SAN FRANCISCO (GenomeWeb) – Sequenom plans to use its expertise in circulating cell-free DNA to develop a test for sequencing circulating tumor DNA, which it will launch in early access in the second half of the year for research use only, the company said today during a presentation at the JP Morgan Healthcare conference.
Sequenom CEO Bill Welch said that during 2015 it will bring "at least" three new laboratory-developed tests to market. Aside from the ctDNA assay, Welch said the company is developing a whole-genome karyotyping test, a carrier screening test that detects more than 250 genetic diseases, and plans to launch VisibiliT — its lower-cost noninvasive prenatal test that screens only for trisomies 21 and 18 — in the US in the first quarter of this year.
During his presentation, Welch also provided an update on the legal landscape in the NIPT field.
In December 2014, Sequenom and Illumina settled their litigation and created a patent pool alliance related to NIPT intellectual property. During his presentation, Welch provided additional details on the patent pool.
Sequenom received $50 million in cash for the settlement with Illumina. Earlier this week, as part of its preliminary financial report for 2014, the company disclosed that it expects to see between $6 million and $14 million in test fees and royalties in 2015 related to the patent pool.
Welch explained today that the patent pool consists of around 425 patents and patent applications, 225 of which Sequenom controls and 200 of which Illumina controls. Illumina is responsible for managing the patent pool and licensing the patents to third parties looking to develop their own tests. Already there are 21 licensees to the patent pool, including both Sequenom and Illumina.
All fees and royalties will be compiled into a pool, which will then be distributed to both Illumina and Sequenom on a quarterly basis. Sequenom will also receive royalties for in vitro diagnostic NIPT kits that are developed with the IP.
Welch said the company expects to receive $80 million in fees and royalties through 2020.
Also as part of the settlement, Illumina will have access to Sequenom's clinical sample database of high-risk pregnancies.
Both companies still have ongoing litigation with both Ariosa and Natera.
Welch said the settlement with Illumina has enabled the company to move forward with additional plans both in reproductive health and oncology. The company is now looking to launch a whole-genome karyotyping test in the second half of the year using the same strategy for shotgun sequencing of cell-free DNA that it uses for MaterniT21 Plus.
The difference, said Welch, is that sequencing will be to higher coverage and the test will look for large deletions and duplications.
"The product is a natural extension of what we've been doing," Dirk van den Boom, Sequenom's chief scientific and strategy officer, said during a Q&A session following the presentation. "In principle, it's the same technology, but [uses] advanced bioinformatics to find the large deletions and duplications," he said, adding that the company will present data on the test's sensitivity and specificity in the future.
He said that the company decided to move in this direction because through the course of running its MaterniT21 Plus test, "there were a significant number of cases with large events" in chromosomes that weren't specifically being tested for. "Events of that size usually have a clinical impact, and the physician wants to know," van den Boom said.
In addition, karyotyping tests are not new, so physicians know how to interpret them. Now, they will simply be able to look first noninvasively and do follow-up confirmatory testing on any positive results.
Sequenom is also looking to expand its cystic fibrosis carrier screening test, HerediT, to screen for more than 250 genetic diseases. Welch said that the company will launch HerediT Universal in the first quarter of the year. Sequenom has partnered with Recombine, a clinical genetic testing company that markets a carrier screening test for 200 diseases.
As part of Sequenom's strategy to tap into the average risk pregnancy market, it developed VisibiliT, a lower-cost NIPT that evaluates only trisomies 21 and 18. Rather than a 'yes' or 'no' for those indications, it gives a risk score.
The test costs $795 and Sequenom launched it outside the US in the fourth quarter of 2014 and plans to launch it in the US in first quarter of this year. Welch said that the company chose to focus on trisomies 21 and 18 because that is what serum screening currently looks for in pregnant women.
One of Sequenom's major goals is to move beyond reproductive health and into the oncology field. Welch said that the transition is a natural one. Sequenom Bioscience, which the company sold off last year, marketed a mass spectrometry-based oncology test. In addition, Sequenom can apply its expertise in analyzing circulating cell-free DNA to analyzing circulating tumor DNA.
In the course of performing NIPT, the firm has so far identified 20 significant incidental findings of confirmed maternal tumor growth, including breast cancer, colon cancer, and lymphoma, Welch said.
Although Sequenom has focused its commercial and marketing efforts on MaterniT21, Welch said that it has built up a clinical advisory board that has been "working behind the scenes" on oncology and that it has partnered with Razelle Kurzrock, director of the Center for Personalized Cancer Therapy & Clinical Trials at the University of California, San Diego.
Welch said that Sequenom would launch a research-use only test to early-access users in the second half of the year. The test will measure ctDNA, initially in advanced cancer patients with solid tumors and patients with metastatic disease where a biopsy is not possible.