, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1002/humu.21612DOI Listing
January 2012

Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA.

BMC Genomics 2012 Jan 18;13:28. Epub 2012 Jan 18.

Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC, Leiden, The Netherlands.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-13-28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3275489PMC
January 2012

A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form.

BMC Bioinformatics 2011 5;12 Suppl 4:S5. Epub 2011 Jul 5.

Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-S4-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194197PMC
December 2011

Literature-aided interpretation of gene expression data with the weighted global test.

Brief Bioinform 2011 Sep 22;12(5):518-29. Epub 2010 Dec 22.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1093/bib/bbq082DOI Listing
September 2011

Describing structural changes by extending HGVS sequence variation nomenclature.

Hum Mutat 2011 May 15;32(5):507-11. Epub 2011 Mar 15.

Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, Nederland.

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http://www.hgvs.org/mutnomen/PMID21309030_PTaschner_HM.pdf
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http://doi.wiley.com/10.1002/humu.21427
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http://dx.doi.org/10.1002/humu.21427DOI Listing
May 2011

LOVD v.2.0: the next generation in gene variant databases.

Hum Mutat 2011 May 22;32(5):557-63. Epub 2011 Feb 22.

Center of Human and Clinical Genetics, Department of Human Genetics, Leiden University Medical Center, Leiden, Nederland.

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http://dx.doi.org/10.1002/humu.21438DOI Listing
May 2011

Dual exon skipping in myostatin and dystrophin for Duchenne muscular dystrophy.

BMC Med Genomics 2011 Apr 20;4:36. Epub 2011 Apr 20.

Center for Human and Clinical Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, Leiden, 2300RC, the Netherlands.

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http://dx.doi.org/10.1186/1755-8794-4-36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107769PMC
April 2011

High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropod.

BMC Mol Biol 2011 Mar 1;12:11. Epub 2011 Mar 1.

VU University Amsterdam, Department of Ecological Science, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2199-12-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060125PMC
March 2011

The value of data.

Nat Genet 2011 Mar 29;43(4):281-3. Epub 2011 Mar 29.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://www.nature.com/doifinder/10.1038/ng0411-281
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http://dx.doi.org/10.1038/ng0411-281DOI Listing
March 2011

Experiences with array-based sequence capture; toward clinical applications.

Eur J Hum Genet 2011 Jan 24;19(1):50-5. Epub 2010 Nov 24.

Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://www.nature.com/articles/ejhg2010145
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http://dx.doi.org/10.1038/ejhg.2010.145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039511PMC
January 2011

New insights in gene-derived therapy: the example of Duchenne muscular dystrophy.

Ann N Y Acad Sci 2010 Dec 1;1214:199-212. Epub 2010 Dec 1.

Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.

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http://dx.doi.org/10.1111/j.1749-6632.2010.05836.xDOI Listing
December 2010

New methods for next generation sequencing based microRNA expression profiling.

BMC Genomics 2010 Dec 20;11:716. Epub 2010 Dec 20.

Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-11-716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022920PMC
December 2010