This bioinformatics bite is going to be a little but more clinically oriented:
A patient is presenting with excess blood clotting, which she thinks might be related to “something that runs in her family”. How do I find known diseases and genes (if any) that are associated with that phenotype?
A good place to start to look for information about symptoms and diseases that are related to genetics is MedGen. This database organizes information related to human medical genetics, like symptoms (clinical features), related genes, diseases, or genomic loci.
A perfectly reasonable approach would be to type “clotting” into the MedGen search box. Here’s what those results look like:
There are 94 results, the first of which is a clotting disorder, but one that is associated with too little clotting rather than too much clotting. If you scroll down, you see records that are not actually diseases:
To find out what type of record you’re looking at, look at the text after concept ID (blue boxes). The screen captures above show a Disease or Syndrome, a Finding, and a Pharmacologic substance. Notice that the diseases has links to other databases (green circle) and the others do not.
So how do we specify that we’re looking for a patient symptom related to a genetic disease? Like all the other NCBI databases, MedGen has field tags.
Here are some useful ones:
- Clinical Features: short stature[clinical features] – records for diseases that are associated with short stature
- Related Genes: LMNB1[gene] – diseases associated with this gene
- Disease name: achrondroplasia[title] – this disease
- Chromosome: 6[chromosome]- diseases associated with alterations to chromosome 6
Also, if you look back at the first screen shot, you can see a link that says “See MedGen results with clotting as a clinical feature (5)“. MedGen automatically sensed that clotting was a clinical feature, or symptom, and narrowed your results down for you.
Now we’ve narrowed the MedGen results to those that have clotting listed as a clinical feature. If you read the description, you see that Factor V deficiency is the only one associated with excess clotting. The record also shows what gene is associated with this disorder (F5) and links to descriptions from other resources like GeneReviews and OMIM, as well as Professional guidelines and Recent clinical studies.
So how do you find out if this is in fact what your patient has? Find out next week!
-C. Tobin Magle, PhD, Biomedical Sciences Research Support Specialist