(1) Stenson, P. D., Mort, M.,Ball, E. V., et al.: The Human Gene Mutation Database: 2008 update. Genome Med. 13, 1 (2009). (2) Johan, T. D., Stylianos, E. A.: ...
MUTation ANnotation Tool (MUTANT)
Uttapong Ruangrit1,2, Anunchai Assawamakin1, Chumpol Ngamphiw1, Bunyarit Uyyanonvara2, Sissades Tongsima1 1Biostatistics
and Informatics Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumtani, Thailand; 2Department of Information and Computer Technology, Sirindhorn International Institute of Technology (SIIT), Pathumtani, Thailand
Background: Scientists have long been interested in studying human mutations which were deposited in public databases or published in article journals. However, reported mutations (mutation nomenclature) do not comply with the standard suggested by Human Genome Variation Society (HGVS) [1]. Mutations from public databases could sometimes be ambiguous which leads to wrong interpretation and prediction of the results in clinical practice. This work attempts to construct a visualization tool, called MUTANT, to assist users annotate their mutations using a standard and unambiguous mutation nomenclature which has largely been accepted by human mutation communities [2]. Results: The MUTANT tool was implemented as a standalone software that can connect to the Internet to retrieve other related genomic information from ThaiMUT database [3]. To generate the mutation nomenclature, the gene sequences and others information including pseudogene information are retrieved from the online ThaiMUT database where users can locally store such information for future use. To facilitate the mutation annotation, MUTANT can graphically display the human genome gene structure (exon, intron, up/downstream regions, etc.) via querying of a target gene symbol. Once the target area is located, users can annotate the mutation by a simple point and click on the location as well as selecting the type of mutation, e.g., substitution, insertion, deletion and others. MUTANT can also display mutations through a popular web-visualizationinterface, named GBrowse [4] as well as offering the listing of annotated mutation results in both nucleotide and amino acid forms. Comparison among different ethnic specific databases can be also be done by using the extensible markup language (XML) exporting feature of MUTANT. Conclusions: The contribution of this work is three-fold. First, MUTANT assists scientists in correctly converting their mutation findings to standard nomenclature recommended by HGVS. The generated nomenclatures can be used in publication or can be used for submitting new mutation data to mutation databases. This work also promote the use of standard nomenclature to others human mutation community in order to improve the integrity and unambiguity of data stored in database. The software is available at http://www4a.biotec.or.th/GI/tools. References: (1) Stenson, P. D., Mort, M.,Ball, E. V., et al.: The Human Gene Mutation Database: 2008 update. Genome Med. 13, 1 (2009) (2) Johan, T. D., Stylianos, E. A.: Mutation Nomenclature Extensions and Suggestions to Describe Complex Mutations: A Discussion. Hum Mutat 15, 7-12 (2000) (3) Ruangrit U, Srikummool M, Assawamakin A, Ngamphiw C, Chuechote S, Thaiprasarnsup V, et al.: Thailand mutation and variation database (ThaiMUT). Hum Mutat 29, E68-75 (2008) (4) Stein, L.D., Mungall, C., Shu, S., et al.: The generic Genome Browser: A Building Block for a Model organism system Database. Genome Res. 12, 1599–1610 (2002)
