Human Mutation Databases
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- 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.
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PDF or HTML at Wiley Online LibraryTable of Contents
- Overview
- Submission of Data to Mutation Databases
- Accessing Data in Mutation Databases
- Literature Cited
- Figures
- Tables
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Figure 1.10.1 Proposed HUGO Mutation Database Initiative allele varient entry form for mutation databases. From http://www.hgvs.org/entry.html. View Image -
Figure 1.10.2 Page from OMIM listing mutations in the phenylalanine hydroxylase ( PAH ) gene. View Image -
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. View Image -
Figure 1.10.4 Page from the Human Gene Mutation Database (HGMD) listing nucleotide substitutions for the phenylalanine hydroxylase gene. View Image -
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. View Image -
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. View Image -
Figure 1.10.7 Home page of PAHdb showing some available features. View Image -
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. View Image
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 |
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