Patrick Koske-McBride
Bioinformatics and Biotechnology Summer Institute
Academic Year 2005/2006
Proposal
Introduction:
The identification of genes and their phenotypes is a crucial first step towards studying the diseases they can cause. Wolfram syndrome, a very rare genetic disease, is caused by mutations at either two genes: one located on chromosome 4p or a gene on chromosome 4q. These are the WFS1 and WFS2 genes, respectively. The WFS1 gene has already been identified, but the WFS2 gene is still unidentified.
Prior researchers identified the WFS2 region to be between base pairs D451591 to D453240 including 53 candidate genes. The WFS2 gene is likely a single base-pair deletion or mutation found in a protein-coding region. Using this information, Dr. Shiang’s lab started sequencing all the known or predicted protein-coding genes in the region. Unfortunately, sequencing is not a cost or time effective method for a wide-search of genetic mutations. To save money and expedite the process, the lab recently made a switch to Single Strand Conformation Polymorphism analysis to detect genetic mutations before sequencing candidate genes. This is a simple, but highly sensitive mutation-detection method that uses polyacrylamide gels to electrophorese denatured DNA strands, which show up as bands on a gel. Using this method to screen gene exons to find was the ultimate goal of the summer’s work.
Progress This Summer:
Unfortunately, we have failed to identify the WFS2 gene this summer. However, we have screened 11 of the candidate genes, adding to the 19 previously sequenced and characterized. This leaves a total of 23 genes left to be screened.
Goals for the School Year:
The primary goal of the academic year is to continue to assist Dr. Shiang’s lab from afar by continuing PCR and SSCP analysis on candidate genes. I will coordinate with the Shiang lab to insure that the same work is not being repeated, and to report genes exhibiting band differences. Should continued SSCP analysis fail to detect the mutation, I will attempt to detect expression changes of the candidate genes using Reverse Transcriptase PCR (RT-PCR).
In addition, I will continue research on genetic diseases with my home mentor
Plan for the Academic Year:
Experiments:
I will continue SSCP analysis of the remaining candidate genes. I may also attempt to detect expression changes through RT-PCR. This method will show if there are changes in genes between affected versus unaffected individuals transcription in any of the candidate genes.[1] This process is financially and technically feasible for any lab with PCR capabilities.[2]
Courses:
Although there are relatively few
courses in genetics at
[1] Dharmaraj,
[2] Shiang, Rita, PhD.
Professional conversation,