Genetics-Gene Identification

Question 1

What are the two ways we can identify diseased genes?

Answer 1

1) Functional cloning: knowledge of the protein function helps you find the gene. 2) Positional cloning: map the disease, find the gene and then figure out the function of the protein.

Question 2

What percent of the human genome actually codes for protein?

Answer 2

1.5%. The rest is involved in control of regulation of gene expression.

Question 3

What percent of the human genome is actually transcribed?

Answer 3

80.00%

Question 4

Although humans don’t have very many genes, what allows us to have a lot of variation?

Answer 4

Splicing

Question 5

What is a genetic marker?

Answer 5

Polymorphic site that has a sequence difference between two or more gene alleles.

Question 6

What are the most common genetic markers?

Answer 6

1) SNPs (single nucleotide polymorphisms) and SNVs (single nucleotide variants, which included polymorphisms, deletions and insertions) 2) Microsatellites (simple sequence repeats) 3) Restriction fragment length polymorphisms (RFLPs, restriction enzyme sites)

Question 7

What is a genetic linkage?

Answer 7

Physical linkage of two genes located on the same chromosome that are inherited together.

Question 8

What are the 3 patterns of gene segregation?

Answer 8

Independent assortment, linkage of loci close together on same chromosome and recombinate gametes.

Question 9

What determines the frequency of recombination between two linked loci?

Answer 9

Recombination fraction.

Question 10

How do you know this was the recombinant gene?

Answer 10

All of the other children have a B if they have an A or a b if they have an a. This last child has a b with an A. Crossing over must have happened. Recombination fraction is 0.1.

Question 11

Recombinant fraction if no recombination occurs

Answer 11

0

Question 12

Recombinant fraction if the loci are unlinked

Answer 12

0.5, there is a 50% chance of any allele pairing with the other.

Question 13

What method do we use to describe genetic linkages?

Answer 13

LOD scores (log of the odds).

Question 14

What LOD score is the threshold for favoring odds of linkage?

Answer 14

Z > 3 (odds of being linked are 10^3, or 1000x > than odds of not being linked)

Question 15

How is recombination frequency determined?

Answer 15

By the distance two genes are away from each other, the closer they are, the lower the recombination frequency. Note that 1 centiMorgan = 1% or in 100 meiotic divisions, 1 will become recombinant.

Question 16

On average, what is the distance of 1cM?

Answer 16

1 centiMorgan is about 1 Megabase pair

Question 17

How do we map disease genes by linkage analysis?

Answer 17

1) Enroll affected families 2) Determine disease status of each family member 3) Determine genotypes at set polymorphic markers across genome 4) Look for correlation between your markers and disease status

Question 18

Did the C allele in the Huntingtin study cause disease?

Answer 18

No, although 22 out of 24 people with Huntingtin disease had the C allele, it does not mean it caused disease. It means that the gene that caused disease is located near the C allele. Hence, people who do not have a family history of Huntingtin disease, but do have the C allele are not at risk for Huntingtin’s.

Question 19

This is a family with Huntingtin disease. The family wants to know the status of the fetus. The family was genotypes for the G8 locus which only has A and B alleles. What is the chance of II-1 to inherit disease? What is the risk the father has the disease? What is the chance the baby is affected? What is the total chance the fetus inherits the disease?

Answer 19

1) 50% 2) 0%, he is unaffected, despite B allele, he is not in the family line 3) 3%, A came from the mom and B came from the dad. Although A is unaffected, G8 and the Huntingtin allele are 3cM apart = 3% chance of recombination. 4) Chance inherits disease allele from mom (1/2) x chance of recombination (3/100) = 3/200 = 1.5%.

Question 20

What is a haplotype?

Answer 20

A set of linked polymorphic alleles that can occur in different combinations across two separate chromosomes. For this person the possible haplotypes are abc, abC, aBc, Abc, ABc, AbC, aBC and ABC (3 genes = 2^3 = 8 types)

Question 21

How do you know haplotypes are in linkage equilibrium?

Answer 21

The percentage of each haplotype is predictable from the individual allele frequencies.

Question 22

How do you know haplotypes are in linkage disequilibrium?

Answer 22

Assortment of haplotypes is not random and there may be many more haplotypes of the original founders.

Question 23

Why do we care about haplotypes?

Answer 23

If a particular haplotype occurs more frequently in affected individuals, a gene contributing to the disease may be located within the haplotype (between b and c shown below)

Question 24

What is responsible for a mosaic structure of haplotypes (haplotype blocks) in chromosomes over time?

Answer 24

There are recombination hotspots where recombination usually occurs and spots where it doesn’t really occur.

Question 25

What can you do to reduce the number of SNPs you are testing for in a study?

Answer 25

Figure out which haplotype block the gene is in and only test for a few SNPs within that block

Question 26

What is the difference between linkage analysis and association studies?

Answer 26

Linkage analysis are best for single gene disorders within families. Association studies are best for multifactorial diseases across different families.