Genetics

question 1: In a particular community in a country a genetically inherited disorder due to a single gene mutation was studied. The disease is due to an autosomal recessive mutation. The disease was mapped to a gene and it was found that within this community, there were frequent allelic variations. Four different alleles of this gene, each with a single nucleotide variant at position 501 within the protein-coding sequence, were found in the population. The allele frequencies are given below:

 

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Allele “T” at position 501: 30%

Allele “G” at position 501: 40%

Allele “C” at position 501: 20%

Allele “A” at position 501: 10%

 

Assuming Hardy-Weinberg equilibrium, what would be the expected frequencies of individuals who are:

  • Homozygous for the “G” allele?
  • Heterozygous for the “T” and the “C” alleles?
  • Heterozygous for the “G” and the “A” alleles?
  • Homozygous for the “A” allele?

 

Show rationale and your calculation.

Question 2: 250 healthy people and 700 people with a disease X were genotyped at two SNP loci (rs001 and rs002). The table below provides the data of genotyping.

SNP locus Genotypes Number of healthy (250) Number of people with the disease

(700)

rs001 GG 90 10
TT 40 567
GT 120 123
rs002 CC 99 318
GG 56 86
GC 95 296

 

Answer the following questions based on the data in the table above (must show your work):

Q2a: How many different alleles of rs001 are present in the healthy population and what are their frequencies?

 

Q2b: How many different alleles of rs001 are present in the diseased population and what are their frequencies?

 

Q2c: How many different alleles of rs002 are present in the healthy population and what are their frequencies?

 

Q2d: How many different alleles of rs002 are present in the diseased population and what are their frequencies?

 

Q2e: The haplotype rs001(G)-rs002(C) was found to be 70% among healthy individuals, and 25% among diseased individuals. All the remaining individuals had different haplotypes. What is the estimated Linkage Disequilibrium between these two alleles in the two populations (healthy versus diseased)?                                                                                              

 

Q2e: What is the allelic ratio in the diseased population for rs001?

 

Q2f: What is the allelic ratio in the normal population for rs002?    

 

Q2g: What is the allelic odds ratio for disease to normal at rs001?  

 

Q2h: What is the allelic odds ratio for disease to normal at rs002?

 

Q2i: The average life-time risk of the disease X for all people is 1/70.  Are people with one G allele at locus rs001 at higher or lower risk of developing this disease than the average risk? How much higher or lower?

 

 

Question 3:

Background: In a hypothetical island in the Pacific Ocean lives a tribe of approximately 500,000 people, with approximate sex ratio of 1:1. They have lived there in isolation for thousands of years, without contact with the external world. You, an explorer, found them for the first time and discovered that about 50 men or women in the island suffer from an incurable disease that manifests as a disorder at the age of approximately 20 years, in which the afflicted men or women suddenly begin to develop neurological symptoms, and die within a month or two. The disease affects males and females roughly equally. Since this disease affects post-pubertal men and women, some of them beget children, nearly all of whom do not get the disease, and it is estimated that on average an affected male or female has about 2% chance of producing a child before they die. Historical data, available from the tribe’s library, written on stone and parchment manuscripts for thousands of years, record that approximately the same number of men or women, about 50 at any time, in the island suffer from the disease, and the records also show that the total population of their people as stable at about 500,000 in that island for as long as the records were kept.

Questions:

3a.       What could be a plausible cause of the disease, genetic or environmental? Give succinct arguments for and against each possibility.

 

 

 

3b.       Assume that the cause of the disease is genetic. Is it due to a sex linked mutation?

 

 

 

3c.       Assuming a genetic disorder, is it likely due to a recessive or a dominant mutation? Explain.

 

3d.       How many mutant alleles of this gene on average go extinct per generation? Explain.

 

3d.       What is the estimated mutation rate of this gene (expressed as the number of mutant genes created per generation)?

 

Question 4. Three single nucleotide polymorphic loci, rs0001, rs0002 and rs0003, are linked in the order shown below, with the physical distance (in DNA nucleotides) separating them as shown on the map.

Below the genetic map are listed values of linkage disequilibrium values, LD, expressed as r2 (which lies between minimum of 0 and maximum of 1.0) between each of the three pairs of  loci as measured within a particular population. Alleles at each locus are in Hardy-Weinberg equilibrium.

 

Explain succinctly one possible reason for the apparent inconsistency between the physical distance and the LD values.

Question 5. In a recent genome-wide association analysis of a type of cancer’s susceptibility genes, 11306022 different SNP markers were followed for evidence of association.

 

5a. Assuming that all SNPs segregate independently of one another in the population, what is an acceptable threshold of significance P-value in this study?

 

5b. A number of SNPs were found to be highly statistically significantly associated with this cancer incidence, and these SNPs mapped nearby the following genes:

NOC2L, HNF4G, HNF1B, HNF1A, SMC2, EDNRA, FOXF1, FOXC2, FOXL1

 

Write a succinct paragraph on the kinds of molecular-genetic functions that might be associated with risk of this type of cancer. Show evidence or justification (you can paste an image, if you like).

 

5c. What is your best guess as to the kind of cancer that were studied in this research work?

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