Can PCR detect chromosomal translocations in cancer?

[TytoAlba95]

How is PCR able to detect chromosomal translocations causing cancer?

I understand it is possible through FISH but how PCR?

 

[Andrew Mason]

Hi SanjuktaGhosh.

I think they are referring to RT-PCR. Both PCR and RT-PCR involve making copies of DNA but in RT-PCR one first uses reverse transcriptase to reverse transcribe a subject RNA strand into its DNA complement (cDNA). One then uses PCR to amplify the cDNA.

AM

 

[Ygggdrasil]

PCR is able to detect specific chromosomal translocations, such as the "Philadelphia chromosome" that produces the BCR-ABL1 fusion in many leukemias. Basically, since the genes for BCR and ABL1 are normally on different chromosomes, a PCR reaction using one primer against BCR and one primer against ABL1 will normally not produce a product. However, if a translocation has occurred which creates the BCR-ABL1 fusion, the PCR reaction will then amplify the BCR-ABL1 gene, enabling detection of the fusion. PCR methods are very sensitive, allowing researchers to detect minute amounts of fused DNA in a mixed population of normal and cancerous cells.

https://www.lls.org/leukemia/chronic-myeloid-leukemia/diagnosis
https://www.cancer.org/cancer/chron...etection-diagnosis-staging/how-diagnosed.html

I think they are referring to RT-PCR. Both PCR and RT-PCR involve making copies of DNA but in RT-PCR one first uses reverse transcriptase to reverse transcribe a subject RNA strand into its DNA complement (cDNA). One then uses PCR to amplify the cDNA.

No, these tests are normally done by conventional PCR, looking for chromosomal translocations at the DNA level.

 

[Andrew Mason]

No, these tests are normally done by conventional PCR, looking for chromosomal translocations at the DNA level.

Would finding the BCR-ABL mRNA be easier than finding the fused DNA? This is not my area, but RT-PCR does seem to be used for this purpose: See for example: https://www.ncbi.nlm.nih.gov/pubmed/17705578

AM

 

[Ygggdrasil]

Would finding the BCR-ABL mRNA be easier than finding the fused DNA? This is not my area, but RT-PCR does seem to be used for this purpose: See for example: https://www.ncbi.nlm.nih.gov/pubmed/17705578

AM

Typically, DNA is more stable than RNA, so I would have thought that it would be preferable to check DNA by qPCR. Upon further investigation, it does appear that you are correct and diagnosis is typically done by RT-qPCR to look for BCR-ABL1 mRNA (e.g. see http://www.bloodjournal.org/content/114/5/937.long?sso-checked=true).

 

[TytoAlba95]

Thank you both of you. So basically to detect BCR-ABL1 fusion gene, a forward primer that anneals to the starting portion of BCR and a reverse primer that anneals to the ending portion of ABL1 are used?