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Human Mutation Databases
Publication Name:
Current Protocols in Human Genetics
Unit Number:
Unit 7.11
DOI:
10.1002/0471142905.hg0711s44
Online Posting Date:
February, 2005
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.
Figures
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Figure 7.11.1 Proposed HUGO Mutation Database Initiative allele varient entry form for mutation databases. From http://www.hgvs.org/entry.html. -
Figure 7.11.2 Page from OMIM listing mutations in the phenylalanine hydroxylase (PAH) gene. -
Figure 7.11.3 Page from the Human Gene Mutation Database (HGMD) showing entries for the phenylalanine hydroxylase (PAH) gene by mutation type and phenotype. -
Figure 7.11.4 Page from the Human Gene Mutation Database (HGMD) listing nucleotide substitutions for the phenylalanine hydroxylase gene. -
Figure 7.11.5 Page from HGVbase showing first half of entry for an SNP in the phenylalanine hydroxylase (PAH) gene. See Figure -
Figure 7.11.6 Page from HGVbase showing second half of entry for an SNP in the phenylalanine hydroxylase (PAH) gene. See Figure -
Figure 7.11.7 Home page of PAHdb showing some available features. -
Figure 7.11.8 HGVS listing of LSDBs and other databases. The encouragement provided by the initiative that created this listing has resulted in over 80 LSDBs.
Videos
Literature Cited
| 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 | |
