Faster Blood Cancer Screening

A team of pathologists at Dana-Farber/Brigham and Women’s Cancer Centre have developed a quick, high-tech genetic test that can provide deep sequencing information on 95 cancer genes in just a few days. We spoke to Jon Aster, a professor of pathology at Harvard Medical School and one of the developers of Rapid Heme Panel (RHP), to find out more.

Why develop a new test?

Before RHP, we had to send out tests for important genes in acute myeloid leukemia (AML), namely, NPM1, FLT3 and CEBPA. The tests had to be performed individually and results could take up to a fortnight. We were also doing bead-selection-based targeted exome sequencing in patients with hematologic malignancies, but these were treated as research and were not recorded in the medical record. We saw a need for a test with a faster turnaround (approximately three to seven days) that would provide sequence variant information to clinicians treating patients with suspected or diagnosed AML, myelodysplastic syndromes (MDS), and myeloproliferative neoplasms (MPN).

How does RHP testing work?

A template is created by primer extension, and the Illumina Mi-Seq platform is used to sequence amplified patient DNA. Once we have the genetic data, an informatics pipeline is used to filter out non-pathogenic single nucleotide polymorphisms. Finally, a report is created that lists pathogenic variants, their allele frequencies and their significance based on the most recent scientific evidence.

Were there any challenges?

RHP relies on analyzing 1,330 amplified DNA sequences that cover 95 genes known to be pathogenic drivers in blood cancers. As you can imagine, developing a test that involves simultaneous amplification of so many sequences is not trivial. It required several rounds of primer design and a lot of testing with cell line and sample controls. In fact, it took about a year to develop and validate. The greatest challenge we are facing now is capacity: we can do up to 42 tests per week with our current equipment – and at present we are at almost 100 percent capacity.

Could you highlight the advantages?

The main advantage is that the test can be performed in five days or less and requires only one tube of blood. It provides information to help pathologists establish a diagnosis, and enable clinicians to select the appropriate therapy in a range of situations; for patients with relapsed refractory disease, RHP includes analysis of genes that may help select suitable candidates for clinical trials. Patients with de novo acute leukemia can be risk stratified based on genetic analysis, and patients who present with abnormal blood counts (who could have myeloid neoplasms or possibly benign hematologic conditions) can be more easily diagnosed. We have now used this test on several hundred samples, and RHP adds value to results beyond our previous capabilities.

What is the impact on pathologists?

Because RHP provides excellent sequencing depth (generally >1000x) it is possible to detect minor clones and to follow clonal evolution during treatment, which may have prognostic importance. In principle, it could also be used to detect and follow chimerism in a post-transplant setting, and it may also be possible to extend its applications to other hematologic malignancies (for example, myeloma and lymphoma).

RHP can also help pathologists establish earlier and more definitive diagnoses, allowing clinicians to better select the best therapy for patients – that actually enhances the value of what the pathologist provides.

Finally, RHP is relatively inexpensive; the price of the deep sequencing information is about a third of the cost of the three tests it is replacing. The sequencing and informatics pipeline we have created only requires the pathologist to consider and interpret a few variations per sample (typically one or two, or at most six or seven), meaning the time required to evaluate and sign out a case is typically only a few minutes – enabling rapid molecular diagnosis.