Genetics 3

Question 0

Endpoint

Answer 0

What you are trying to predict.

Question 1

What is needed to develop a biomarker?

Answer 1

1. Subjects
2. Endpoint
3. Biological specimen
4. Assay/Dataset
5. Prediction

Question 2

Sample

Answer 2

biological material used to perform a measurement

Question 3

Feature

Answer 3

Anything you can measure about a subject (continuous or categorical).

Question 4

Biomarker

Answer 4

a feature that is relevant to a specific clinical endpoint.

Question 5

What is most important about Statistical Significance with biomarker models?

Answer 5

How many subjects are misclassified.

Question 6

What is overfitting?

Answer 6

When a model is optimized too much and allows for too much noise.

Question 7

What is cross validation?

Answer 7

I dunno.

Question 8

What is a somatic mutation?

Answer 8

One that does not happen in the germline. It is not inherited.

Question 9

How do you detect somatic mutations?

Answer 9

1. Compare two different tissues from the same individual.
2. Sequence genome and align to reference.
3. Remove germline mutations (they will be present in both samples)
4. Somatic mutations will be present in only one sample

Question 10

What are 5 DNA repair mechanisms?

Answer 10

1. Mismatch Repair (MMR)- mismatches and indels trigger a single-strand incision.
2. Base-Excision Repair (BER)- damaged base is recognized and removed.
3. Nucleotide Excision Repair (NER)- helix distorting base lesions are removed in a 22-30 base oligonucleotide.
4. Non-Homologous End-Joining (NHEJ)- double stranded breaks are repaired, can happen at any stage of cell cycle.
5. Homologous Recombination- happens at S and G2, use sister chromatid for repair, BRCA 1/2 genes are involved in this pathway.

Question 11

Can somatic mutations lead to mosaicism?

Answer 11

Yes. It all depends on when and where the mutation takes place.

Question 12

What is a major concern regarding ESC therapies?

Answer 12

If the cell spontaneously makes a deleterious mutation, then we could be injecting or transplanting somebody with cancer.

Question 13

Can environmental factors cause more Transversions (pyr to pur and vice versa) than Transitions (pur to pur and pyr to pyr)?

Answer 13

Yes. Smoking is an example.

Question 14

Are somatic mutations that occur in germline cellls inheritable?

Answer 14

Yes.

Question 15

What is a progenitor cell?

Answer 15

Committed cells, expand extensively.
Cannot reconstitute the entire organ.
Can reconstitute a specific cell line.

Question 16

What is a terminally differentiated cell

Answer 16

Cannot dividie, short half-life.

ie- neutrophils, monocytes, platelets

Question 17

What is a stem cell?

Answer 17

Reconstitute all cellular component of a specific organ, scarce, self renewal.

Question 18

Pluripotent cells can become what?

Answer 18

Brain, organs, skin, bones, etc. They can even become germ cells (with some coaxing).

Question 19

Can progenitors self-renew?

Answer 19

No.

Question 20

What is pluripotent vs. multipotent

Answer 20

Pluripotent can give rise to every tissue.

Multipotent can give rise to certain tissue, but cannot give rise to the whole brain, for example.

Question 21

What’s the difference between stem cell and progenitor cell?

Answer 21

Stem cells self-renewal and differentiate, self-renew and differentiate.

Progenitors only differentiate, there fore have a short half-life.

Question 22

Difference between Totipotent and Pluripotent?

Answer 22

Totipotent can give rise to placenta.

Question 23

What do niche do?

Answer 23

They support stem cells. (Look it up.)

Question 24

What happens if you can’t differentiate stem cells appropriately?

Answer 24

They can turn malignant.

Question 25

What are niche cells?

Answer 25

They support the growth of stem cells. They regulate many processes.