Leiden Muscular Dystrophy pages^©

Help us - projects for students

(last modified February, 2007)

With the growing amount of data that are displayed on the Leiden Muscular Dystrophy pages, updating this information becomes an increasingly difficult and time-consuming task. There are many possibilities for trainees (students, stagiaires) of different types of background (biomedical, medical, journalism, bioinformatics) to assist us in this task and thereby to complete a practical training. Below some possibilities.

Disease genes - the disease gene pages contain information including;

• DNA:    gene structure (exon & inron / size & location), gene region, chromosome, genome

• RNA:    transcript (size, differential splicing, promoter(s), polyA-addition site(s)), expression

• protein:    size, characteristics, domains, homologies, folding, potential processing and interaction sites, function

• disease(s):    brief description, general findings in relation to pathogenic changed identified
  

• sequence conservation:    DNA, RNA and protein (multiple sequence alignments)

• diagnostics:    possibilities for diagnosis (methods, primers, markers, etc.)

In many cases this information needs updating to include the latest findings, insights and important links. In other cases this information is still missing totally (see LOVD databases hosted in Leiden).  Updates need to be retrieved from active searches, inlcuding database queries (e.g. using Blast in dbEST for transcript information or all genomes for multiple protein algnments). Similarly primer lists for diagnostics need to be checked and possilbe SNPs have to be marked. Cross-species comparisons need to be performed to determine where evolutionary conserved sequences reside, directing and complementing regions to be screend in patients.

To aid the conclusion "pathogenic or not" when a new change is found we want to display important and helpful information like multiple protein sequence alignments, splice site strength, etc.

The Leiden Muscular Dystrophy pages actively collaborate with the ISNO Dutch Neuromuscular Research Support Centre, e.g. by contributing a range of disease gene summary pages (see e.g. DMD). For most genes the content of these pages still needs to be completed. In addition we would like to offer Dutch translations of the information displayed.

DNA variation databases

The Leiden Muscular Dystrophy pages host many gene-specifc DNA variation databases. These databases need continuous attention to;

• check & update content
• literature searches for missing publications (to be added)
  
• check description (nomenclature) of variations in the database (using Mutalyzer)
• deduce & predict "pathogenic or not" - are all reports consistent
  
• write summary on collected information (for Disease gene page or to be published)

• set up using LOVD-based database
• generate reference sequences for residue numbering (DNA, RNA, protein)
• enter data, derived from publications and private data collections (requires good skills with spread sheet software)
  

LOVD database

LOVD, an "LSDB-in-a-Box", is a software tool to maintain a fully web-based gene-specific sequence variation database. LOVD has been written using open source software and is freely available for everybody to use. Currently, LOVD provides basic functionality only and there is a whole list of options to add, especially regarding automated data entry checking and display of the data (e.g. location of mutations, type of mutations, protein domains, multiple sequence alignments, etc.).

Interested, please contact us;

Dr. Johan T. den Dunnen
Center for Human and Clinical Genetics
Leiden University Medical Center
Wassenaarseweg 72
2333AL LEIDEN
Nederland
Tel.: +31 - 71 - 527 6105 / 6293
Fax.: +31 - 71 - 527 6075
E-mail: ddunnen @ LUMC.nl

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