fresh York Department of Health Guidelines for Assist Labs in Cancer Testing
You may be wondering what type of guidelines has been developed by the fresh York Department of Health for labs. This particular can be from the developing NGS based cancer assays. NGS stands for Next Generation Sequencing.
Of all the many topics under discussion at the NCI Clinical NGS for Cancer conference, perhaps the most contentious was the issue of which tests should be performed along with how they should be reported. In This particular instance, the great advantage of the fresh technology—inexpensive along with high-volume sequence data—can be also in some ways its Achilles heel.
The guidelines, which cover somatic variant detection for molecular oncology testing, were issued in August by the department's Clinical Laboratory Evaluation Program, or CLEP, which monitors the quality of testing conducted by clinical laboratories along with blood banks from the state as well as out-of-state labs which accept clinical samples coming from fresh York.
The document complements existing department guidelines for molecular oncology tests, following "the same basic principles for validating most some other complex molecular diagnostics procedures," along with are supposed to evolve "as the field matures along with gains experience," according to the document.
Erasmus Schneider, director of CLEP's oncology section at the department's Wadsworth Center in Albany, told Clinical Sequencing News which the need for the guidelines arose because next-gen sequencing can be producing its way into clinical diagnostics along with the department had received requests coming from laboratories wanting to know how to validate their tests in order to gain fresh York State approval.
Input for the guidelines came coming from meetings Schneider along with his colleagues attended where the clinical use of NGS was discussed along with coming from feedback coming from interested parties on a draft document.
NGS-based molecular oncology testing differs coming from most some other tests in This particular area because This particular interrogates panels of tens to hundreds of mutations in parallel rather than individually. Schneider said the only some other high-throughput genotyping assay currently used for oncology mutation detection can be the Sequenom MassArray assay, although which This particular "has not been widely adopted" by clinical laboratories from the state, in part because of the big investment required. "I think most people are much more familiar with sequencing-based assays," he said.
So far, the majority of clinical laboratories offering somatic mutation detection for cancer in fresh York have expressed an interest in NGS-based assays, Schneider said. Overall, 104 labs from the state hold a permit for molecular oncology testing, although not all of them offer somatic mutation detection, he added.
No NGS-based oncology tests have been approved yet, although several applications are pending.
Cyrus Hedvat, director of the diagnostic molecular pathology lab at Memorial Sloan-Kettering Cancer Center, said which the guidelines provide "a solid starting point for labs from the process of developing clinical next-generation sequencing-based tests."
His lab can be currently developing an assay for solid tumors which runs on Illumina's MiSeq along with uses the firm's TruSeq Amplicon Cancer Panel, which includes 212 amplicons coming from 48 cancer genes (CSN 10/17/2012).
Among some other requirements, fresh York State's guidelines call for a laboratory to define the minimum coverage required for calling a variant with high confidence along with for calling an amplicon normal. According to Hedvat, This particular can be similar to guidelines published by the College of American Pathologists This particular summer (CSN 8/1/2012), although fresh York offers "no specific guidance on the coverage depth required or the minimum allelic frequency to report a positive result."
"This particular will be a significant advantage for common mutations in genes with hotspots such as EGFR, KRAS, along with BRAF, although more problematic for a tumor suppressor such as P53," Hedvat said.
He also said which the guidelines are unclear about how many positive controls need to be included in each run, along with whether they have to cover mutations coming from all regions tested. The guidelines do state which a positive control has to be included during validation "along with periodically thereafter," along with suggest using a control containing "multiple known somatic alterations of each kind to be detected."
With regard to reports, the guidelines state which they should include all detected somatic variants, even those of unknown significance. "This particular could result in a long list of variants which could be difficult for a clinician to interpret," Hedvat said, although on the some other hand, if later publications make such variants clinically interpretable, the lab could not need to issue an updated report.
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