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BillionToOne to Launch Noninvasive Prenatal Screening Test; Plans Liquid Biopsy Products


NEW YORK (GenomeWeb) – San Francisco Bay Area startup BillionToOne is getting ready to launch a prenatal genetic screening test that combines maternal carrier screening for five single-gene recessive disorders with a reflex noninvasive prenatal test (NIPT) of the fetus.

The company plans to make the test, called Unity, available to a limited number of clinics under an early-access program next month. The assay uses next-generation sequencing and a molecular counting technology developed by the firm. Later on, it also plans to move into liquid biopsy cancer testing.

In late March, BillionToOne, based in Menlo Park and founded by CEO Oguzhan Atay and CTO David Taso, announced a $15 million Series A funding round that was led by Hummingbird Ventures and NeoTribe Ventures. Additional participants were Y Combinator, a business accelerator in the Bay Area that also provided seed funding to the firm; Civilization Ventures; Fifty Years; 500 Startups Istanbul; and HOF Capital.

The name of the company, which has approximately 10 employees, comes from the fact that many recessive disorders result from a single base change in the more than 3 billion bases of the human genome.

Unity uses cell-free DNA from a single maternal blood sample for both assays and relies on amplicon sequencing as well as multiplex ligation probe amplification (MLPA). It first determines the woman's carrier status for cystic fibrosis, spinal muscular atrophy, sickle cell disease, alpha thalassemia, and beta thalassemia — conditions that the American College of Obstetricians and Gynecologists recommends all women should undergo carrier screening for. 

If she is a carrier for one of the diseases, which is expected to happen in about 11 percent of cases, a reflex NIPT is automatically performed that determines whether the fetus is likely to have the condition, an estimated 1 percent of cases.

Tsao said the company chose the five disorders because guidelines recommend carrier screening for them and because there is currently no noninvasive screening test available when the parents are found to be carriers.

In traditional carrier screening, if the mother tests positive, the father is tested next, and only if he is also a carrier, the pregnant woman undergoes invasive diagnostic testing to see if the fetus is affected, he said. However, it is not always possible to obtain DNA from the father, given, for example, that 40 percent of pregnant women in the US are single mothers. In other cases, only the mother but not the father has health insurance that covers carrier screening, leaving a woman who tests positive worried throughout her pregnancy, even though her baby will most likely be healthy. Unity gets around that by not requiring any paternal DNA to assess the fetal disease risk.

Since Medicaid and private payors generally cover carrier screening in pregnant women, the test "will be accessible and affordable to everyone," said Shan Riku, BillionToOne's head of products. She said that the company plans to bill only for the carrier screening portion of the test, allowing the firm to provide it more effectively to the Medicaid population.

Underlying Unity is a molecular counting technology that was developed by BillionToOne scientists and described in a preprint in BioRxiv last month. The approach, for which the firm has filed four patent applications so far, uses so-called quantitative counting template (QCT) synthetic DNA molecules that serve as a reference. They are spiked into the cell-free DNA prior to PCR amplification and are designed to amplify at the same rate as their corresponding gene of interest, with which they share certain regions. The number of QCT molecules added can be calculated from the sequencing data, and they can help to determine the number of DNA molecules that are derived from a particular gene in the sample.

"Typically, when people look at abundance information, they say, I have this many reads, [and] the read count from this allele is different from this other allele, but you don't know how many molecules that is," explained Tsao, who holds a PhD in bioengineering from Rice University. "We're able to convert read counts to numbers of molecules, so we can get absolute counts of DNA."

Knowing the absolute number of each allele in a sample allows the researchers to determine whether a fetus is affected by disease or not. For example, for a pathogenic variant for sickle cell disease, "if you have a 10 percent fetal fraction in that [maternal] blood tube, then the allele fraction would be 0.55 for an affected child," Tsao said. "For a fetus that's only a carrier, though, the allele fraction is 0.50. So distinguishing between the 0.55 and the 0.50 scenarios is how we can tell whether the fetus is affected."

The main advantage over digital PCR, which also provides absolute molecular counts, is that BillionToOne's NGS approach allows for more multiplexing, so it can test for more conditions and variants in parallel.

The company plans to provide Unity, which can be performed from 10 weeks of gestation, as a lab-developed test and is currently setting up a CLIA laboratory in Menlo Park. The goal is to provide test kits to clinicians, who will send maternal blood samples for testing to the company. The anticipated turnaround time for the test, which will initially not be available in New York, is about two weeks.

“We do think our first customers will be Medicaid-heavy practices, because that’s where the most need is for noninvasive prenatal testing, and also because it can be reimbursed in that patient population,” Tsao said.

In an initial clinical validation study described in the BioRxiv preprint, the researchers, in collaboration with scientists at the University of California, San Francisco; Baylor College of Medicine; and Yashoda Super Specialist Hospitals in Ghaziabad, India, tested the ability of the method to detect a heterozygous or homozygous variant in the beta-globin (HBB) gene in the fetus, using maternal blood samples from India. They found that in all 27 cases tested, the results were concordant with the newborn HBB genotype.

Another study in India, a country the company chose because the beta thalassemia carrier rate is quite high there, also showed 100 percent concordance, Riku said.

In addition, BillionToOne has an ongoing study with Baylor College of Medicine, funded by the National Institutes of Health, in which the researchers use Unity to test for sickle cell disease. Because that disease is included in the newborn screening program in Texas, they can match their NIPT results with the newborn screening results once the children are born.

Tsao said larger studies will be needed to determine the clinical sensitivity and specificity of Unity but those will likely be conducted after the test is commercially available, similar to how existing NIPTs were evaluated.

Pricing information for the test is not yet available but Riku said that the company is working on a financial assistance program, so patients’ out-of-pocket costs will be kept low. According to Tsao, the list price is expected to be less than that of the least expensive currently available NIPT for chromosomal aneuploidies.

Tsao said that BillionToOne may expand the Unity test if professional guidelines start recommending carrier screening for additional conditions. Next year, the company also plans to launch an NIPT for chromosomal aneuploidies that would compete with many of the existing NIPTs for fetal trisomies. "With our technology, because it's so quantitative, we believe we can come up with a trisomy NIPT that's very cost effective," Tsao said.

In addition, the firm is looking into liquid biopsy testing for cancer. One advantage of its absolute counting technology is that it could lower the detection limit for cancer mutations. Detection limit is typically expressed in percent allele fraction right now, Tsao said, but with absolute quantification, "you could set your limit of detection as the number of molecules instead, which physically makes a lot more sense. So you could say, if there are 10 molecules or more of an oncogene, for instance, then we would be able to detect that."

Another advantage, he said, is the ability of the counting method to detect gene amplifications, or copy number variants, with greater sensitivity. This could be clinically important, for example in breast cancer for detecting HER2 amplifications, he added.