NEW YORK (GenomeWeb) – KellBenx, a Great River, New York-based firm developing technology that can identify fetal cells in maternal blood, is about to launch a 1,000-person clinical validation study in collaboration with Columbia University with the hopes of subsequently commercializing a noninvasive prenatal diagnostic based on the technology.
According to KellBenx CEO Hassan Bennani, tests that analyze these fetal cells could be more accurate than those that analyze cell-free fetal DNA.
Previously, the company had been looking to launch a FISH-based test to detect chromosomal abnormalities in DNA from fetal cells, but now Bennani said the firm would launch a test either on Thermo Fisher's Ion Torrent PGM or on a microarray platform.
The goal is to develop a test that goes beyond current noninvasive prenatal screening tests and offers information akin to a karyotype. Aside from the standard chromosomal aneuploidies offered by NIPTs, Bennani said KellBenx's test would also detect microdeletions and would be able to diagnose single-gene disorders. Eventually, the hope is to be able to replace invasive diagnostic tests altogether.
"To enter the market, we have to show something that's superior to NIPT," Bennani said. "We want to offer something relevant to diagnostics that would be able to detect everything that you would look for in a karyotype today."
Besides Columbia, the company is also collaborating with researchers at Memorial Sloan Kettering Cancer Center, Bennani said.
Others are also looking to commercialize tests based on analyzing fetal cells and several academic and commercial research groups presented their work at the Advances in Prenatal Molecular Diagnostics annual meeting in Boston last month.
KellBenx's technology relies on being able to detect a cell surface marker called 4B9, which is an antibody that is unique and specific to fetal cells. The marker is present on fetal nucleated red blood cells, but not maternal cells.
In its clinical study with Columbia, KellBenx is trying to verify that it can detect and isolate fetal cells and analyze them for clinically relevant chromosomal aneuploidies like trisomies 21, 18, and 13.
In addition, Brynn Levy, director of the clinical cytogenetics laboratory at Columbia who is collaborating with KellBenx on the study, said the team would "assess the accuracy of genome-wide clinically significant copy number changes as well as monogenic disorders."
Levy's team at Columbia also collaborated with KellBenx on the proof of principal, testing the method on 213 cells from 108 samples of maternal blood from between four and 20 weeks gestation. The samples included both high- and low-risk pregnancies as well as women of multiple ethnicities.
Bennani said that KellBenx purchased the intellectual property and patent rights from Alere for the techniques used to identify and isolate the fetal cells, and said that the company did not have to license technology from Illumina or Sequenom since it was dealing with fetal cells as opposed to circulating cell-free DNA.
The company first separates out nuclear cells from maternal blood and then stains the cells, so that those with the B49 marker can be identified. Those cells are then separated out using cell separation techniques like magnetic-activated cell sorting and fluorescent-activated cell sorting. Bennani said the firm has also used micromanipulation to select the individual cells.
The company can work with single cells or can pool multiple fetal cells together for analysis. The DNA is extracted and the company performs whole-genome amplification.
Bennani said the firm is testing whole-genome amplification kits from Sigma-Aldrich and Rubicon Genomics. After whole-genome amplification, analyses can be done by microarray or NGS. Bennani said the company has been testing both. For NGS applications, he said the firm has been working with Thermo Fisher's Ion Torrent PGM.
An advantage of testing fetal cells, as opposed to circulating cell-free DNA, said Levy, is that it "opens up the avenue for offering a true diagnostic test as opposed to a screening test." One reason current NIPTs are used as a screening test and not a true diagnostic is that the cell-free DNA that they analyze comes from the placenta, not the fetus, while invasive procedures like amniocentesis sample the amniotic fluid, which does contain fetal tissue.
Another advantage would be that tests would not have the problem of confined placental mosaicism, in which the chromosomal make up of placental cells is different from that of the actual fetal cells. Confined placental mosaicism has been attributed as the cause for many false positives in current NIPTs that analyze cell-free DNA shed into the blood from the placenta.
However, Levy cautioned that one key to developing the method as a diagnostic will be having a built-in method to validate that the cell being tested is in fact fetal.
Levy said he has tested a number of so-called fingerprinting methods to demonstrate the cells are of fetal origin, including STR analysis and SNP arrays.
For STR analysis, there are commercial kits that analyze between 16 and 23 markers. But, one problem with these kits is that the input requirements are typically larger than the amount of DNA present in a single cell, so the genome would first have to be amplified.
Levy is now working on developing a SNP array that would generate a fingerprint profile for the cell. He first established threshold comparing genomic DNA derived from single cells to self, a child, and a non-related individual and then demonstrated that the method could accurately separate out fetal cells.
Levy said he is continuing to refine and validate this SNP fingerprinting method. Another option, he said, would be to use next-generation sequencing results for both aneuploidy analysis as well as genotype-based fingerprinting.
Bennani said KellBenx is aiming to commercialize a test based on the PGM shortly after the clinical study with Columbia wraps up, which he expects will be in about nine months to one year. While it is too early to say exactly what the price of such a test would be, he said he is aiming to have it in the range of current karyotyping tests — around $1,000 to $1,200.
He also anticipates offering the test in waves. For instance, he said, a physician could order the test initially for aneuploidy screening, he said, and could later request additional information from the results.
"Since we'll have the whole genome, we'll have access to all abnormalities, so if physicians want to see only the trisomies, we can offer that, or if they also want the more frequent microdeletions, that will be up to them," he said.