CHROMOSOME 18 CLINICAL RESEARCH CENTER

Chromosome 18 Gene Dosage Annotation

The goal of the Chromosome 18 Clinical Research Center is to perform and facilitate clinical and basic research relating to chromosome 18 abnormalities, with a focus on the development of treatments and therapies.   In order to facilitate research at other institutions, we have created a set of genome annotation tracks on the UC Santa Cruz Genome Browser.  These tracks contain information about the genes on chromosome 18 and their potential role in generating an abnormal phenotype when present in a non-diploid copy number.  The Gene Dosage Track indicates the positions of specific genes and contains links to their gene dosage information.  The Phenotype Track indicates critical regions for specific phenotypic features for which the causative gene and pathogenic mechanism have not yet been identified.

Gene Dosage Track
Users can enter the genomic coordinates of a copy number variation (CNV) in order to visualize the genes in the region. The genes are color coded based on the likelihood of the gene to have a phenotypic effect when duplicated or deleted. By clicking on a specific gene, a “details page” will appear with additional information. Only information relating to the effects of gene dosage are described in this track, as there are numerous other resources (OMIM, PubMed etc.) for information on the biological role of the gene’s product and potential role in disease through mechanisms other than copy number changes.

As our understanding of the effects of CNV’s evolves, the gene dosage codes will be updated to reflect the latest knowledge.  For example, if a haplosufficient code is assigned based on a CNV in a control population and is then found to be a causative of an adult onset condition by a haploinsufficiency mechanism, the code will be changed from not dosage sensitive (green) to dosage sensitive (pink).

The gene dosage codes are as follows:

Green

This gene is unlikely to cause a phenotype when there is a copy number change.

Pink

This gene is dosage sensitive. There can be either high or low penetrance of the abnormal phenotype.  

Yellow

A copy number change in this gene ONLY results in a phenotype in the presence of a second event (eg. drug exposure or a second genetic change).

Red

This gene is thought to be haplolethal.

Grey

The consequences of a copy number change in this gene are unknown.

 

Phenotype Track
This custom track synthesizes and presents existing data linking a specific phenotype to a region of chromosome 18. The data here are from various datasets, including linkage studies and GWAS data as well as studies presenting molecularly defined critical regions for specific phenotypes. The Phenotype Track regions are color coded using the same scheme as used for the Gene Dosage Track.

Once the specific gene is identified for a phenotype, the data will be removed from this set of tracks.  If the molecular mechanism of the disease is either haploinsufficiency or supersufficiency, the information will be linked to the appropriate gene on the “Gene Dosage” tracks.  The Phenotype track will be regularly curated as new data become available.  As chromosome 18 is relatively gene-poor, we expect to be able to regularly update the track with the latest information.  This is in contrast to the OMIM phenotype data, which will identify a region and a phenotype with the first report and only update when the causative gene is identified.   Thus, we hope to provide a unique resource for the research community.  

 

Gene Dosage Map

Phenotype

Clinical Dosage Map

 

For additional information about:

  • The chromosome 18 conditions (18q-, 18p-, Ring 18, Tetrasomy 18p, Trisomy 18 etc.) go to The Chromosome 18 Registry & Research Society website at www.chromosome18.org
  • The biology of a gene of interest or links to other datasets with gene-specific information follow these steps.
  • When looking at either of our tracks, scroll down below the track image to the track controls.
  • Expand the “Genes and Gene Prediction Tracks” list
  • Click on “UCSC Genes” and open it in “pack” and click on any “refresh” button.
  • Click on your gene of interest and the UCSC Gene Details page will open with summary information and links to other databases.

 

We invite anyone with additional information that could improve this site to contact us. We do our best to keep abreast of the literature, but we also recognize that this is a large project.  We welcome your input!  Contact us at chromosome18@uthscsa.edu