(a) What do the numbers across the X axis correspond to? (b) Why are some of the

Question

(a) What do the numbers across the X axis correspond to?

(b) Why are some of these dots green?

(c) For a given disease (say Crohn’s disease), what does it mean that most dots aren’t green?

(d) Provide a hypothesis for why some diseases (like bipolar) have very few signficant associated loci.

(e) Compare and contrast the findings of associated genes for coronary artery disease, and Crohns disease.

(f) Which disease would you expect to have more variable symptoms than the other?

(g) Use the data shown to explain your reasoning.

(h) Compare the findings for rheumatoid arthritis and type 1 diabetes. Is there something unexpected in these findings?

(i) Use the internet to do a quick search on what causes symptoms for both of these conditions. Use what you find to develop and support a hypothesis for the unexpected pattern

Bipolar disorder 15 10 Coronary artery disease 15 15 10 Crohn's disease 15 10 Rheumatoid arthritis 15 10 Type 1 diabetes 15 10 Type 2 diabetes 15 10

Explanation / Answer

The figure/ Manhattan plot represents a data from a genome-wide association study (GWAS). All dots represent SNPs.

A. The numbers across the X-axis represent chromosome number.

B. Green dots are SNP variants strongly associated with the disease at particular chromosomal loci.

C. All the non-green dots are also SNPs in the genomic location but their association with the disease is very low or in other way, they are low confidence SNPs as compared to the green one. Thus they are not vary tightly linked with the investigated disease, such as Crohn’s disease.

D. For Bipolar disease the green dots associated with chromosomes are less and scattered, because for this disease the environment play very important role and there are several factors like social status or social interactions, body hormones. Because of that, even though there are few genetic links but that were not were strong as compared to other disease like coronary artery disease, etc.

E. The results for Crohn’s and coronary artery disease contrast. For Crohn’s, more than one genetic loci or variants are identified and theyare distributed over chromosomes such as 1, 2, 5, 6, 10 and 16. Their fore its an quantitative or polygenic trait with more than one QTL hot spot. In contrast, there was strong association of coronary artery disease with chromosome number 9, which shown very high confidence SNP variants at this chromosome at same loci.

F. The Crohn’s and bipolar disorder would like to have variable symptoms. For instance, Crohn’s disease is controlled by multiple loci, thusinvolves multiple genes. Thus their cumulative effect will results variable phenotypes/symptoms

H. The SNPs variation associated with both disease are common are highly significant residing at chromosome 1 and 6. Both rheumatoid arthritis (RA) and type-1-diabetes are strongly related and may be consequence from each other. At the same time one disease can promote the severity or occurrence of other.

I. There is a strong correlation between type 1 diabetes and rheumatoid arthritis. Both of them areautoimmune diseases. The immune system's kill the cartilage tissue located at the joints in rheumatoid arthritis. Type 1 diabetes targets the cells in the pancreas that produce insulin, a hormone that However, helps in case of type 1 diabetes they target the pancreatic cell causing reduced production of insulin. In more detail, type 1 diabetes is regulated by a PTPN22 as a susceptibility gene, which is likely to be control rheumatoid arthritis. Thus, there is a huge possibility that type 1 diabetes patient can develop another autoimmune disease rheumatoid arthritis.

Note . the overall answer represent the question no. G

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