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First Veterans Affairs MDx Lab Launches NGS-Based Cancer Panel; Others to Follow


NEW YORK (GenomeWeb) – The Veterans Affairs of Greater Los Angeles Health System last month became the first institution within the VA to begin performing next-generation sequencing-based cancer testing, starting with a panel for hematologic malignancies.

The move is part of a broader push by the VA to bring advanced molecular testing in house in order to make it more cost-effective, streamline and standardize the process for doctors, and gauge markers that are relevant to the veteran population.

The NGS test, which uses Thermo Fisher Scientific's Ion Torrent Oncomine Myeloid Research Assay, reports markers in genes clinically relevant to the veteran population and was deployed into patient care in late February. The test, which runs on Thermo Fisher’s Ion GeneStudio S5 Prime sequencer, can detect gene mutations, fusion transcripts, and gene expression associated with myeloid cancers, such as acute myeloid leukemia, myelodysplastic syndromes, and myeloproliferative neoplasms. Oncologists can use the molecular data with other patient information to determine the most appropriate care for them or direct them to clinical trials.

"Testing for hematologic malignancies has been moving toward NGS for a few years now," said Carmen Kletecka, medical director for the molecular diagnostics laboratory at the Pathology and Laboratory Medicine Service at the VAGLAHS. "The oncologists at the VA have been asking for it."

The VAGLAHS serves a region with 1.4 million veterans. The lab in LA that Kletecka leads is the largest molecular diagnostics lab within the VA system and will be accepting and analyzing samples from vets locally, as well as from other VA healthcare systems in Southern California and a handful of other states.

There are multiple molecular markers that are prognostic for hematologic malignancies. For example, AML patients with NPM1 or CEBPA mutations tend to have a good prognosis, while those with FLT3 mutations tend to fare worse. The list of FDA-approved drugs with molecularly defined indications is also growing. Examples include Novartis' Rydapt (midostaurin) and Astellas Pharma's Xospata (gilteritinib) for AML patients with FLT3 mutations; Celgene's Idhifa (enasidenib) for AML patients with IDH2 mutations; and Novartis' Gleevec (imatinib) for those with myelodysplastic or myeloproliferative diseases and PDGFR rearrangements. Patients without molecularly informed treatment options could qualify for clinical trials investigating specific markers linked to hematologic malignancies.

The myeloid NGS panel assesses markers for all these purposes. The test report features a section on prognostic markers, markers that can predict response to FDA-approved drugs, markers in treatment guidelines, and markers that are being explored in clinical trials. "This gives the clinicians a lot of options," Kletecka said.

The VA decided to bring NGS testing in house as part of a concerted effort to streamline and standardize testing access. As knowledge about molecular markers increased, the VA recognized a few years ago that doctors would be challenged to keep current with the latest evidence, guidelines, and test offerings. As a result, the VA Pathology and Laboratory Medicine Service formed the Molecular Genetics Pathology Workgroup, putting it in charge of reviewing the evidence and coming up with recommendations that the Veteran Health Administration's hospitals and clinics could adopt.

The workgroup's hematopathology subcommittee published recommendations for molecular testing in Federal Practitioner in 2017, in which it called for expanding the resources of VA labs that are already doing such testing and having VA hospitals use those labs instead commercial reference labs, which have varying standards and results. "What the [VAGLAHS] is doing is a follow-on from the identification of the need and the recommendations," said Michael Icardi, national director of Pathology and Laboratory Medicine Services at the Veterans Health Administration and an author of the recommendations.

Prior to setting up the NGS test for myeloid disorders in the LA molecular testing lab, oncologists at the VA had sent out testing to firms that had contracts with the VA. "A lot of times, [the panels] might be missing markers you want to have for veterans based on their exposure histories," said Icardi, noting that this forced doctors to order analysis for specific genes of interest from different labs. "This is very difficult to figure out if you're a frontline physician."

The hematopathology subcommittee within the VA's Molecular Genetics Pathology Workgroup chose to report genomic markers in 34 genes included in the 72-gene Oncomine panel that are associated with myeloid malignancies and are clinically relevant and actionable within the veteran population.

One of the advantages of in-house testing is having better control over turnaround time. Some commercial labs that were previously doing testing for the VA, for example, had turnaround times that were longer than a month, which is bad for patient care. In comparison, the LA lab has been able to return results in around 10 to 15 days, according to Kletecka. "That's a huge improvement and patients can get their treatments much faster," she said.

The VA organizes healthcare services into regions, and the LA molecular diagnostics lab is currently accepting samples from Veterans Integrated Service Network-22 members, which include healthcare systems serving veterans in New Mexico, Arizona, and southern California. The lab is also accepting samples from the VA healthcare system in Las Vegas, though it is outside the VISN-22 network. Although the LA facility is the first to offer NGS testing to veterans, Icardi noted that other VA labs will eventually come online with NGS tests that serve other regions and provide back-up in emergencies.

Based on the recommendations of the Molecular Genetics Pathology Workgroup's other subcommittees, the VA is looking to similarly deploy an NGS panel for solid tumors and to implement pharmacogenetic testing. The same day this article was published, the VA and Sioux Falls, South Dakota-headquartered health system Sanford Health announced a program to provide free PGx testing to 250,000 vets.

Kletecka is also currently validating the 52-gene NGS Oncomine Focus Assay for solid tumors and similar to the myeloid panel, the lab will be reporting markers in genes that are clinically relevant for veterans based on their exposures, which differ from the general population. This panel is expected to go live in the next couple of months.