Genetics 3 Flashcards
Endpoint
What you are trying to predict.
What is needed to develop a biomarker?
- Subjects
- Endpoint
- Biological specimen
- Assay/Dataset
- Prediction
Sample
biological material used to perform a measurement
Feature
Anything you can measure about a subject (continuous or categorical).
Biomarker
a feature that is relevant to a specific clinical endpoint.
What is most important about Statistical Significance with biomarker models?
How many subjects are misclassified.
What is overfitting?
When a model is optimized too much and allows for too much noise.
What is cross validation?
I dunno.
What is a somatic mutation?
One that does not happen in the germline. It is not inherited.
How do you detect somatic mutations?
- Compare two different tissues from the same individual.
- Sequence genome and align to reference.
- Remove germline mutations (they will be present in both samples)
- Somatic mutations will be present in only one sample
What are 5 DNA repair mechanisms?
- Mismatch Repair (MMR)- mismatches and indels trigger a single-strand incision.
- Base-Excision Repair (BER)- damaged base is recognized and removed.
- Nucleotide Excision Repair (NER)- helix distorting base lesions are removed in a 22-30 base oligonucleotide.
- Non-Homologous End-Joining (NHEJ)- double stranded breaks are repaired, can happen at any stage of cell cycle.
- Homologous Recombination- happens at S and G2, use sister chromatid for repair, BRCA 1/2 genes are involved in this pathway.
Can somatic mutations lead to mosaicism?
Yes. It all depends on when and where the mutation takes place.
What is a major concern regarding ESC therapies?
If the cell spontaneously makes a deleterious mutation, then we could be injecting or transplanting somebody with cancer.
Can environmental factors cause more Transversions (pyr to pur and vice versa) than Transitions (pur to pur and pyr to pyr)?
Yes. Smoking is an example.
Are somatic mutations that occur in germline cellls inheritable?
Yes.
What is a progenitor cell?
Committed cells, expand extensively.
Cannot reconstitute the entire organ.
Can reconstitute a specific cell line.
What is a terminally differentiated cell
Cannot dividie, short half-life.
ie- neutrophils, monocytes, platelets
What is a stem cell?
Reconstitute all cellular component of a specific organ, scarce, self renewal.
Pluripotent cells can become what?
Brain, organs, skin, bones, etc. They can even become germ cells (with some coaxing).
Can progenitors self-renew?
No.
What is pluripotent vs. multipotent
Pluripotent can give rise to every tissue.
Multipotent can give rise to certain tissue, but cannot give rise to the whole brain, for example.
What’s the difference between stem cell and progenitor cell?
Stem cells self-renewal and differentiate, self-renew and differentiate.
Progenitors only differentiate, there fore have a short half-life.
Difference between Totipotent and Pluripotent?
Totipotent can give rise to placenta.
What do niche do?
They support stem cells. (Look it up.)
What happens if you can’t differentiate stem cells appropriately?
They can turn malignant.
What are niche cells?
They support the growth of stem cells. They regulate many processes.