Imagine you are studying the genetic basis of gout using GWAS and have available molecular markers (single nucleotide polymorphism tags or SNP tags) located all over the genome. Your results are displayed below. -log, P-value 30 25 8 15 10- 5 ABCG2 I SLC2A9 ī Chromosome MYL2-CUX2 i O 11 12 13 14 15 16 17 18 19202122 a) From the plot above. Which chromosome/s would be the focus of your future studies in search of the genes that might be responsible for gout? Chromosome/s b) Briefly justify your choice/s for item a: I choose those chromosomes because c) You have made some assumptions to answer the previous item, please share them by filling in the blanks below: i) I am interpreting the results as: most of the patients that show gout symptoms also show allele/s for the SNP tag on chromosomes different alleles for the SNP tags on the other chromosomes. (the same/different) (please supply chormosome/s number/s as above), but an array of ii) My assumption about the relationship between gene distance (distance between the SNP tag and the candidate genes proposed as potential disease genes) and linkage disequilibrium (LD) is that the smaller the distance, the (higher/lower) the LD. iii) My assumption about the relationship between recombination rate and LD is that the higher the recombination rate, the (higher/lower) the LD.
Imagine you are studying the genetic basis of gout using GWAS and have available molecular markers (single nucleotide polymorphism tags or SNP tags) located all over the genome. Your results are displayed below. -log, P-value 30 25 8 15 10- 5 ABCG2 I SLC2A9 ī Chromosome MYL2-CUX2 i O 11 12 13 14 15 16 17 18 19202122 a) From the plot above. Which chromosome/s would be the focus of your future studies in search of the genes that might be responsible for gout? Chromosome/s b) Briefly justify your choice/s for item a: I choose those chromosomes because c) You have made some assumptions to answer the previous item, please share them by filling in the blanks below: i) I am interpreting the results as: most of the patients that show gout symptoms also show allele/s for the SNP tag on chromosomes different alleles for the SNP tags on the other chromosomes. (the same/different) (please supply chormosome/s number/s as above), but an array of ii) My assumption about the relationship between gene distance (distance between the SNP tag and the candidate genes proposed as potential disease genes) and linkage disequilibrium (LD) is that the smaller the distance, the (higher/lower) the LD. iii) My assumption about the relationship between recombination rate and LD is that the higher the recombination rate, the (higher/lower) the LD.
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Transcribed Image Text:Imagine you are studying the genetic basis of gout using GWAS and have available molecular markers (single nucleotide polymorphism tags or SNP tags) located all over the genome. Your results are displayed below.
**Graph/Diagram Explanation:**
The graph depicted is a Manhattan plot, a common visualization in Genome-Wide Association Studies (GWAS). It shows the -log10 p-values on the y-axis, which indicates the significance of associations, plotted against the chromosome number on the x-axis. Each dot represents a SNP, colored by chromosome.
Significant peaks that are above the horizontal line (often representing a significance threshold) indicate potential genetic associations with gout. Particularly notable peaks are labeled with gene names, such as:
- **ABCG2** on chromosome 4
- **SLC2A9** also on chromosome 4
- **MYL2-CUX2** on chromosome 11
a) From the plot above. Which chromosome/s would be the focus of your future studies in search of the genes that might be responsible for gout? Chromosome/s _______ .
b) Briefly justify your choice/s for item a: I choose those chromosomes because _______ .
c) You have made some assumptions to answer the previous item, please share them by filling in the blanks below:
i) I am interpreting the results as: most of the patients that show gout symptoms also show __________ (the same/different) allele/s for the SNP tag on chromosomes _______ (please supply chromosome/s number/s as above), but an array of different alleles for the SNP tags on the other chromosomes.
ii) My assumption about the relationship between gene distance (distance between the SNP tag and the candidate genes proposed as potential disease genes) and linkage disequilibrium (LD) is that the smaller the distance, the (higher/lower) _______ the LD.
iii) My assumption about the relationship between recombination rate and LD is that the higher the recombination rate, the (higher/lower) _______ the LD.
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