Human Mutation Databases

Ourania Horaitis1, Richard G.H. Cotton2

1 Genomic Disorders Research Centre, St. Vincent's Hospital Melbourne Fitzroy, 2 The University of Melbourne, Melbourne
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 7.11
DOI:  10.1002/0471142905.hg0711s44
Online Posting Date:  February, 2005
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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.

     
 
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Table of Contents

  • Overview
  • Submission of Data to Mutation Databases
  • Accessing Data in Mutation Databases
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

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.
   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.
   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
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