Researchers used a genome wide association study to investigate the effectiveness of paclitaxel treatment for women with ovarian cancer. Their goal was to identify novel genetic variants that might be used to inform chemotherapeutic treatment decisions for women with ovarian cancer. The Manhattan plot showing results of their research is provided below. What does the highest dot found above the number 1 indicate?
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Shown in the figure below is a Manhattan plot of a Genome-Wide Association (GWA) study of a certain disease. This study involved the genotyping of 500,000 Single Nucleotide Polymorphisms (SNPs) in 1000 patients and 3000 controls. Please explain in your own words and in simple terms, what does each point on the plot stand for and what is the meaning of the height of the peaks? How many SNPs were significantly associated with the disease? What is the standard criterion of significance for this kind of study and what reasoning led to the establishment of this particular criterion?
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An article in Nature Genetics ["Treatment-specific Changes in Gene Expression Discriminate in Vivo Drug Response in Human Leukemia Cells" (2003, Vol. $34(1),$ pp. $85-90$ ) ] studied gene expression as a function of treatments for leukemia. One group received a high dose of the drug, while the control group received no treatment. Expression data (measures of gene activity) from one gene are shown in Table $6 \mathrm{E} .1$. Construct a box plot for each group of patients. Write an interpretation to compare the information in these plots.
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