Curating Gene Variant Databases (LSDBs): Toward a Universal Standard

Human Mutation

Volumn 33, Issue 2, 2012, Pages 291-297

  Celli, Jacopo ^a   Dalgleish, Raymond ^b   Vihinen, Mauno ^c   Taschner, Peter E M ^a   den Dunnen, Johan T ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF LEICESTER   (United Kingdom)

^c Institute of Biomedical Technology   (Finland)

Author keywords

Curation; Database; Guidelines; Sequence variants

Indexed keywords

ARTICLE; DNA SEQUENCE; EXON; GENE EXPRESSION; GENETIC DATABASE; GENETIC VARIABILITY; GENOME; GENOMICS; GENOTYPE; HUMAN; LOCUS SPECIFIC DATABASE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; RNA SEQUENCE;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENES; GENETIC VARIATION; HUMANS; INTERNET; SOFTWARE;

EID: 84857772267     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.21626     Document Type: Article

References (26)

1. Amberger J, Bocchini C, Hamosh A. 2011. A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®). Hum Mutat 32:564-567.
2. Arnold S, Buchanan DD, Barker M, Jaskowski L, Walsh MD, Birney G, Woods MO, Hopper JL, Jenkins MA, Brown MA, Tavtigian SV, Goldgar DE, Young JP, Spurdle AB. 2009. Classifying MLH1 and MSH2 variants using bioinformatic prediction, splicing assays, segregation, and tumor characteristics. Hum Mutat 30:757-770.
3. B́eroud C, Hamroun D, Collod-B́eroud G, Boileau C, Soussi T, Claustres M. 2005. UMD (Universal Mutation Database): 2005 update. Hum Mutat 26:184-191.
4. Claustres M, Horaitis O, Vanevski M, Cotton RGH. 2002. Time for a unified system of mutation description and reporting:Areview of locus-specificmutation databases. Genome Res 12:680-688.
5. CottonRGH, HoraitisO2000. Quality control in the discovery, reporting, and recording of genomic variation. Hum Mutat 15: 16-21.
6. Cotton RGH, Auerbach AD, Brown AF, Carrera P, Christodoulou J, Claustres M, Compton J, Cox DW, De Baere E, den Dunnen JT, Greenblatt M, Fujiwara M, Hilbert P, Jani A, Lehvaslaiho H, Nebert DW, Verma I, Vihinen M, Members of the Human Genome Variation Society, Human Variome Project Diagnostic Laboratory Working Group. 2007. A structured simple form for ordering genetic tests is needed to ensure coupling of clinical detail (phenotype) withDNA variants (genotype) to ensure utility in publication and databases. Hum Mutat 28:931-932.
7. Dalgleish R, Flicek P, CunninghamF, Astashyn A, TullyRE, ProctorG, ChenY, McLaren WM, Larsson P, Vaughan BW, B́eroud C, Dobson G, Lehv̈aslaiho H, Taschner PEM, den Dunnen JT, Devereau A, Birney E, Brookes AJ, Maglott DR. 2010. Locus Reference Genomic sequences: An improved basis for describing human DNA variants. Genome Med 2:24.1-24.7.
8. den Dunnen JT, Antonarakis SE. 2000.Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat 15:7-12.
9. den Dunnen JT, Sijmons RH, Andersen PS, VihinenM, Beckmann JS, Rossetti S, Talbot Jr CC, Hardison RC, Povey S, Cotton RGH. 2009. Sharing data between LSDBs and central repositories. Hum Mutat 30:493-495.
10. Fokkema IFAC, den Dunnen JT, Taschner PEM. 2005. LOVD: easy creation of a locusspecific sequence variation database using an "LSDB-in-a-box" approach. Hum Mutat 26:63-68.
11. Fokkema IFAC, Taschner PEM, Schaafsma GCP, Celli J, Laros JFJ, den Dunnen JT. 2011. LOVD v.2.0: the next generation in gene variant databases. Hum Mutat 32:557-563.
