GWAS Practice Quiz Answer Key

GWAS Practice Quiz Answer Key - BIOL14 Practice Quiz Name...

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Unformatted text preview: BIOL14 Practice Quiz Name_______________________ Design your own GWAS study of some type of cancer. Discuss your plans in a group of 2-­‐4, but you can each write your own individual answers to the questions. 1. What one type of cancer do you want to study? Any one type of cancer can be listed here. 2. Do you want to look for somatic mutations, or germ-­‐line genetic variation? Either approach can provide useful information. Choose one, and explain what you will learn from that approach. Somatic mutations: I want to learn what mutations occurred, and in what genes, in the cells that made them cancerous. I want to know what genetic differences are responsible for making the cancer cells misbehave. This will not give me information on inherited predispositions to cancer. Germline genetic variations: I want to learn what genes are involved in the inherited cancer risk for this type of cancer. This will not give me information about the genetica changes (somatic mutations) that make the cancer cells behave differently than normal cells. 3. What are your case and control groups? What individual people, and what cells from those people are in each group (cancer cells, normal cells, or both)? Explain how this approach will meet the goal (what you would want to learn) you stated above. Somatic mutations: Best design is to recruit people who have the cancer you are interested in, and take two types of cells from these people: their cancer cells will be the “case” group; their normal cells will be the “control” group. Ideally, you keep these samples (conceptually) paried, so that you compare each cancer genotype directly with the normal genotype of the seame person. This way, differences between case and control are the somatic mutations that occurred in development of the cancer. Germline genetic variation: Compare non-­‐cancer cells (more similar to germline, because fewer somatic mutations than cancer cells have) from two different groups of people: the case group is people who have developed that type of cancer. The control group is people of similar age and environment who have not developed that type of cancer. BIOL14 Practice Quiz Name_______________________ 4. What molecular assay will you choose to use, and why? Be sure to relate this to what sort of molecular differences you want to be able to observe. There are multiple possible correct answers. For example: -­‐ Microarray to genotype SNPs across the genome -­‐ Microarray to detect CNVs across the genome -­‐ Next generation DNA sequencing of “whole exome” is a good choice if you want to look for somatic mutations The following are not realistic to do for so many loci in so many samples: -­‐ Sequencing the whole entire genome is not (yet) realistic to do for so many individual samples. -­‐ Southern blot detection of RFLPs -­‐ PCR, digest and gel to detect RFLPs -­‐ Allele-­‐specific PCR to detect SNP alleles -­‐ Fluorescence in situ hybridization (FISH) ...
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