Deletions Project

Project Member

Tom Carpel

The goal of this quarter

A working computer program which will detect deletions resulting from Mendelian errors and identify regions of many deletions as danger areas. As a result, will enable researchers to identify regions of deletions in individuals (given their parents' genotypes are known) and populations.

The Schedule for the quarter

Week 4: Pick topic + setup wiki page
Week 5: Look and data + start working on data parsing
Week 6: Work on basic deletion detection
Week 7: Fix any issues + start looking to expand
Week 8: Complete expansion of deletions to include either sibling or cancer data
Week 9: Finish last minute touches + make presentation
May 30: Project Presentation!
Week 10: Update program, presentation, and write 2-page paper, and submit them by June 10th.

Project Description

The project will be written in C, and will take HapMap data as input and parse for family relations to find Mendelian errors to mark as possible deletions. If long regions of deletions are found, there was a deletion in that region, will return at what SNP the deletion started and where it ended. A possible extension to the project is calculating whether an error is likely due to a genotype error or is a true deletion/Mendelian error. Paper summarizing the project is attached at the bottom (results section).

Related Papers

  • Estimation of genotype error rate using samples with pedigree information—an application on the GeneChip Mapping 10K array by K Hao, C Li, C Rosenow, W Hung Wong - Genomics, 2004
  • Mendelian error detection in complex pedigree using weighted constraint satisfaction techniques by S de Givry, I Palhiere, Z Vitezica, T Schiex - Proceedings of WCB05 Workshop on Constraint Based Methods for Bioinformatics, pp. 53 - 61, 2005
  • Detection and Integration of Genotyping Errors in Statistical Genetics by E Sobel, JC Papp, K Lange - The American Journal of Human Genetics, 2002
  • Identification and Analysis of Error Types in High-Throughput Genotyping by KR Ewen, M Bahlo, SA Treloar, DF Levinson, B Mowry … - The American Journal of Human Genetics, 2000

April 20 2008

Deletions Project started!

April 21-27 2008

  1. What I did this week: Picked a topic and set up the wiki page
  2. What I'll do next week: Begin examining the data that will be given to the program, and perhaps start working on data parsing.
  3. How what you did compared to what you planned to do: Perfectly :).
  4. What grade you think you deserve for your work on the project for the week: A+.

April 28 - May 4 2008

  1. What I did this week: Refined my topic and the goal of the quarter for the project. Examined the HapMap data output and family data relations, to see what data in needed for my program in what format. Thought about how to handle input. First devise the meat of the program's initial functionality - a function or set of functions to find Mendelian errors. Then figure out how to handle the input, then expand the program functionality.
  2. What I'll do next week: Work on code to identify Mendelian errors assuming I have family HapMap data in convenient format. Work on getting/parsing large HapMap data input.
  3. How what you did compared to what you planned to do: Overall advanced the project, especially in terms of it's theory. Didn't quite do exactly what I planned on, but made comparable progress on the project.
  4. What grade you think you deserve for your work on the project for the week: A (especially since we had the midterm to prepare for ;)).

May 5-11 2008

  1. What I did this week: Wrote and thoroughly tested a C function to identify Mendelian errors given the genotype of parents and child in 2-letter format (AC, GT, CC…).
  2. What I'll do next week: Work on parsing HapMap data.
  3. How what you did compared to what you planned to do: I made progress in the areas I thought I would. I didn't get the input processing done yet, but I didn't consider that debugging takes longer than coding, and that small mistakes are inevitable, so the small C function took longer than I'd figured.
  4. What grade you think you deserve for your work on the project for the week: A

May 12-18 2008

  1. What I did this week: Reevaluated how I was doing things and how I thought I was going to handle input. Will now work with 0, 1, 2 shorthand for genotype as we did in class. Rewrote the Mendelian error function to handle 0's, 1's, and 2's instead of letters. Came up with setup for reading in letter genotypes, translating them to 0, 1, or 2, and preserving what the translation was.
  2. What I'll do next week: Code the reading from file, translation, retention, etc.
  3. How what you did compared to what you planned to do: I had to do something other than what I planned on because I learned of a better way to do what I was doing. Thus I had to redo some previous work and didn't get to the work that was supposed to be done this week.
  4. What grade you think you deserve for your work on the project for the week: A (problem solving and critical-reevaluation is important)

May 19-25 2008

  1. What I did this week: Worked on reading in/parsing/translating, etc the data.
  2. What I'll do next week: Continue debugging this and finish the coding of it, as well as work on the presentation and present on May 30th.
  3. How what you did compared to what you planned to do: This would be what I planned to do this week, plus working on the presentation.
  4. What grade you think you deserve for your work on the project for the week: A

May 26-June 1 2008

  1. What I did this week: Worked on the presentation and presented on May 30. Continue working on the input processing, although less devoted to that this week because of the presentation.
  2. What I'll do next week: Finish all coding/debugging especially with relation to input processing. Also do test cases to see how well this lovely little program works. Also, upgrade the presentation and write the final 2-page paper and submit all final materials on the website.
  3. How what you did compared to what you planned to do: Compared very well. Gave a good presentation! (updated version posted below in results section).
  4. What grade you think you deserve for your work on the project for the week: A

June 2-June 8 2008

  1. What I did this week: Finished all coding/debugging. Specifically the cross-translating locations of trios in the SNP data. Tested the program - it works! Also, updated the presentation to reflect all recent work and wrote a summarizing paper on the project.
  2. What I'll do next week: Turn everything in when it's due and enjoy the summer :)
  3. How what you did compared to what you planned to do: Exactly what I planned on doing.
  4. What grade you think you deserve for your work on the project for the week: A

June 12 2008

  1. Project finally turned in.

Results

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