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        Human Mutation Databases

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        1190
        • Abstract
        • Table of Contents
        • Figures
        • Literature Cited

        Abstract

         

        The first part of this unit compares general and locus?specific mutation databases. The second section deals with submitting data. The third part provides guidance for accessing mutation data. The final section offers advice on database construction.

             
         
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library

        Table of Contents

        • Overview
        • Submission of Data to Mutation Databases
        • Accessing Data in Mutation Databases
        • Literature Cited
        • Figures
        • Tables
             
         
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library

        Materials

         
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library

        Figures

        •   Figure 1.10.1 Proposed HUGO Mutation Database Initiative allele varient entry form for mutation databases. From http://www.hgvs.org/entry.html.
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        •   Figure 1.10.2 Page from OMIM listing mutations in the phenylalanine hydroxylase ( PAH ) gene.
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        •   Figure 1.10.3 Page from the Human Gene Mutation Database (HGMD) showing entries for the phenylalanine hydroxylase ( PAH ) gene by mutation type and phenotype.
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        •   Figure 1.10.4 Page from the Human Gene Mutation Database (HGMD) listing nucleotide substitutions for the phenylalanine hydroxylase gene.
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        •   Figure 1.10.5 Page from HGVbase showing first half of entry for an SNP in the phenylalanine hydroxylase ( PAH ) gene. See Figure for second half of entry.
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        •   Figure 1.10.6 Page from HGVbase showing second half of entry for an SNP in the phenylalanine hydroxylase ( PAH ) gene. See Figure for first half of entry.
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        •   Figure 1.10.7 Home page of PAHdb showing some available features.
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        •   Figure 1.10.8 HGVS listing of LSDBs and other databases. The encouragement provided by the initiative that created this listing has resulted in over 80 LSDBs.
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        Videos

        Literature Cited

           Antonarakis, S.E. and the Nomenclature Working Group. 1998. Recommendations for a nomenclature system for human gene mutations. Hum. Mutat. 11:1‐3.
           Beroud, C., Collod‐Beroud, G., Boileau, C., Soussi, T., and Junien, C. 2000. UMD (Universal Mutation Database): A generic software to build and analyze locus‐specific databases. Hum. Mutat. 15:86‐94.
           Brown, A. and McKie, M. 2000. MuStaR and other software for locus‐specific mutation databases. Hum. Mutat. 15:76‐85.
           Claustres, M., Horaitis, O., Vanevski, M., and Cotton, R.G.H. 2002. Time for a unified system of mutation description and reporting: A review of locus specific mutation databases. Genome Res. 12:680‐688.
           Cotton, R.G.H. and Horaitis, O. 2000. Quality control in the discovery, reporting, and recording of genomic variation. Hum. Mutat. 15:16‐21.
           Cotton, R.G. and Scriver, C.R. 1998. Proof of “disease causing” mutation. Hum. Mutat. 12:1‐3.
           den Dunnen, J.T. and Antonarakis, S.E. 2000. Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion. Hum. Mutat. 15:7‐12.
           den Dunnen, J.T. and Antonarakis, S.E. 2003. Mutation nomenclature. In Current Protocols in Human Genetics (N.C. Dracopoli, J.L. Haines, B.R. Korf, C.C. Morton, C.E. Seidman, J.G. Seidman, and D.R. Smith, eds.) pp. 7.13.1‐7.13.8. John Wiley & Sons, Hoboken, N.J.
           Fredman, D., Siegfried, M., Yuan, Y.P., Bork, P., Lehväslaiho, H., and Brookes, A.J. 2002. HGVbase: A human sequence variation database emphasizing data quality and a broad spectrum of data sources. Nucleic Acids Res. 30:387‐391.
           Hamosh, A., Scott, A.F., Amberger, J., Valle, D., and McKusick, V.A. 2000. Online Mendelian Inheritance In Man (OMIM). Hum. Mutat. 15:57‐61.
           Horaitis, O., Scriver, C.R., and Cotton, R.G.H. 2001. Locus‐Specific Mutation Databases. In The Metabolic and Molecular Bases of Inherited Disease, 8th ed. (C.R. Scriver, A.L. Beaudet, W.S. Sly, and D. Valle, eds.) Ch. 1, App. 1‐2. McGraw‐Hill, New York.
           Krawczak, M., Ball, E.V., Fenton, I., Stenson, P.D., Abeysinghe, S., Thomas, N., and Cooper, D.N. 2000. Human Gene Mutation Database: A biomedical information and research resource. Hum. Mutat. 15:45‐51.
           Patrinos, G.P., van Baal, S., Petersen, M.B. and Papadakis, M.N. 2005. Hellenic National Mutation Database: A prototype database for mutations leading to inherited disorders in the Hellenic population. Hum. Mutat. 25:327‐333.
           Riikonen, P. and Vihinen, M. 1999. MUTbase: Maintenance and analysis of distributed mutation databases. Bioinformatics 10:852‐859.
           Scriver, C.R., Nowacki, P.M., and Lehväslaiho, H. 1999. Guidelines and recommendations for content, structure, and deployment of mutation databases. Hum. Mutat. 13:344‐350.
           Scriver, C.R., Nowacki, P.M., and Lehväslaiho, H. 2000. Guidelines and recommendations for content, structure, and deployment of mutation databases. II. Journey in progress. Hum. Mutat. 15:13‐15.
           Scriver, C.R., Hurtubise, M., Konecki, D., Phommarinh, M., Prevost, L., Erlandsen, H., Stevens, R., Waters, P.J., Ryan, S., McDonald, D., and Sarkissian, C. 2003. PAHdb2002: What a locus‐specific knowledgebase can do. Hum. Mutat. In press.
           Sipila, K. and Aula, P. 2002. Database for the mutations of the Finnish disease heritage. Hum. Mutat. 19:16‐22.
           Teebi, A.S., Teebi, S.A., Porter, C.J., and Cuticchia, A.J. 2002. Arab genetic disease database (AGDDB): A population‐specific clinical and mutation database. Hum. Mutat. 19:615‐621.
        Internet Resources
           http://www.agddb.org
           AGDDB: Arab Genetic Disease Database
           http://www.bioc.aecom.yu.edu/bgmut/index.htm
           Blood Group Antigen Mutation Database
           http://www.ncbi.nlm.nih.gov/SNP/
           dbSNP: NCBI Single Nucleotide Polymorphism database
           http://www3.ncbi.nlm.nih.gov/omim/
           OMIM: Online Mendelian Inheritance in Man
           http://globin.cse.psu.edu/
           A Syllabus of Human Hemoglobin Variants and A Syllabus of Thalassemia Mutations
           http://archive.uwcm.ac.uk/uwcm/mg/hgmd0.html
           HGMD: Human Gene Mutation Database
           http://www.hgvs.org
           HGVS: Human Genome Variation Society
           http://hgvbase.cgb.ki.se/
           HGVbase: Human Genome Variation Database
           http://www.hgu.mrc.ac.uk/Softdata/Mustar/
           MuStar: Mutation Storage and Retrieval
           http://bioinf.uta.fi/mutdatbas.html
           MUTbase: Mutation Database
           http://www.pahdb.mcgill.ca/
           PAHdb: Phenylalanine Hydroxylase Locus Know ledgebase
           http://www.shox.uni‐hd.de/
           SHOX Mutation Database
           http://www.umd.necker.fr/
           UMD: Universal Mutation Database
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library
         
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