Thermo Fisher Scientific Inc. released updated software and new instructions for its Taqpath COVID-19 Combo Kit, a widely used COVID-19 test kit that is also the basis for several other coronavirus diagnostics, following issuance of a letter to clinical laboratory staff and health care providers by the U.S. FDA about the risk of false results with the test. Separately, the Waltham, Mass.-based company has released the first in a series of hematology-oncology assays designed to run on its Ion Torrent Genexus system.

The FDA identified two problems with the Taqpath test and its related interpretive software. The first issue arises from “inadequate vortexing and centrifugation of RT-PCR reaction plates,” which can lead to false positive results, according to the agency. Thermo fisher issued updated instructions to prevent insufficient mixing or centrifugation.

“We are working with the FDA to make sure that laboratory personnel understand the need for strict adherence to the instructions for use,” Thermo Fisher said in a statement provided to BioWorld. “Our goal is that every sample is collected and tested with the high level of accuracy associated with 1PCR-based tests, which are the gold standard for molecular diagnostic testing.”

The FDA encouraged labs to implement the updated instructions issued by the company and to “review the amplification curves within the instrument software for controls and patient specimens to determine whether the plate should be retested due to inadequate vortexing and centrifugation.” In addition, the agency recommended implementation of routine plate level checks of the amplification curves “to ensure your laboratory appropriately adheres to specimen processing instructions.”

The assay’s internal positive control also had issues, the FDA letter said. To fix the problem, the agency urged laboratory staff to stop using older versions of the Applied Biosystems COVID-19 Interpretive Software and to “upgrade their software to reduce the risk of invalid, potential false negatives, or inconclusive tests and decrease the potential need to retest.”

“Manufacturers’ protocols for any COVID-19 assay or test must be followed and run by qualified and trained laboratory technicians to provide the public with the certainty needed to respond to test results in a safe and effective manner,” the company said. “We strongly encourage laboratories to participate in the training that we offer to make sure all workflow processes are followed. We also provide 24-hour support for labs that are processing COVID-19 test kits.”

The updated software and new instructions also apply to any diagnostic tests based on Taqpath and to other coronavirus tests that use the Applied Biosystems software and instrumentation.

Hematology-Oncology portfolio

Thermo Fisher’s initial entry in what is touted as an expansive portfolio of assays to detect targetable mutations and more accurately assess risk in patients with blood cancers is the Oncomine Myeloid Assay GX. The new clinical research assay enables simultaneous next generation sequencing (NGS) analysis of DNA mutations and RNA fusion transcripts in myeloid samples with 24-hour turnaround. It total, the assay will allow researchers to profile 40 DNA targets and 29 fusion driver genes, facilitating detection of more than 600 fusion isotypes associated with three types of myeloid malignancies: myeloproliferative neoplasms (MPNs), acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS).

Among the biomarkers detected by the new assay are TP53, CEBPA, NPM1, RUNX1, PML-RARA, IDH 1, IDH 2 and FLT3-ITD.

AML often progresses very rapidly, making quick turnaround of genetic results essential.

“In the case of AML, oncologists are really driven by the genetics of the disease when informing the treatment plan,” Kojo Elenitoba-Johnson, director of the Center for Personalized Diagnostics and Division of Precision and Computational Diagnostics at the University of Pennsylvania’s Perelman School of Medicine told BioWorld. “There are several protocols, including extensive amounts of genetics and immunophenotyping, which are required to establish the appropriate approach to treat patients. The sooner we can get results and deliver treatment, the better the outcomes.”

Until recently, clinicians would request single gene testing, but with the explosion in the number of biomarkers in hematologic oncology and other cancers, that can unnecessarily delay appropriate treatment.

“The advantage of having NGS is that you can test for multiple targets at once. However, you need to weigh the ability to do this with the infrastructure needed and the ability to report clinical results in a relevant timeframe,” Elenitoba-Johnson added. “The advantage is that instead of approaching each abnormality as a singular problem, you’re able to target them all and report in context.”

Thermo Fisher plans to add assays for B-cell and T-cell clonality and somatic hypermutation assessment through immune repertoire sequencing to study lymphoid malignancies such as chronic lymphocytic leukemia, acute lymphoblastic leukemia, multiple myeloma, and Hodgkin’s and non-Hodgkin’s lymphomas as well as a comprehensive lymphoid gene panel. All the tests will run on the Genexus system.

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