Episode 005: Heme Path Series Pt. 4 - Molecular Testing
Major Points Covered:
In Part 4 of our Heme Path series, we thoroughly examine the details of molecular testing and how it relates to hematologic and oncologic malignancies
Molecular Testing Basics
Provides a means of assessing patient’s genotypes, specifically at smaller changes in the genetic information
How is it performed?
Polymerase chain reaction (PCR)-based testing, which involves using a specific primer that is complementary to the area of interest on the patient’s DNA
PCR can allow for both amplification and quantification of gene of interest
Can look for either single gene mutations (faster) or a panel of mutations (slower but more information) also known as NGS
Clinical Utility of Molecular Testing
Very useful in risk stratification based on the mutations noted (some mutations are unfavorable and some are favorable)
Certain genetic mutations have drugs that are effective against them, therefore provides information about targeted therapeutic options
In hematologic malignancies, can be used to also assess response to treatment
You can determine minimal residual disease or MRD
Can look for a gene mutation that was present in the original cancer clone and see if there is any amount of residual cancer left over on the order of 1 in a million cells
In solid cancers, used to determine presence of genetic changes that have prognostic and targeted treatment implications
BRAF V600E mutation in melanoma → BRAF inhibitor pill treatment
EGFR mutation in lung cancer → EGFR inhibitor pill treatment
How is molecular testing different than FISH?
Both require choosing probes and understanding what you are looking for before running the test
FISH (discussed in part 3!) reports out of 200 cells and provides information about only larger kilobase sized genetic changes (translocations, inversions, deletions)
Molecular testing analyzes a much larger number of cells and can detect changes at the single base pair level. Much more detailed and microscopic evaluation of genetic changes
Single Gene Molecular Testing
Look for a specific gene mutation (i.e. EGFR for lung cancer, BRAF for melanoma, FLT3-ITD for AML)
Pros:
Faster turnaround time
Has a higher resolution and effective for detecting MRD
Cons:
Only looks for one genetic mutation as opposed to a panel like in NGS
Some diseases ideally require understanding of multiple mutations not just one for prognostication and treatment planning
Next Generation Sequencing (NGS)
Allows to sift through a larger part of the genome to identify a panel of mutations
Panel of mutations chosen is based on the clinical context
For example: NGS for acute myeloid leukemia is much different than NGS testing for lung cancer as each cancer has a much different genetic mutation profile
Overview of technical aspects of running NGS
Massively parallel sequencing meaning that many tiny primers are used and the areas that primers encode may be overlapping
A computer takes all of the smaller pieces and puts them together to determine the correct sequence
Pros:
Gives us an understanding of many different mutations present based on the panel chosen
Again, this has both prognostic and predictive treatment implications
Cons:
May find mutations of undetermined significance meaning we currently do not understand how these mutations will affect prognosis and treatment decisions
Very time consuming (~2-4 week turnaround time)
Costly
References:
https://jamanetwork.com/journals/jamaoncology/fullarticle/2734828 - Quick overview of NGS
https://ashpublications.org/blood/article/125/26/3996/34323/Minimal-residual-disease-diagnostics-in-acute - Look at table 1 to see the difference in sensitivity for MRD testing
https://www.oncotarget.com/article/27602/text/ - Emphasizes prognostic relevance of EGFR mutations in NSCLC
https://www.nejm.org/doi/full/10.1056/NEJMoa1612674 - Phase 3 trial showed that targeted treatment for EGFR mutation in NSCLC was superior to chemotherapy
https://www.nejm.org/doi/full/10.1056/nejmoa1614359 - Phase 3 trial showed that targeted treatment of FLT3 mutation in AML improved outcomes