Tutorial

NCBI supplies an integrated site that allows users to search for genomic data in a number of ways, ranging from BLAST searches to published FISH tags on each of the human chromosomes, to "browsing" individual chromosomes.  This tutorial exmines three gene families associated with disease ands is designed to give you experience with the vast quantity of information available.

The entry to this pathway can be found at

http://www.ncbi.nlm.nih.gov/genome/guide/human/
 

Open the site in a new window and first go to the interactive tour.  This page provides an overview of the types of information that are available.

I.  Click on

Is there something like Lmx1b in humans?
 

This link brings you to a combined BLAST/human chromosome view.
 

How many matches are there?
What chromosomes have similar sequences?
What is the difference between a paralogue and an orthologue? (see Nature article)

Click on Map element NT_004648

What is shown at this link?  What is shown when you click on the link for Blast Hit? Why is this type of information useful for the study of human disease?
 
 

II.      Go back to the interactive tour page and Click on
            What genes are at the 13q14 breakage hotspot?

What is the significanceof the 13q14 breakage hotspot?
 

Note there are several genome maps shown in the main window.  The map on the left shows a close up of the physical banding mapping in thge area of the region of interest.  The next maps are the Mitelman, Gene sequence, and Morbid maps.  Right click to open in a new window Human Maps Help link on the far left.

Describe the significance and differences between information provided by the Mitelman, Gene sequence, and Morbid maps.  Also describe the information provided for in the contig map.
 
 
 

Now examine the Mitelman map in the area of the 13q14.13 where there is a cluster of sites.  Move the mouse pointer over these sites.

What do all these sites have in common?
 
 

III.      Go back to the interactive tour page and  Click on

         Show me the ADAM family in the genome.

What is ADAM?

How many matches are found in the human genome?

Are there any linked to a human disease?  What is the disease?  What are the symptoms?
 
 

IV.  Go back the human genome home page at
 http://www.ncbi.nlm.nih.gov/genome/guide/human/

Type into the search, LocusLink, BRCA1

You will come up with several hits.  Scroll down to BRCA1.

What is this gene?
 

Open the link 17q21 in a new window.

What chromosome is this gene on?
 

Click on the link for BRCA1.

What are some of the proposed roles for the BRCA1 gene product?

Where in the cell would you expect to find the protein?
 

Scroll down to NCBI Reference Sequences (RefSeq).

What are these sequences?  Compare and contrast sequences 5 and 8.
 

Go back to the "hit" page.  To the right of BRCA1 you will find a series of lettered links.
What information is provided at these links? (just a quick scan will do - open in a new window so you don't lose the hit page.

P
O
R
G
P
H
U
V
 
 
 
 

Go back to the "hit" page and open the "O" link again.
 

Describe the diseases linked to this gene.
Any surprises for guys?
 
 
 
 

Read over the section on Genetic Counseling.

What individulas are advised to undergo the mutation test?

What is the proposed course of action for those found to be at risk?

What is the increased risk for breast cancer for women who carry the mutant gene?

Are  BRCA1 mutations the only risk factor described here?
 

Describe two of the variants that are found for the gene.
Do these variants necessarily correlate with increased risk to breast cancer?