Cellular Research, a Bay Area company established a year ago by the cofounders of Affymetrix and Fluidigm, has received federal funding to develop a non-invasive test for detecting Down syndrome in prenatal samples using a new array-based DNA molecule counting approach.
According to the abstract of the $360,000 National Institutes of Health grant, Cellular Research aims to develop a "faster and cheaper single-molecule counting system" that will rival a non-invasive massively parallel sequencing test to detect trisomy 21 in fetal DNA present in maternal plasma.
While the competitive product is not named in the grant, Sequenom launched its MaterniT21 test for Down syndrome in 2011, and that assay is run on Illumina's HiSeq 2000 sequencing platform. Other companies such as Ariosa Diagnostics, Natera, and Verinata Health (which Illumina said this week that it plans to acquire), claim they can provide such information to patients as part of their sequencing-based prenatal screening services.
According to Cellular Research, while such sequencing-based tests produce a "definitive prognosis for aneuploidy without risk to the fetus," they are at the same time "expensive," and "expectant parents usually have a long wait time of ten days or more."
Sequenom offers its test to uninsured patients for $1,700, but charges a copay of $235 to insured patients. It bills insurance companies $2,900. Ariosa markets its test for $795 while Verinata's is $1,200.
Palo Alto, Calif.-based Cellular Research aims to deliver a system that can provide the same information as these sequencing-based tests but at a lower price and with a faster turnaround time. According to the grant abstract, the firm's method includes using a collection of sequence barcodes to randomly label individual DNA molecules. Following amplification, various barcodes are detected and counted to reveal the number of copies of identical molecules originally present.
"We transform the difficult task of counting individual copies of identical molecules into a simple one of detecting the number of different barcodes present," Cellular Research wrote in the abstract.
In previous work, Cellular Research claimed it had used a microarray detector to count barcodes, and showed "precise and accurate digital, absolute quantitation of chromosomal copies starting with very low, sub-nanograms of sample input." For its proposed pilot study, the firm plans to "further define the barcoding and amplification reaction conditions," and "construct a suitable microarray barcode counter to enable the detection of very small increases of additional copies of chromosome 21."
Additionally, Cellular Research aims to investigate the "measurement accuracy and statistical confidence" of the test to "demonstrate feasibility for a subsequent commercial product development phase."
The company did not provide a timeline in its grant abstract for when it hoped to commercialize its test, but claimed that its method is "faster and less expensive than massively parallel DNA sequencing methods," while still exceeding the statistical power required for the accurate diagnosis of fetal chromosomal anomalies such as trisomy 21.
Some main elements of Cellular Research's approach were developed at Affymetrix. Glenn Fu, Affy's former director of genotyping research, is principal investigator on the new grant. And Affy cofounder and longtime chairman Stephen Fodor is listed on the grant as a founder of Cellular Research. Fu and Fodor were coauthors on a PNAS paper published in May 2011 entitled, "Counting individual DNA molecules by the stochastic attachment of diverse labels."
In that paper, the authors described a strategy for single-molecule counting that they termed "stochastic labeling," where the "random attachment of a diverse set of labels converts a population of identical DNA molecules into a population of distinct DNA molecules suitable for threshold detection."
Fu and Fodor are also inventors on patent application 20110160078, "Digital counting of individual molecules by stochastic attachment of diverse labels," which was filed with the US Patent and Trademark Office in June 2011.
In a filing with the US Securities and Exchange Commission last year, Affy acknowledged that it had assigned "one patent application and related know-how" to Cellular Research, and that Fodor owns "a majority of the shares" in the new company. As part of that agreement, Cellular Research agreed to pay single-digit royalties to Affy on sales of products covered by the technology, and, starting in December 2015, an annual minimum fee of $100,000. Affy also retains a "right of first refusal" to collaborate with Cellular Research to develop certain new products and to supply arrays to Cellular Research under certain terms and conditions.
According to the new grant abstract, Cellular Research also counts Stephen Quake, a Stanford University biophysicist, as a founder. Quake is also cofounder of South San Francisco, Calif.-based Fluidigm, as well as Verinata, which has commercialized a sequencing-based prenatal test for multiple chromosomal aneuploidies. As BioArray News sister publication GenomeWeb Daily News has reported, Illumina this week announced plans to acquire Verinata for up to $450 million.
Additionally, Cellular Research said it is collaborating with Ronald Davis at Stanford's Genome Technology Center, and has access to "instruments and expertise" via the partnership. Fu is listed as a visiting scholar on the GTC website.
The $360,000 funding amount attached to the grant, which began on Jan. 1, is intended to support the project through the end of 2013. The grant is expected to expire in September 2014. It is unclear what additional funding Cellular Research will require to achieve its goals in that time.
BioArray News was unable to reach the firm, which does not have a website and did not provide contact information on the grant, for comment.