Put It on the Board, 6/15

NIST releases first ‘genome in a bottle’

The National Institute of Standards and Technology has released the first reference material from its Genome in a Bottle project (see “Groups closing the gap in reference materials for sequencing assays,” CAP TODAY, March 2015, page 1).

Reference material 8398, human DNA for whole-genome variant assessment, “is intended to provide a whole human genome sample and accompanying reference values to assess performance of variant calling from genome sequencing,” NIST said in a technical document released April 15.

Laboratories can use the material to test the performance of their whole-genome and whole-exome sequencing, as well as more targeted sequencing such as gene panels. The material can be used to obtain estimates of true positives, false positives, true negatives, and false negatives for variant calls. Because the material is extracted DNA, it cannot be used to assess preanalytical steps such as a lab’s DNA extraction. While the reference material can assess sequencing library preparation, sequencing machines, and the bioinformatic steps of mapping, alignment, and variant calling, it cannot be used to gauge the performance of functional or clinical interpretation.

The material will be valid until 2024. Additional reference materials for sequencing are reportedly under development.
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For blood supply safety, time for technology mandate

Improvement in proper use of blood is having the unintended effect of making it more difficult for blood centers to implement new blood-safety interventions, says a New England Journal of Medicine perspective article co-written by physicians from Yale University
and American Red Cross Blood Services.

“Blood management and utilization programs ensuring that blood is used only when needed and in the smallest quantity possible have become widespread, but their adoption is a double-edged sword,” said the article (Snyder EL, et al. 372[20]: 1882–1885). “Blood centers are facing a 20 percent decline in blood use, which translates into decreased cost recovery.”

“Consequently, centers are downsizing infrastructure, reducing staff, closing facilities, and merging to remain fiscally sound. Individual centers are unable to absorb the additional costs of implementing new blood-safety interventions unless they are reimbursed by hospitals. Hospitals are not directly reimbursed for blood products and will purchase blood from the lowest-cost provider. All these factors inhibit the pursuit of safety innovations.”

The authors said “The historical process of reactive, pathogen-specific test development is not sufficient to protect patients” and that proactive pathogen-reducing technologies—such as the Cerus Intercept Blood System—for blood components should be mandated. “This mandate should be supported by a reimbursement process that recognizes the benefits of proactive strategies and offsets the costs,” the article said.
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CE for NSCLC liquid biopsy

Qiagen earlier this year announced the CE-IVD marking and launch of its novel liquid biopsy-based companion diagnostic that analyzes circulating nucleic acids obtained from blood samples to assess an important genomic mutation in patients with non-small cell lung cancer.

Qiagen said the registration, which applies to more than 30 European countries, makes the new Therascreen EGFR RGQ Plasma PCR kit the first-ever regulated companion diagnostic assay that has demonstrated clinical utility for guiding treatment decisions in patients with solid tumors based on the analysis of molecular biomarkers obtained from a body fluid.

The Therascreen EGFR RGQ Plasma PCR kit helps physicians identify advanced NSCLC patients who could benefit from treatment with Iressa (gefitinib) when a suitable tumor sample is not available. The test is performed on Qiagen’s Rotor-Gene Q PCR detection platform.

Qiagen also recently filed a U.S. regulatory submission for a tissue-based EGFR test using an FFPE sample as a proposed companion diagnostic to guide treatment with Iressa.
FDA clears two Roche tests

The Food and Drug Administration has provided 510(k) clearance for Roche’s Cobas Cdiff Test to detect Clostridium difficile in stool specimens. The test targets the toxin B gene found in toxigenic C. difficile strains directly in specimens from symptomatic patients.

The agency also approved Roche’s Cobas KRAS Mutation Test for diagnostic use. The real-time PCR test is designed to identify KRAS mutations in tumor samples from metastatic colorectal cancer patients and help clinicians determine a therapeutic path for them. The test is intended to help identify patients for whom treatment with cetuximab or panitumumab may be effective if no KRAS mutation is present. It is a TaqMelt assay, a PCR-based diagnostic test intended for the detection of mutations in codons 12 and 13 of the KRAS gene. The test can be performed in less than eight hours on the Cobas 4800 System.

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Siemens launches handheld coagulation analyzer

Siemens Healthcare Diagnostics has introduced a handheld coagulation analyzer for point-of-care monitoring and management of oral anticoagulation therapy with warfarin.

The Xprecia Stride Coagulation Analyzer was designed to meet the growing demand for fast and reliable PT/INR results in physician offices and walk-in clinics. It is about as big as a large-screen smartphone, weighs 300 g, and can be held at any angle and brought directly to the patient’s finger for blood-sample application. An integrated barcode scanner simplifies data capture for accurate calibration of new lot numbers prior to testing.

The analyzer uses fresh capillary whole blood, and results are expressed in PT seconds or as a PT/INR. It uses the same reagent as that used by Siemens central laboratory analyzers to minimize the potential for varia­bility. Siemens cited studies showing the performance to be equivalent to that of a reference laboratory hemostasis system, with results available in minutes.