Molecular Testing PearlsIn Part 4 of our Heme Path series, we thoroughly examine the details of molecular testing and how it relates to hematologic and oncologic malignancies I. Molecular Testing BasicsA. Provides a means of assessing patient’s genotypes, specifically at smaller changes in the genetic information B. How is it performed?1. Polymerase chain reaction (PCR)-based testing, which involves using a specific primer that is complementary to the area of interest on the patient’s DNA2. PCR can allow for both amplification and quantification of gene of interest C. Can look for either single gene mutations (faster) or a panel of mutations (slower but more information) also known as NGSII. Clinical Utility of Molecular TestingA. Very useful in risk stratification based on the mutations noted (some mutations are unfavorable and some are favorable)B. Certain genetic mutations have drugs that are effective against them, therefore provides information about targeted therapeutic options C. In hematologic malignancies, can be used to also assess response to treatment1. You can determine minimal residual disease or MRD2. 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 cellsD. In solid cancers, used to determine presence of genetic changes that have prognostic and targeted treatment implications1. BRAF V600E mutation in melanoma → BRAF inhibitor pill treatment2. EGFR mutation in lung cancer → EGFR inhibitor pill treatmentIII. How is molecular testing different than FISH?A. Both require choosing probes and understanding what you are looking for before running the testB. FISH (discussed in part 3!) reports out of 200 cells and provides information about only larger kilobase sized genetic changes (translocations, inversions, deletions)C. 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 changesIV. Single Gene Molecular TestingA. Look for a specific gene mutation (i.e. EGFR for lung cancer, BRAF for melanoma, FLT3-ITD for AML)B. Pros: 1. Faster turnaround time 2. Has a higher resolution and effective for detecting MRDB. Cons:1. Only looks for one genetic mutation as opposed to a panel like in NGS2. Some diseases ideally require understanding of multiple mutations not just one for prognostication and treatment planningV. Next Generation Sequencing (NGS)A. Allows to sift through a larger part of the genome to identify a panel of mutations B. Panel of mutations chosen is based on the clinical context1. 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 profileC. Overview of technical aspects of running NGS1. Massively parallel sequencing meaning that many tiny primers are used and the areas that primers encode may be overlapping2. A computer takes all of the smaller pieces and puts them together to determine the correct sequenceD. Pros:1. Gives us an understanding of many different mutations present based on the panel chosen2. Again, this has both prognostic and predictive treatment implicationsE. Cons:1. May find mutations of undetermined significance meaning we currently do not understand how these mutations will affect prognosis and treatment decisions2. Very time consuming (~2-4 week turnaround time)3. CostlyReferences:1. https://jamanetwork.com/journals/jamaoncology/fullarticle/2734828 - Quick overview of NGS2. 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 testing3. https://www.oncotarget.com/article/27602/text/ - Emphasizes prognostic relevance of EGFR mutations in NSCLC4. https://www.nejm.org/doi/full/10.1056/NEJMoa1612674 - Phase 3 trial showed that targeted treatment for EGFR mutatio