Thomas Jefferson University Hospitals is partnering with Singapore-based molecular diagnostic company Vela Diagnostics to develop both next-generation sequencing-based and quantitative PCR-based molecular diagnostics in the fields of oncology and infectious disease.
The tests will be developed based on the clinical research and expertise at Thomas Jefferson University, while VelaDx will be responsible for commercializing and gaining regulatory approval of the tests.
Thomas Jefferson University currently has Roche's 454 GS Junior, and it recently installed Life Technologies' Ion Torrent PGM for the purpose of the VelaDx collaboration. It has also ordered an Illumina MiSeq.
Stephen Peiper, chair of the university's department of pathology, anatomy, and cell biology, told Clinical Sequencing News that the university recently started doing next-gen sequencing and that one of its "front line goals" is to bring the technology into a CLIA-certified environment.
Last May, Peiper presented on a pilot project testing the GS Junior for cancer mutational profiling in colorectal adenocarcinoma patients (CSN 5/16/2012).
In that project, researchers tested a panel that encompassed 275 exons from 51 genes that represent mutational hotpsots in colorectal adenocarcinoma. The panel was designed using existing companion diagnostics and other existing tests with clinical and diagnostic utility.
Despite the initial work on the GS Junior, Peiper said that he plans to validate both the PGM and the MiSeq in a CLIA laboratory and has not yet decided whether he would validate the GS Junior for clinical use or continue to use it solely for research purposes.
He said he wanted to partner with VelaDx because "there aren't a lot of the major diagnostic companies that are making a clear commitment, a boots-on-the-ground commitment, to push sequencing forward successfully."
VelaDx announced an agreement with Life Tech last fall to develop diagnostics on the PGM in the areas of infectious disease and oncology (CSN 10/10/2012). Under that agreement, the companies plan to codevelop products on the PGM that VelaDx would commercialize. The companies plan to convert existing PCR-based tests that VelaDx currently markets and also to develop new tests on the PGM based on "innovative biomarkers."
Peiper added that VelaDx's "relationship with a major next-gen sequencing manufacturer" contributes to "a vision that is very attractive for us."
The two entities will develop tests based on research from Thomas Jefferson's clinical research laboratory with VelaDx primarily responsible for commercializing and gaining regulatory approval of the tests. However, Peiper said that the agreement allows for some flexibility in this regard. The partners may develop tests based solely on intellectual property held by either VelaDx or Thomas Jefferson, or tests could be developed based on combined IP.
Additionally, while VelaDx will be responsible for bringing in vitro diagnostic versions of the test through any accrediting or approval agency such as the US Food and Drug Administration or for IVD approval in Europe, in some cases, the university may launch a lab-developed test through its CLIA laboratory.
And, while VelaDx plans to only develop tests on the PGM, Peiper said that the university is open to developing tests on either the PGM or the MiSeq.
"I think the different platforms have different strengths, and we want to be positioned to do all," Peiper said.
The entities are planning to develop tests based on both PCR and next-gen sequencing. The clinical question being asked will determine the technology used. For instance, oncology patients "require the clinicians to consider multiple biological pathways containing many mutations, indels, and translocations," VelaDx's CEO Michael Tillman explained via email. In these cases, it's advantageous to use "higher multiplex technologies" such as next-gen sequencing, in order to "derive the desired data in an accurate and timely manner."
Peiper said that the university has identified a number of assays that it will move forward with for its initial tests, although he would not give specifics. "We're ready to move forward with test validation and we have a library of samples that we're going to interrogate," he said.
Tillman added that while project timelines have not been finalized, the goal is to begin test development within the first part of 2013.