Julies Recitation 9 QA

Julies Recitation 9 QA - Recitation 9 Questions and...

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Recitation 9 Questions and Answers 1. How do you calculate a high negative log value? (Do we have to?) How does negative log value and low p value come into play? In a Manhattan plot, there are two lines, which one do we pay attention to? a. You don’t have to calculate high negative log value from GWAS data, but you should be able to read a Manhattan plot. b. c. For the GWAS “Manhattan plot”, pay attention to the top blue line, the line the arrow is pointing to in the figure above. Points above this line are SNPs that show significant association with the disease you are studying. The x-axis shows which chromosome the SNPs are found. The y-axis shows the −log10 P values of 100,000s of SNPs. In the graph above, the statistical cutoff point is -log 10 (7.5) which is about equal to 5x10 -8 . P values lower than 5x10 -8 show significant association. 2. What is DNA typing? What are variable number tandem repeats and how do they relate to DNA typing? What is a restriction fragment length polymorphism (RFLP)? i. Repetitive sequences: VNTRs & STRs
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1. 2. For this class, you only need to know short tandem repeats (STRs). ii. Copy number variations (CNVs) 1. 2. CNVs consist of variation in the number of copies of large segments of the genome, ranging in size from 1000 bp to many hundreds of kilobase pairs. 3. About 12% of the genome contains CNVs. 4. The CNVs in a person’s genome can be detected by PCR followed by gel electrophoresis or microarray. iii. Restriction Fragment Length Polymorphisms (RFLPs) 1. Restriction fragment length polymorphisms, or RFLPs, are differences among individuals in the lengths of DNA fragments cut by enzymes. Restriction enzymes are proteins that cut DNA at short, specific sequences called restriction sites. After a segment of DNA has been cut into pieces with restriction enzymes, researchers can examine the fragments using gel electrophoresis (and Southern blotting, as shown below). If two individuals have differences in their DNA sequences at particular restriction sites, then the restriction enzymes will cut their DNA into fragments of
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different lengths. There may also be differences in the number of DNA fragments observed among two or more individuals. RFLP analysis can be used as a form of genetic testing to observe whether an individual carries a mutant gene for a disease that runs in his or her family.
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