Cancer Genomics

Cancer Genomics

Project Member:

Olivera Grujic

Project Description from Slides:

Using allele and haplotype frequencies, compute how likely deletion or amplification samples are (if there is a deletion, long run of homozygous mutation can be observed).

Goal:

Create method to simulate the homozygous regions (implant deletions) and another method to find those homozygous regions that appear to be too long to be homozygous, and are therefore likely to be deleted regions. If this only happens on one SNP, it may be an error. Find performance and determine the false positive rate through simulations. Assume that SNPs are independent at first, and (if time allows) relax this assumption. Phase HapMap data and use haplotypes. Use Bonferoni correction to decide how long a region is too long to be homozygous.

Preliminary Schedule:

Week 4: Pick topic and setup wiki page.
Week 5: Download and get familiar with HapMap data. Research current work on this topic.
Week 6: Learn Python.
Week 7: Parse HapMap data.
Week 8: Create program that simulates deletions.
Week 9: Create program that outputs regions where deletions might have occured.
Week 10: Determine performance, possibly improve method. Presentation.
Week 11: Improve method. Project Report.

Weekly Log:

April 25, 2008:

What I did this week: Chose topic, set up this wiki page.
What I'll do next week: Download and get familiar with HapMap data. Research current work on this topic.
How what you did compared to what you planned to do: Good.
What grade you think you deserve for your work on the project for the week: A

May 2, 2008:

What I did this week: Downloaded and familiared myself with HapMap data. Discussed the project with Dr. Eskin and updated details on this wiki page.
What I'll do next week: Learn Python and (if time) start working on the program that parses HapMap data.
How what you did compared to what you planned to do: Good.
What grade you think you deserve for your work on the project for the week: A

May 9, 2008:

What I did this week: Learned Python.
What I'll do next week: Parse HapMap data.
How what you did compared to what you planned to do: Good.
What grade you think you deserve for your work on the project for the week: A-

May 16, 2008:

What I did this week: Parsed HapMap data.
What I'll do next week: Create program that simulates deletions.
How what you did compared to what you planned to do: Good.
What grade you think you deserve for your work on the project for the week: A-

May 23, 2008:

What I did this week: Created program that simulates deletions.
What I'll do next week: Create program that outputs regions where deletions might have occured.
How what you did compared to what you planned to do: Created deletion simulator, but realized it was simulating deletions at SNP regions, not haplotypes.
What grade you think you deserve for your work on the project for the week: I give myself an A as an encouragement

May 30, 2008:

What I did this week: Recreated and improved the program that simulates deletions. Discussed with Dr. Eskin statistics I need to use for program that outputs regions where deletions might have occurred.
What I'll do next week: Create program that outputs regions where deletions might have occured.
How what you did compared to what you planned to do: Good, I worked hard on this.
What grade you think you deserve for your work on the project for the week: A

June 6, 2008:

What I did this week: Created program that outputs regions where deletions might have occurred. Created project presentation and presented in class.
What I'll do next week: Improvements to the method and complete final paperwork that needs to be turned in by June 11.
How what you did compared to what you planned to do: Good, I spent a substantial amount of time on this.
What grade you think you deserve for your work on the project for the week: A

June 11, 2008:

Please see the attachments for Project Report, Project Presentation Slides, and Source Code!

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