Flashcards
Week 8: Translocation & fusion genes
Flashcards do conjunto (23)
- 1What are these intrachromosomal abberations called?Left= Inversion
Middle= Deletion
Right= duplication - 2what is the difference between intrachromosomal and inter chromosomal abberations?Intrachrom. ab are changes within the same chromosome, in interchrom abberations, changes occur among multiple chromosomes
Interchromosomal > translocation or insertion - 3What is the difference between a balanced and an unbalanced translocation?Balanced = exchange of DNA between non-homologous chromosomes
Unbalanced= 2 non-homologous chromosomes get attached, no exchange
- 4Which 3 steps are required for gene fusions?1. ds DNA break
2. Illegal (wrong) recombination
3. Clonal expansion
- 5Name 3 reasons for gene fusionsRadiation (causes ds breaks)
Recombination events that have gone wrong (B and T cells)
Vulnerable places lie close to each other in the nucleus - 6What are 3 consequences of oncogenic chromosomal translocations1. fusion protein as tyrosine kinase forms
2. Fusion protein as transcription factor forms
3. Oncogenes are translocated to a place where they are under the control of a stronger promoter (like the promotor of the BCR) - 7Which 3 methods can be used to detect translocations and fusions?Karyotyping > only on high quality material
FISH
RNA based > RT-PCR and Archer RNA seq - 8Can FISH be done on FFPE or only of FF materialFISH can be done on both FFPE and FF
- 9What is the difference between a break apart FISH and a fusion FISHBreak apart: When gene is broken into pieces (translocated), the yellow dots form separate green and red dots.
Fusion: Red and green dots lie close to each other. Each color marks a different genomic region
- 10What chromosomal abberations can be seen with FISH?Chromosomal breaks > translocation
Fusions
CNVs (amplification) - 11Why would you used RNA seq instead of DNA seq (NGS/ Sanger)?Generally, RNA sequencing provides information about expression of genes. In addition, it gives information about the level of expression and at what moment genes are switched on or off.
In tumor cells, RNA sequencing provides information about the (functionality of) fusion of genes, alternative splicing and/or exon skipping. - 12For translocation detection: When do you use RNA seq, and when FISHFISH: When you need results quick (1 day), cheaper, but only applicable for 1/2 targets
RNA seq: more info of multiple genes in 1 assay
Both possible with FFPE - 13How does Archer RNA seq work?Archer can determine the unknown fusion partner of your target gene
- 14Name 2 pros and 2 cons of ArcherPros:
1. Unknown fusion partners can be detected
2. Fusion gene detection of multiple genes in 1 assay
Cons:
1. Takes 1 week
2. Expensive per sample - 15What is Nanostring used for?Gene expression
miRNA expression
Fusion gene detection
CNV detection
SNV detection
Protein expression - 16Name 2 pros and 2 cons of NanostringPros:
1. Relatively cheap
2. No amplification step needed
Fast, can be done on FFPE etc.
Cons:
1. Expensive machines needed
2. No detection of unknown fusion genes - 17Name 2 pros and 2 cons of RNA sequencingPros:
1. Transcriptome wide
2. Detects both over translocation, expression and SNVs
Cons:
1. Only works well on FF
2. Slow (2 weeks)
extra: Complex bio-informatics needed - 18What markers are used for the detection of B and T cells in IHC?B cells: CD19, CD20
T cells: CD3 - 19BCR rearrangement involves combinations of different fragments. Which fragments are combined in the light and which in the heavy chainLight: V and J
Heavy: V, D and J
- 20On which region of the BCR gene do primers bind to detect clonality for B cell malignancies?On the V region of heavy chain
Consensus primer binds to the J region of the heavy chain
- 21What are the pitfalls of gene rearrangement analysis using TCR/BCR?1. Low amount of T or B cells might look like monoclonality
2. difficult to distinguish between reactive B/T cells or malignant T/B cells
3. In case of a high mutation load, primers will not bind and no peak is shown for the malignant cells - 22What is the difference between lymphomas and leukemia?Leukemia: lymphoid malignancy with involvement of bone marrow and usually peripheral blood
Lymhomas: lymphoid malignancy arising as a discrete tissue mass - 23What 3 molecular things are testen in lymphomasTCR/BCR gene rearrangement > reactive or malignant
Translocations > classification and treatment
Mutations > classification and treatment
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- Tentamenvragen Molecular Pathology FlashCards sobre Week 8: Translocation & fusion genes, criado por Leanne van den Berg em 12-04-2022.
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- Leanne van den Berg
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