(draft, final assignments will be provided by the respective instructor)
Assignment 1. NGS - Technologies and Design
(P. Park, Due: 3/7/11)
Write a research proposal for a study that utilizes NGS. Assume that you have a budget of 20K for basic biological experiments or 100K for clinical-oriented projects. Some suggested page lengths for each section is noted, but these are guidelines only. The main objective is for you to think hard about each step.
1. Start with a description of the problem of interest, including the hypothesis that you would like to test. [~1 page]
2. Find out what sequencing facilities are available to you and how much each type of sequencing will cost. (One example is http://pcpgm.partners.org/research-services/dna-sequencing/pricing). [~.5-1 page.]
3. Describe your experimental design in detail, including (i) type(s) of experiments you will do, (ii) how you will collect samples, (iii) what controls you will have, (iv) how many samples you will have and how deeply you will sequence each; and (v) what type of sequencing you will do, e.g., read length, SE vs PE. Please give reasons for the choices you made whenever possible. [~1-2 pages]
4. Discuss how the funds will be allocated and what you might do if additional funds might become available. [~.5 page]
5. Briefly describe the steps in preparing libraries for sequencing. [~.5 page]
6. Describe your plans for analysis, including (i) how you will verify the quality of the data, (ii) which aligners might be appropriate, and (iii) what software packages might be available for the analysis of your interest. [~1-2 pages]
Assignment 2. NGS – Data Analysis and Computation
(D. Wall, Due: 4/4/11)
Find an NGS data set, analyze the data, identify 10 mutations with known side-effects, and write a research report detailing each aspect of the analysis.
NGS data is freely available to the public through the 1000 Genomes website (http://www.1000genomes.org/) and GenomeQuest provides a valuable platform for NGS data analysis. These resources are only suggestions. You are free to use NGS data and analysis tools of your choice. The aim of the assignment is for you to apply the NGS data analysis strategies covered in the class lectures and practicum and thereby extract pertinent information from the enormous amount of data generated by NGS technologies.
Assignment 3. NGS – Applications and Implications
(P. Tonellato, Due: 5/2/11)
State a scientific hypothesis concerning a fundamental translational medicine question concerning the use of NGS in clinical application (e.g. arising from assignment 2). Develop an experimental design and data collection plan that will provide the data required to address the question and test your hypothesis. Review the literature relevant to the background and current scientific state of the question and hypothesis. Review any data sources that already exist that are relevant to the question. Write a research report (minimum ten pages) on the question, background, data collection design and methods relevant to the analysis of the data. Outline a program plan, timeline and milestones associated with the execution of your experimental design. Prepare a budget. The plan period should be no more than three years and the budget no more than $200,000/year. Obtain feedback on your proposal from an HMS faculty member. Write up the feedback and submit with the proposal.
1- "UNESCO-L’Oreal Morocco, Imane Allali received the first prize of the best PhD student"
2- "Sequencing Step Now 'Trivial' Part of Clinical Genomics Pipeline amid Analysis, Reimbursement Challenges"
3- Bioinformatics, Medical information and Translational Medicine,