Ambry Genetics and GE Healthcare, who each released a new 26-gene sequencing service last week, have disclosed that both of their new services are based on Illumina's TruSight Tumor panel for somatic variant detection in solid tumors on the MiSeq platform.
Illumina launched TruSight Tumor earlier this month as a research use-only sequencing panel of 26 oncogenes and tumor suppressor genes selected for their implication in common solid tumors including lung, colon, gastric, and ovarian cancers, and melanoma.
At the same time as Illumina's announcement of the panel, Ambry Genetics announced that it would be offering a 26-gene sequencing service for somatic mutations in solid tumors developed in collaboration with Illumina. GE Healthcare announced a similar assay a few days later (CSN 4/10/2013).
Both companies told Clinical Sequencing News this week that their assays use the Illumina TruSight panel. Neither is currently being offered for clinical use, but both firms said they are planning to conduct validation work to allow them to offer the panel as a clinical diagnostic in the future.
The TruSight Tumor panel is designed for use with formalin-fixed paraffin-embedded tissue samples, with sensitivity below five percent even with "limited DNA inputs," across 175 exonic regions with 1000x minimum coverage, according to Illumina.
The company has said the panel has showed 99.9 percent sensitivity and specificity in in-house verification and pilot studies.
Ardy Arianpour, Ambry Genetics' vice president of business development, said that Ambry "co-developed" the panel with Illumina.
"We ran multiple sample sets for a two-plus month evaluation period to launch it as a product, [and] we plan to translate it to our clinical diagnostics menu at some point in 2013," he said.
He said the company is "gathering more data from [its] current pipeline of samples and doing internal testing," but he said the panel of genes itself would not be changed for clinical use.
While Illumina announced reliable sensitivity below five percent, Ambry is claiming its offering can reliably detect minor allele frequencies below three percent.
Scott Lerman, Global Public Relations Manager at GE Healthcare, said in an email to CSN that GE's use of TruSight Tumor also grew out of a collaboration with Illumina.
He stressed that GE is currently offering the panel only for research purposes for its pharma services customers, including for clinical trial research.
"Due to the complexity of reimbursement for multi-gene panels," he said, the company is taking a "wait and see" position in terms of its plans for expanding the test to clinical diagnostic use. But, Lerman wrote, Clarient believes that when it does "eventually launch the panel in the clinical lab setting it will be important that we've been involved in the development and validation of the assay."
Arianpour said Ambry believes it will distinguish its version of TruSight Tumor testing through the use of additional bioinformatics and in how it reports results. "We co-developed this, so we know the panel better than anyone," he said. "We know how to run it to get the best data."
Lerman said that Clarient is working on its end to optimize the pre-analytic steps of the assay, including sample selection and nucleic acid extraction, to better maximize the number of samples that the company can analyze with the test.
Though clinical labs have long used RUO reagents, like the TruSight Tumor kit, as the basis for lab-developed tests, the US Food and Drug Administration has signaled it may begin cracking down on the practice, issuing a draft guidance document last year that warned labs and vendors that such products should not be used for clinical applications (PGx Reporter 6/8/2011).
While GE and Ambry did not detail their specific plans for validating TruSight Tumor as a clinical diagnostic, labs adapting RUO products for clinical use often follow guidelines from the College of American Pathologists (CSN 4/11/2012).
Ambry's Arianpour said the company is confident about the process, having developed "300-plus diagnostic tests that were research use-only to begin with," including versions of its exome sequencing service.