Wk 1,2 Molecular Methods Appendix and Case Studies

Question 1

What are 3 categories of things that are measured from a patient sample?

Answer 1

1. RNA or DNA
2. Specific proteins
3. Metabolites (small molecues involved in metabolism)

Question 2

What are 5 ways of measuring a DNA sequence?

Answer 2

1. quantitative PCR
2. FISH
3. microarray
4. direct hybridization
5. high throughput genomic sequencing

Question 3

When can PCR work w/ translocation?

Answer 3

When looking for known translocation so the two primers can detect them.
Ex t(9;22) BCR-ABL in CML (chronic myeloid leukemia)
-Could also use FISH
-This particular transfusions can occur at different regions of BCR to same site on ABL1 kinase gene –> may need different/multiple primers for varying possible transcripts

Question 4

What gives most info but can cost more: PCR, FISH, karyotyping?

Answer 4

Karyotyping - can show other chromosomal abnormalities, gains and losses to potentially help w/ tx course. Others may cost less, but give less info and can only confirm translocation.

Question 5

When would we use FISH fusion probe strategy?

Answer 5

When looking for two signals that have come together (translocation w/ two chromosome pieces coming together)
-fusion is the abnormal state created by translocation
-use if there are 2 partners involved

Question 6

When do we use FISH break apart strategy?

Answer 6

Chromosome parts break apart when abnorm
-good for “promiscuous translocators” that have several translocation partners - this detects any one of them

Question 7

How do karyotyping, FISH and PCR compare?

Answer 7