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

  1. Ivo F. A. C. Fokkema‡,
  2. Peter E. M. Taschner‡,*,
  3. Gerard C. P. Schaafsma,
  4. J. Celli,
  5. Jeroen F. J. Laros,
  6. Johan T. den Dunnen

Article first published online: 22 FEB 2011

DOI: 10.1002/humu.21438

Issue

Human Mutation

Human Mutation

Special Issue: Bioinformatics for Human Genetics: Promises and Challenges, A Human Variome Project Special Issue

Volume 32, Issue 5, pages 557–563, May 2011

Additional Information

How to Cite

Fokkema, I. F. A. C., Taschner, P. E. M., Schaafsma, G. C. P., Celli, J., Laros, J. F. J. and den Dunnen, J. T. (2011), LOVD v.2.0: the next generation in gene variant databases. Hum. Mutat., 32: 557–563. doi: 10.1002/humu.21438

Author Information

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

  1. ‡

    Both authors contributed equally.

*Department of Human Genetics S-4-P, Center for Human and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300RC Leiden, Nederland

  1. †

    For the HVP Bioinformatics Special Issue

Publication History

  1. Issue published online: 21 APR 2011
  2. Article first published online: 22 FEB 2011
  3. Accepted manuscript online: 25 JAN 2011 02:56PM EST
  4. Manuscript Accepted: 14 DEC 2010
  5. Manuscript Received: 12 OCT 2010

Funded by

  • The European Community's Seventh Framework Programme. Grant Number: FP7/2007-2013 under grant agreement no. 200754—the GEN2PHEN project
  • Re-use of this article is permitted in accordance with the Terms and Conditions set out at [http://wileyonlinelibrary.com/author resources/onlineopen.html]

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References

  • Beales PL, Badano JL, Ross AJ, Ansley SJ, Hoskins BE, Kirsten B, Mein CA, Froguel P, Scambler PJ, Lewis RA, Lupski JR, Katsanis N. 2003. Genetic interaction of BBS1 mutations with alleles at other BBS loci can result in non-Mendelian Bardet-Biedl syndrome. Am J Hum Genet 72:1187–1199.
  • Béroud C, Collod-Béroud G, Boileau C, Soussi T, Junien C. 2000. UMD (universal mutation database): a generic software to build and analyze locus-specific databases. Hum Mut 15:86–94.
    Direct Link:
  • Claustres M, Horaitis O, Vanevski M, Cotton RGH. 2002. Time for a unified system of mutation description and reporting: a review of locus-specific mutation databases. Genome Res 12:680–688.
  • Cotton RG, Auerbach AD, Beckmann JS, Blumenfeld OO, Brookes AJ, Brown AF, Carrera P, Cox DW, Gottlieb B, Greenblatt MS, Hilbert P, Lehvaslaiho H, Liang P, Marsh S, Nebert DW, Povey S, Rossetti S, Scriver CR, Summar M, Tolan DR, Verma IC, Vihinen M, den Dunnen JT. 2008. Recommendations for locus-specific databases and their curation. Hum Mutat 29:2–5.
    Direct Link:
  • Den Dunnen JT, Antonarakis SE. 2000. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat 15:7–12.
    Direct Link:
  • Den Dunnen JT, Paalman MH. 2003. Standardizing mutation nomenclature: why bother? Hum Mutat 22:181–182.
    Direct Link:
  • Den Dunnen JT, Sijmons RH, Andersen PS, Vihinen M, Beckmann JS, Rossetti S, Talbot Jr CC, Hardison RC, Povey S, Cotton RG. 2009. Sharing data between LSDBs and central repositories. Hum Mutat 30:493–495.
    Direct Link:
  • Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SM. 2010. Ensembl's 10th year. Nucleic Acids Res 38:D557–D562.
  • Fokkema IF, den Dunnen JT, Taschner PE. 2005. LOVD: easy creation of a locus-specific sequence variation database using an “LSDB-in-a-Box” approach. Hum Mutat 26:63–68.
    Direct Link:
  • Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. 2005. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33:D514–D517.
  • Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12:996.
  • Riikonen P, Vihinen M. 1999. MUTbase: maintenance and analysis of distributed mutation databases. Bioinformatics 15:852–859.
  • Ring HZ, Kwok PY, Cotton RG. 2006. Human Variome Project: an international collaboration to catalogue human genetic variation. Pharmacogenomics 7:969–972.
  • Scriver CR. 2000. Guidelines and recommendations for content, structure, and deployment of mutation databases: II. Journey in progress. Hum Mutat 15:13–15.
    Direct Link:
  • Scriver CR, Nowacki PM, Lehväslaiho H. 1999. Guidelines and recommendations for content, structure, and deployment of mutation databases. Hum Mutat 13:344–350.
    Direct Link:
  • Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308–311.
  • Tarpey PS, Smith R, Pleasance E, Whibley A, Edkins S, Hardy C, O'Meara S, Latimer C, Dicks E, Menzies A, Stephens P, Blow M, Greenman C, Xue Y, Tyler-Smith C, Thompson D, Gray K, Andrews J, Barthorpe S, Buck G, Cole J, Dunmore R, Jones D, Maddison M, Mironenko T, Turner R, Turrell K, Varian J, West S, Widaa S, Wray P, Teague J, Butler A, Jenkinson A, Jia M, Richardson D, Shepherd R, Wooster R, Tejada MI, Martinez F, Carvill G, Goliath R, de Brouwer AP, van Bokhoven H, Van Esch H, Chelly J, Raynaud M, Ropers HH, Abidi FE, Srivastava AK, Cox J, Luo Y, Mallya U, Moon J, Parnau J, Mohammed S, Tolmie JL, Shoubridge C, Corbett M, Gardner A, Haan E, Rujirabanjerd S, Shaw M, Vandeleur L, Fullston T, Easton DF, Boyle J, Partington M, Hackett A, Field M, Skinner C, Stevenson RE, Bobrow M, Turner G, Schwartz CE, Gecz J, Raymond FL, Futreal PA, Stratton MR. 2009. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Nat Genet 41:535–543.
  • Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PE. 2008. Improving sequence variation descriptions in mutation databases and literature using the Mutalyzer mutation nomenclature checker. Hum Mutat 29:6–13.
    Direct Link:
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