NEW YORK – A whole-genome sequencing test developed by researchers at Washington University School of Medicine in Saint Louis (WUSTL) has received coverage from the US Centers for Medicare and Medicaid Services, allowing the assay to be employed across a wider group of patients.
The ChromoSeq test is a high-coverage whole-genome assay for patients with myeloid neoplasms that runs on Illumina sequencers, said Eric Duncavage, a professor of pathology and immunology at the university and one of the developers of the test. The team has been using the assay to test patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) in its hospitals since 2021, but its CMS coverage will allow the university to widen its pool of potential patients.
A key problem in the field of myeloid malignancy testing, Duncavage noted, is that there are multiple technologies used to perform comprehensive testing, none of which fill all of hematologists' needs. It is particularly difficult to integrate data received from each test, and the developers of ChromoSeq wanted to simplify the process. Whole-genome sequencing (WGS) can detect single-nucleotide variants, insertions and deletions, translocations, and "everything you would need to rigorously classify an AML patient," he said.
The researchers developed informatics tools to determine which WGS data is clinically significant, and in 2021 published a study in the New England Journal of Medicine validating the test on 263 patients, 235 of whom had undergone cytogenetic analysis. In that study, the test detected all 40 recurrent translocations and 91 copy-number alterations that had previously been identified by cytogenetic analysis, and identified new clinically reportable genomic events in 17 percent of patients who underwent cytogenetic analysis. In addition, the test was used to stratify patients with inconclusive cytogenetic analysis results into risk groups.
The researchers also performed prospective sequencing on 117 patients, which provided new genetic information for 29 patients and changed the risk category for 19 patients.
Currently, the test is being run in WUSTL's CLIA-certified laboratory on every patient admitted to the hospital with high-grade myeloid neoplasms and paid for via hospital-based reimbursement, but Duncavage said that the CMS coverage now allows the team to run the test in an outpatient setting. Patients that are not acutely ill and hospitalized, such as those with lower-grade MDS, will be able to utilize the test, even if they don't live in Missouri.
Duncavage said that the team "is happy to take cases from outside" the health system, noting that there is "no technical reason why we can't" do the test for other patients.
By broadening the patient population that can use the test, the CMS coverage may also push forward efforts to adapt the test for use with blood samples instead of bone marrow. The team has primarily tested bone marrow thus far, since patients in the hospital already provide those samples, but in an outpatient setting blood is the easier sample type to collect.
Duncavage noted that the test is usually more sensitive with bone marrow samples, but sequencing offers "pretty good" positive and negative predictive values regardless of sample type, meaning either could be used for the test. Using blood may also allow clinicians to detect disease earlier, since patients can provide a blood sample before they become acutely ill.
The Medicare approval will "allow us to test these patients potentially earlier from a blood sample, rather than waiting until they go through the referral process and end up here to get a bone marrow biopsy," he said.
The test takes advantage of the falling cost of sequencing technologies and reagents, costing approximately $3,300 — about the same price as the comprehensive testing for AML performed as part of the current standard of care as well as the comprehensive cancer panels used for solid tumor testing, Duncavage said. WGS requires less technician time, as much of the analysis is automated, and that decrease in workload combined with continued lowered sequencing costs makes the test "very attractive," he said.
ChromoSeq runs on Illumina's NovaSeq 6000 sequencers, although Duncavage said the team will be transitioning the test to the NovaSeq X Plus platform. It uses commercially available reagents from Illumina, and sample preparation takes about four hours. The current turnaround time is between 10 and 14 days, which includes the time it takes to accession the case and do the insurance pre-certification, Duncavage said. It also takes into account that the team batches its cases, doing two runs per week. Running the technical part of the assay takes three days with the NovaSeq 6000 and two days with the NovaSeq X Plus, he noted.
"As prices continue to fall … we'll see a movement away from traditional testing," he said. "If the sequencing costs continue to drop the way they are, it's going to be hard to make an economic argument not to switch to whole-genome [sequencing]."
The assay is covered under Medicare's MolDx program for myeloid neoplasms, but the team is also pursuing other indications, he added. Right now, the lab is validating the assay for use with B-cell acute lymphoblastic leukemia, myeloma, and other hematologic neoplasms, although the test would not be covered under MolDx for those indications and the team would have to resubmit it for coverage, he said.
The researchers have already validated the test for use with B-ALL in nearly 100 patients and have received a grant from the Alliance for Clinical Trials to integrate testing for the disease into one of the organization's existing protocols. For myeloma there has been slightly less progress, with only a few samples tested so far, he added.
Christopher Hourigan, a senior investigator at the National Institutes of Health's National Heart, Lung, and Blood Institute, said that the key innovation of ChromoSeq is that it can serve as a substitute for disease-specific tests. The current standard of care to diagnose myeloid neoplasms requires multiple different kinds of tests, such as targeted DNA sequencing, cytogenetic analysis, and fluorescence in situ hybridization tests. The innovation of ChromoSeq is that it uses "simple, ubiquitous" whole-genome sequencing and "adds this filter of disease-specific information on top to get the information that you would get" from standard clinical testing.
Hourigan, who used a version of the test before it became clinically available, said he sees value in the test, not as a replacement for the current clinical standard of care but as a fail-safe when conventional metaphase cytogenetic testing doesn't work.
The potentially longer turnaround time for ChromoSeq compared to other forms of testing makes it less appealing as a replacement for standard-of-care testing, at least for patients outside of the WUSTL system, he added. Because it currently doesn't provide substantially more information than standard-of-care testing, there may be less incentive to use the test on all patients, he said.
Hourigan also said that he doesn't know of anything else like ChromoSeq, noting that while it uses whole-genome sequencing, "a tool we're all familiar with," it's the first "clinical application of this technique for acquired genetic abnormalities" in AML and MDS.
The assay could also have broader implications for rare cancers in general, Hourigan said. In the future, rather than doing multiple disease-specific tests on all rare tumor types, a laboratory could run WGS on DNA from a tumor and then use bioinformatics solutions like ChromoSeq that incorporate domain-specific knowledge to identify the most important prognostic or actionable mutations.
ChromoSeq is an "illustration of potential" for that future, but Hourigan noted that there are significant logistical and regulatory challenges before it would be possible. However, as the cost of WGS and computation continues to decrease, "you could imagine the future of genetic-based diagnostic testing increasingly being more comprehensive and then adding the specificity after the test, rather than investing early in specific tests."