Reference no: EM132266879

Exercise: Using public databases

For this assignment you will gather information about a human genetic disease from an online source. First you will go through this exercise using the example of Achondroplasia. Then you will gather information about a different disease selected from the list on p. 4. Turn in answers to questions 3-8 for the disease that you select.

There are many public databases that are excellent sources of information, and for data mining. This exercise will introduce you to one of these sites, called Online Mendelian Inheritance in Man (OMIM). There are also sites for other organisms that are supported by NCBI (National Center for Biotechnology Information). NCBI also maintains PubMed, a searchable database of biomedical publications.

1. Connect to the OMIM site.

2. Near the top of the page, type in achondroplasia in the Search box. Click on Search.

3. The next page should have a list of entries associated with achondroplasia. You may notice that among the first entries you will find a number preceded by "#", such as those shown below. This is a constantly updated database, so the first entries you may see may differ. Click on the first three of these entries. Has the mutated gene been identified? If so, what chromosome is it located on? How many loci are involved?

4. On the web page, click on the number #100800. You should see a new page entitled "ACHONDROPLASIA; ACH". As you read down the page, you will obtain information to answer the following questions.

a. What does the # sign indicate?

b. What gene is involved? (The name of the gene will be listed both as an abbreviation and as a number.)

c. What is the phenotype of affected individuals?

d. Is this a recessive or dominant condition?

e. What is known about homozygous individuals?

f. Are there any cognitive developmental effects?

g. What is the penetrance of the trait?

h. What did Weinberg (of Hardy-Weinberg fame) report about this condition and in what year did he report it?

5. After you have answered the questions above, go back to the top of the page and click on the chromosomal location (i.e., 4p16.3, under the word "location").

a. In the 5th row in this table is the information on "FGFR3, ACH". FGFR3 is the gene that when mutated causes Achondroplasia. Click on the number in the far left column. A highly detailed genetic map will appear. At the top is a drawing of chromosome 4; a small vertical red bar on the left side of this chromosome shows where the gene for Achondroplasia resides. Underneath this image is a series of maps presented as horizontal lines. Each presents information about this region that has been "annotated" on the assembled human genome. The location (in base pair) on the chromosome arm is indicated by numbers at the top.

b. Several alternative mRNAs from the FGFR3 gene are depicted. How are introns, exons, coding and noncoding portions of a message depicted?

c. Underneath these is a row of colorful bars. What do these represent?

d. A track depicting enrichment for H3K27Ac (a histone modification associated with regulatory regions) is next. Where is H3K27Ac most abundant?

e. Below this are several tracks depicting sequence conservation of homologous genes in other species. What parts of the gene that are most highly conserved?

f. Near the bottom of the page a track labeled "common SNPs" is presented as lines in various colors. What does "SNP" stand for? Click on this track to expand a list of genetic variants of FGFR3. What do the different colors indicate? The vast majority of SNPs are black. Why is this? How might you use this information if you had a patient with Achondroplasia?

6. Now go to the top of the page with the chromosome drawing. Click on the 10X "zoom in" button at the top of this page. Look carefully at the maps as you do this. What happens? And what happens if you keep clicking on the 10X button? How detailed is the information that you can obtain? What is the smallest unit of genetic information that can be identified here?

7. Now click several times on the 10X zoom out button. What happens to the vertical red line on the left side of the chromosome? What happens to the map information beneath the chromosome? How big can the "big picture" get?

8. Now click on one of the buttons to the right of word "move" (to the left of "zoom in"). What happens to the red box? How much detail can you see for genes that are to the left and to the right of the FGFR3 gene? How do you think that a website, such as OMIM, benefits researchers and clinicians?

Now research a different disease -

Generate a document that answers questions 3-8 from the example above using one of the congenital diseases or conditions from the list below. If the question is not applicable to the disease you choose, please note this in you answer.

1. Beta thalassemia

2. Sickle cell anemia / Hemoglobin C disease

3. Phenylketonuria (PKU)

4. Alkaptonuria

5. Albinism

6. Hunter's syndrome

7. Alpha thalassemia

8. Galactosemia

9. Tay Sach's disease

10. Trichothiodystrophy / Cockayne Syndrome / Xeroderma Pigmentosum complementation group D

11. Color blindness

12. Hemophilia

13. Duchenne / Becker muscular dystrophy

Attachment:- Assignment File.rar