12. Gout AM, ADPKD Gene Variant Consortium, Ravine D, Harris PC, Rossetti S, Peters D, Breuning M, Henske EP, Koizumi A, Inoue S, Shimizu Y, ThongnoppakhunW, Yenchitsomanus PT, Deltas C, Sandford R, Torra R, Turco AE, Jeffery S, FontesM, Somlo S, Furu LM, Smulders YM, Mercier B, FerecC, Burtey S, Pei Y, Kalaydjieva L, Bogdanova N, McCluskey M, Geon LJ, Wouters CH, Reiterova J, Stekrov́a J, San Millan JL, Aguiari G, Del Senno L. 2007. Analysis of published PKD1 gene sequence variants. Nat Genet 39:427-428.
13. Jordan DM, Kiezun A, Baxter SM, Agarwala V, Green RC, Murray MF, Pugh T, Lebo MS, Rehm HL, Funke BH, Sunyaev SR. 2011. Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy. Am J Hum Genet 88:183-192.
14. Kohonen-Corish MRJ, Macrae F, Genuardi M, Aretz S, Bapat B, Bernstein IT, Burn J, Cotton RGH, den Dunnen JT, Frebourg T, Greenblatt MS, Hofstra R, Holinski-Feder E, Lappalainen I, Lindblom A, Maglott D, Møller P, Morreau H, M̈oslein G, Sijmons R, Spurdle AB, Tavtigian S, Tops CMJ, Weber TK, deWind N, Woods MO. 2011. Deciphering the colon cancer genes-Report of the InSiGHT-Human Variome ProjectWorkshop, UNESCO, Paris 2010. Hum Mutat 32:491-494.
15. Kuipers R, van den Bergh T, Joosten H-J, Lekanne dit Deprez RH, Mannens MMAM, Schaap PJ. 2010. Novel tools for extraction and validation of disease-related mutations applied to Fabry Disease. Hum Mutat 31:1026-1032.
16. MitropoulouC, WebbAJ, MitropoulosK, Brookes AJ, PatrinosGP. 2010. Locus-specific database domain and data content analysis: Evolution and content maturation toward clinical use. Hum Mutat 31:1109-1116.
17. Murphy JA, Barrantes-Reynolds R, Kocherlakota R, Bond JP, Greenblatt MS. 2004. The CDKN2A database: integrating allelic variants with evolution, structure, function, and disease association. Hum Mutat 24:296-304.
18. Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA. 2009. BioPortal: Ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 37(Web Server issue):W170-173.
19. Povey S, Al Aqeel AI, Cambon-Thomsen A, Dalgleish R, den Dunnen JT, Firth HV, Greenblatt MS, Barash CI, Parker M, Patrinos GP, Savige J, SobridoM-J, Winship I, Cotton RGH, Ethics Committee of theHuman Genome Organization (HUGO). 2010. Practical guidelines addressing ethical issues pertaining to the curation of human locus-specific variation databases (LSDBs). Hum Mutat 31:1179-1184.
20. Pruitt KD, Tatusova T, Klimke W, Maglott DR. 2009. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 37:D32-D36.
21. Riikonen P., Vihinen M. 1999. MUTbase: Maintenance and analysis of distributed mutation databases. Bioinformatics 15:852-859.
22. 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.
23. Stenson PD, Mort M, Ball EV, Howells K, Phillips AD, ThomasNST, CooperDN. 2009. The Human Gene Mutation Database: 2008 update. Genome Med 1:13.1-13.6.
24. Tavtigian SV, Byrnes GB, Goldgar DE, Thomas A. 2008. Classification of rare missense substitutions, using risk surfaces, with genetic- and molecular-epidemiology applications. Hum Mutat 29:1342-1354.
25. VihinenM, den Dunnen JT, Dalgleish R, Cotton RGH. Guidelines for establishing locus specific databases. Hum Mutat (in press).
26. Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PEM. 2008. Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Hum Mutat 29:6-13.