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BillionToOne Secures $83.5M in Private Funding, Loan Facility; Shows Clinical Performance of NIPT

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This article was corrected on Dec. 17, to clarify the number of Unity sgNIPS tests sold to date. That number is over 100,000, as opposed to over 9,000 as previously stated.

NEW YORK – BillionToOne said on Wednesday that it has raised an additional $48.5 million in funding from existing investors and increased its term loan facility to $35 million, extending the firm's cash runway to the end of 2024 and enabling it to further develop and commercialize its noninvasive prenatal screening test and oncology products.

Also, in a recently published study, the firm's Unity test, which combines a maternal carrier screen and reflex single-gene noninvasive prenatal test (NIPT), accurately estimated fetal risk for a number of recessive conditions without the need for paternal samples, indicating the test's potential as an alternative to traditional carrier screening.

BillionToOne has already launched a follow-on validation study, for which it is gathering data, and hopes to eventually win inclusion of Unity into clinical guidelines.

The new funding follows a $125 million Series C round earlier this year and came from existing investors in that round, including Libertus Capital, Hummingbird Ventures, Baillie Gifford, Adams Street Partners, Neotribe Ventures, Fifty Years VC, Norwest Venture Partners, and Time BioVentures. BillionToOne also upsized its term loan facility with existing lender Bridge Bank and now has access to up to $35 million in loans.

The cash infusion, consisting of dilutive and non-dilutive capital, will give the firm more space to scale up its Unity screening test and to commercialize its Northstar Select and Northstar Response liquid biopsy tests in early 2023.

Jennifer Hoskovec, senior director of medical affairs at BillionToOne, estimated that the company has sold more than 100,000 Unity sgNIPT tests so far and that peer-reviewed research studies like the current one should give providers confidence in the screening test that will help the company grow. Pricing for the Unity test has not been established yet, she said, adding that traditional carrier screening is typically covered by insurance.

BillionToOne's study, published earlier this month in Genetics in Medicine, evaluated the clinical performance of the company's Unity test, which combines maternal carrier screening and reflex single-gene noninvasive prenatal screening (sgNIPS), among 9,151 pregnant women, screening them for being carriers of cystic fibrosis (CF), alpha and beta thalassemia, and spinal muscular atrophy (SMA).

Unity provided an informative result — either negative carrier status or being heterozygous for a pathogenic variant — to 98.7 percent of the cohort, leaving a 1.3 percent no-call rate.

While overall Unity showed a negative predictive value (NPV) of 99.4 percent and a positive predictive value (PPV) of 48.3 percent, Hoskovec commented that the test's performance was better demonstrated in individual risk quartiles.

"Overall PPV," Hoskovec said, "[isn't] overly useful, particularly to the patient themselves. What they want to know is … how confident can I be that that's truly the chance that my baby's affected? And that's what our data showed."

All four pregnancies estimated to have a risk of 90 percent or more for one of the assayed conditions, for instance, were in fact affected. Of the 17 pregnancies with risk estimated at between 50 and 66 percent, 47 percent were affected. One quarter of pregnancies with risk between 1 and 20 percent were affected, and finally, only one of 162 pregnancies with a less than 1 percent risk was affected.

Unity provides an alternative to the traditional carrier screening workflow of testing the mother first and then, should she test positive, the father. If the father also tests positive, then the mother, if she is already pregnant, would be referred for more invasive diagnostic testing.

In real-world scenarios, however, paternal DNA is not always available, such as when the father is not present or does not have insurance that covers carrier screening. These complications limit the usefulness of traditional carrier screening and can lead to undue concern on the part of the expectant mother throughout her pregnancy.

In its study, BillionToOne argued that implementing maternal carrier screening with reflex sgNIPS, as enabled by Unity, could serve an important role in improving healthcare equity.

Mary Norton, professor and vice chair for clinical and translational genetics, obstetrics, gynecology and reproductive sciences at the University of California, San Francisco, commented, though, that while certainly a useful tool, Unity's role in the healthcare system shouldn't be overstated.

"The biggest equity issue is lack of insurer coverage for carrier screening," she said, "particularly for the male partner. However, this approach is a clever solution for patients who are known carriers of a common known variant for a common disorder and in which the partner is not available and/or the patient declines diagnostic testing but does want some further analysis."

She also noted that the study's claim that traditional carrier screening may be ineffective in many cases is "unclear depending on the outcomes being sought."

"For the disorders in this report," she said, "traditional carrier screening is extremely effective in identifying tested individuals as carriers."

Another limitation stems from the study's relatively small sample size, she said.

The study, Norton said, "only had follow-up on 200 cases of over 9,000 studied. These data are helpful as this company has been offering this test for a few years without any published data, but with a 2 percent follow-up rate, the overall performance in clinical settings is uncertain."

Nonetheless, the present data does provide useful information regarding Unity's analytic validity, she added, although it doesn't address the test's utility in population screening, which she sees as a critical question.

Hoskovec acknowledged that the conclusions drawn from this study must be corroborated in further validation studies, adding that these are now taking place.

BillionToOne is currently collecting data from an ongoing multisite chart review study of over 1,300 carriers of at least one of the tested conditions. Although the two studies are similar in size, Hoskovec said that the multisite study collection methodology is different and should result in significantly more affected fetuses among eligible patients. 

"Our hope is that not only the patients and providers recognize that this is a useful approach and useful information, but that ACOG, for example, will recognize the utility of this [test] for when providers or partners are unavailable."

BillionToOne's proprietary quantitative counting template (QCT) technology drives the Unity sgNIPT assay. QCT involves spiking synthetic DNA molecules into a cell-free DNA sample prior to PCR amplification. The synthetic molecules share some DNA sequence with the genes of interest and amplify at the same rate, enabling BillionToOne to calculate the number of target DNA molecules in a sample, and therefore to assess gene dosage in cases where it is medically relevant, such as in SMA.

Because the synthetic molecules must be uniquely designed for each variant, however, carriers of uncommon variants in conditions with a high number of them, as in the case of the F508del variant in CF, can slip under the radar. The F508del mutation accounts for approximately 65 percent of carriers in CF, with the next most common variant accounting for an allele frequency of approximately 2.5 percent.

"CF has about 1,700 variants," Hoskovec said, "and we don't have 1,700 different assays."

BillionToOne is planning to design probes for more CF variants, she said, but will decide how to prioritize those based on observed frequencies. Further development, she added, "needs to be really strategic," in order to maximize patient benefit while containing test development costs.

BillionToOne has also been adapting its QCT technology to other disease indications, such as detecting actionable cancer mutations and monitoring cancer patients' drug response or resistance to therapy. Additionally, Hoskovec mentioned that the company is looking into Rh and fetal antigen testing via the same technology.

"I think [Unity] is really game changing similar to the way NIPT was game changing for aneuploidy," Hoskovec said. "We're really excited that with this particular paper, we were able to show that everything we're doing is performing as expected in the real world."

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