Cytogenetics

Question 1

What are the 2 most common leukemia translocations?

Answer 1

• t(9;22) = Chronic Myelogenous Leukemia (CML), which can be treated with tyrosine kinase inhibitors
• t(15;17) = acute promyeloid leukemia (PML), which can be treated with retinoic acid

Question 2

What are the common cytogenetic findings in childhood B-cell leukemia and prognoses?

Answer 2

• LOW hypodiploidy or near triploidy = POOR prognosis (loss of tumor suppressor, for instance)
• HIGH hyperdiploidy (trisomy 4, 10, 17) = GOOD prognosis (maybe silencing mechanism)

Question 3

What are FISH probes used for?

Answer 3

Initial DDx, monitor treatments or disease progression.

enumerate number of a specific chromosome OR identify translocation

Question 4

What are 3 types of FISH probes?

Answer 4

CEN centromere: enumeration (e.g. cen 4, 8, 10, 17, 21)
LSI Locus specific: deletion (e.g. one copy of p53 means cancer)
F Fusion: translocations (e.g. BCR;ABL PML;RARA)
All used in diagnosing leukemias

Question 5

How does CMA work?

Answer 5

Sample and control DNA is labeled with green & red dye respectively. Hybridize to plate. If red = loss, green = gain (target is ~60bp)

Question 6

What does CMA detect?

Answer 6

Chromosomal gains and losses ONLY

It cannot detect balanced rearrangement or single bp changes

Question 7

What is the test protocol for diagnoses?

Answer 7

1. If deletion or duplication is detected by CMA consult DGV
2. If 4+ contiguous oligo clones are deleted or duplicated (and they are not considered as a common CNV in DGV) the finding will be confirmed by FISH using labeled BAC (bacterial artificial chromosome)-labeled DNA probe.
3. Parental FISH studies will be offered to determine if this finding is rare, ​normal, familial variant.
   ​4. If a deletion or duplication is found in one or both parents, other family members may be tested by FISH. Often extensive consultation between
   the clinical geneticist, genetic counselors and cytogeneticist are required.
4. If the deletion or duplication is NOT found in either parent, and it is not found in the genomic variants Database, further data-base mining, literature searches are performed. Often a gene or genes mapped in the region of deletion or duplication reveals a syndromic association (see Decipher website/database).