Course Requirements (Email firstname.lastname@example.org)
Problem Sets (20%)
Problem set 1. Out April 3. Due April 17.
Problem set 2. Out April 17. Due May 1.
Choose one of the following projects.
a. One page write up of association of how a SNP is linked with a particular trait. The format is the same as used at SNPedia.com. For example, see http://www.snpedia.com/index.php/Rs1800497. This should be a new SNP, not currently listed at DTC companies or on SNPedia. (Previous traits can be written with permission from Stuart Kim and your write up has to be significantly different than ones available on the web. )
b. First draft due on May 15, 2014. Instructors and TAs will provide comments on your write-up.
c. Write-ups will be published on SNPedia.com by the last day of class, May 22, 2014.
2. Special Project
In the past, some students have found a specific interest in some aspect of Personalized Medicine. This may come from your interest in some aspect of your own genetics, the ethics of genetic testing, or entrepreneurial possibilities in Personalized Medicine. You may come up with an individualized project for class credit by discussing your idea with one of the course directors. Past examples include:
a. A 5 page proposal was submitted to the Research Program for Genes, Environment and Health. One student working on schizophrenia for her PhD thesis wrote a proposal to RPGEH to request genotype/phenotype data from 110,000 patients of Kaiser Permanente in San Francisco. The goal was to perform a large GWAS on schizophrenia.
b. One student wrote a manuscript for the New England Journal of Medicine about his experience from what he learned from genetic testing.
Personalized Medicine Blog
Write a 750 word essay on one of the 10 reasons why the human genome matters in medicine. The essay counts as a class project (e.g. instead of a SNPedia write-up) or it can count as extra credit for the course (up to 10%). The essay is due April 11th.
Besides course credit, you can also enter your essay into a contest run by 23andme. The contest entry is also due April 11th. Everyone will receive a free t shirt for entering. Winners will get $100 Amazon gift card and a 23andme kit. Class will get $300 for a class social event.
Final Exam (40% credit) take home.
- Scenario is that you are an MD diagnosing a patient.
You will be given the genotypes of a hypothetical family. The final will have various scenarios.
You need to discuss how the genotype of the patient affects the diagnosis of the patient. You will use the tools from the class website to analyze the patient's genome, and provide informative feedback to the patient.
Extra credit. (10%)
a. You will be given the genotypes of 7 people (SK, KK, RT, NT, NZ, MPS, GC).
b. You will be told ancestry and specific traits for these 7 people.
c. You need to match the genotype with the person.
In the past, some students have taken this introductory class even though they are highly advanced in human genetics and bioinformatics. These students can do a more advanced project by consulting one of the course instructors. Students that undertake a super-project do not need to take the final exam. Possible super-projects topics include:
a. Annotate whole-genome sequence for Stuart Kim or Aaron Gitler (adopted).
b. Write a grant for Kaiser-Permanente GWAS (n=110,000 patients)
c. Analyze exome sequence data from ALS patients
d. Write an algorithm for choosing minimal n number of people to sequence to get all sequence data in a population