In 2001, the Human Genome Project completed the sequencing of the entire human genome. A byproduct of this effort was the identification and mapping of more than 1,000 human disease genes. The large amounts of data generated by the Human Genome Project have been organized and made available to scientists and the general public via several databases. Online Mendelian Inheritance in Man (OMIM) is one example. OMIM is a catalog of human genes and genetic disorders developed for the World Wide Web by the National Center for Biotechnology Information (NCBI). The database contains information about the research history of the disease gene, inheritance patterns, a clinical synopsis of the disorder, and information about the molecular nature of the mutation or defect that leads to the disorder.
Activity
In this activity you will access the resources provided by the National Center for Biotechnology Information and research the details of a genetic disease using OMIM.
Part 1.
Under the section "Genetics and Medicine" choose "Genes and Disease."
Choose the section near the bottom titled Chromosome Map and read the introduction to chromosome mapping.
*What are the three main parts of a chromosome, as viewed under a microscope?
It will be handy to know these as you are looking at maps of chromosomes- these will be part of the “address” for each gene! The first one is the telomere which is the ends of the chromosome. The second one is the centromere which is the primary constriction of the chromosome, the centromere also divides the chromosome into a short arm (p) and a long arm (q). Then the chromatidwhich is a single molecule of DNA
Select the X chromosome from the list of chromosomes on the right side of the page and read the summary of the genes found on the X chromosome.
*List at least four human diseases that have been mapped to the X chromosome.
I was looking at chromosome 1 and it has UROD (Porphyria Cutanea Tarda) which is a group of acquired and familial disorders (passed on from generation to generation). Another disease is GBA (Gaucher Disease) which is an inherited disorder that affects many of the body's organs and tissues. Then there is GLC1A (Glaucoma), what this disease is technically when you are losing your eyesight. Then there is PS2 (Alzheimer Disease) this is when you lose your memory and you forget things that you have done. It happens when you get older.
Notice that this database has information about the DNA and proteins for many species (including platypus!).
Choose the latest build for human (homo sapiens) chromosomes.
Select the X chromosome.
At this point you will be looking at the most current map of the known DNA sequences on the human X chromosome! And yes, its complicated : )
You can browse through the map of the X chromosome if you wish, zooming in and out. You may find the “You are here:” diagram on the left side of the page to be handy (or not).
Perhaps an easier way to experience the map of the X chromosome is to do a search for one of the disease genes that you discovered earlier. Do that now using the search box above the chromosome map.
Once you get the results, click on the Map Element that looks most promising to you. This link will take you to a more detailed map of the X chromosome showing where the disease gene is located.
Click on one of the reference numbers for that gene to see if you can get some useful information about it (and there will be a lot of scientificnonsense, so keep digging or find a summary!)
*Read the summary section for that gene to find out what functions, processes, and components it is thought to be involved in (what’s it do?).
I was looking at the contig map and it shows the chromosomal placement of contigs that have been assembled at NCBI using finished and draft high-throughput genomic (HTG) sequence data. Any individual contig can be assembled from finished sequence (phase 3 HTG), draft sequence (phase 1 and 2 HTG), or a mixture of both.
Part 2.
Choose a topic from the menu at the left (Cancer, Immune System, Metabolism, and so on).
Read the introduction to the disease type you have chosen, thenchoose a specific disease to study.
Read the information about the disease you picked and use it to answer the following questions:
1-What disease did you choose and what gene is/genes are associated with this disease?
I chose to look at cancer. The genes that are associated with this disease is that the predominant mechanisms for the cancers featured here are (i) impairment of a DNA repair pathway (ii) the transformation of a normal gene into an oncogene and (iii) the malfunction of a tumor suppressor gene.
2-On what chromosome are these genes/is this gene located?
Well I had looked at the breast cancer article and where this cancer is located at is in the woman's breasts.
Use the link at the side of the disease page to go to the OMIM entry for the disease you chose.
*Read the text section and the clinical synopsis in the OMIM entry and answer the following questions:
When was the disease first reported in the scientific literature?
It does not say but probably a long time ago because people were smoking back in the days and they probably started to have problems with their respiratory system.
What are some of the clinical symptoms of this disease?
Some of the clinical symptoms are inhalation of toxic agents, accidents, and harmful lifestyles, such as smoking. Infections, genetic factors, and anything else that affects lung development, either directly or indirectly, can cause respiratory symptoms.
What lab findings (gene function or biochemical data) are associated with the disease?
The respiratory function involves gas exchange — the transfer of oxygen from the air into the blood and the removal of carbon dioxide from the blood. Non-respiratory lung functions are mechanical, biochemical, and physiological
What type of inheritance governs this disease?
It has to do more with the lifestyle that you live in. For example say that you smoke, then you will end up having this disease because it is messing with your lungs and then instead of being healthy lungs, they will look black and it will be harder to breath.
