NCBI MedGen is a centralized resource that organizes information about medical genetics, focusing on conditions influenced by genetic factors. Researchers and clinicians can use MedGen to find details about genetic conditions, genes, and associated medical attributes. This guide demonstrates how to search for information related to the LCT gene as an example, providing step-by-step instructions for accessing and navigating MedGen. By the end, you’ll understand how to leverage MedGen for medical genetics research and integrate insights from other related NCBI resources, such as ClinVar and the 1000 Genomes Browser

NCBI Human Genetics

This guide shows a sample of the resources available in human genetics available from NCBI.

MedGen

NCBI MedGen

Organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution. (from website).

The MedGen website can be reached at http://www.ncbi.nlm.nih.gov/medgen/.

The example shown will find medical information about problems in the LCT gene.

NCBI provides an MedGen tutorial at http://www.ncbi.nlm.nih.gov/books/NBK159970/

Start by searching for LCT in MedGen:

The page returned shows various types of medical data:

By selecting the first entry, we see various literature about the clinical findings for LCT mutations:

The 2nd entry returns more detailed information about the gene, including the mode of inheritance, gene location, description of mutation, and other clinical information:

Looking further down the page, we see literature on therapy and diagnosis:

ClinVar

NCBI ClinVar

ClinVar aggregates information about genomic variation and its relationship to human health. (from NCBI website)

This resource can be accessed at http://www.ncbi.nlm.nih.gov/clinvar

NCBI has an Introduction to this resource at http://www.ncbi.nlm.nih.gov/clinvar/intro/

This example will step through looking for the same LRC variation that we looked at in the dbSNP guide – rs121908936.

Search for LCT and rs121908936:

Which returns more information on this allele:

1000 Genome

1000 Genome Browser

The 1000 Genome Browser is an interactive graphical viewer that allows users to explore variant calls, genotype calls and supporting evidence (such as aligned sequence reads) that have been produced by the 1000 Genomes Project. (from the NCBI web site).

It can be reached directly at http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/. As in most of these resources, there are many ways to find this tool. In the dbSNP Guide there is an example via the Variant ID.

NCBI has provided a tutorial on this tool at http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/help/

Once again this example will continue to use the LCT gene, using variation rs121908936.

From the 1000 Genome Browser page:

There are a few things to notice – At the top of the page there is indication of what genomic assembly was used for this data.  This is important because unlike literature databases, the data for bioinformatics is always changing.  Also, the default chromosome is 1.

Next we add the variation that we are interested in.  In this case it is rs121908936, a SNP that we found in the dbSNP example and click the arrow following the field:

We are now on Chromosome 2 in the Region of LCT, which confirms that we found the correct variation.

This display highlights the region of variation within the 1000 Genome project population.  It can be used to determine allele variation percentages within specific groups and across the whole data set.