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Armed With $10M in Funding, Phosphorus Plans to Expand Genetic Testing, Bioinformatics Footprint


NEW YORK (GenomeWeb) – Newly minted computational genomics firm Phosphorus is hoping to build its business around bioinformatics solutions that support genetic testing laboratories as well as clinical tests for identifying patients' predispositions to cardiovascular disease and other conditions.

The company is preparing to launch two new genetic tests in 2017 and helping a number of unnamed clinical labs implement its lab management and variant analysis and reporting software, Phosphorus Founder and CEO Alexander Bisignano told GenomeWeb this week.

Specifically, Phosphorus plans to launch two new tests for cardiovascular disease in January. The first of these, called HeartMap, will test for a predisposition to sudden cardiac death due to cardiomyopathies and arrhythmias, while its second test will focus on familial hypercholesterolemia, a genetic disorder associated with high cholesterol levels in the blood and early-onset cardiovascular disease in patients.

Bisignano told GenomeWeb that the company will use funds from its recently closed $10 million Series A funding round to launch the two planned cardio tests — the financing will also be used to hire new computer scientists, engineers, and geneticists. The company has completed developing and validating the tests as well as associated analysis infrastructure and is currently working on obtaining the appropriate licenses for its new lab. Those procedures should be completed sometime in the next five months, he said.

These initial tests cover genes for which there are medical guidelines and which are covered by some of the major private insurers. Bisignano declined to provide specifics on the company's billing because Phosphorus is still in negotiations with a few payers. He did say that the company does bill a few thousand dollars for each test but generally patients will pay under $500 in out-of-pocket costs. 

A portion of the incoming funds will go towards setting up Phosphorus' software at the first set of laboratory customers, which is interested in using the software to support its tests. Phosphorus is initially trying to get the software installed at a few beta sites before offering the solution to more customers, Bisignano said. However, the demand for these sorts of solutions is quite high, he told GenomeWeb. "We see a lot of hospitals and regional labs wanting to bring testing in house …  yet dealing with this data, building their own labs, [storing data] in the cloud, how to curate variants, these are high-complexity problems," he said. "Our software is a turnkey solution that solves it for them."

Phosphorus software is built on Amazon Web Services infrastructure so customers have access to ample space for storing NGS data. The software includes tools for automatically annotating variants found in samples and includes a variant decision-tree model that helps curators easily identify and make calls on newly seen mutations. There are also tools for generating customized clinical reports as well as for performing laboratory operations including tasks such as sample accessioning, laboratory tracking and assay management, and digitization and storage of requisitions. Lastly, Phosphorus offers a family pedigree tool for structuring familial relationships and for analyzing trio data as well as for ordering and managing results, Bisignano told GenomeWeb. The same tool also assists genetic counselors with taking and recording family and disease histories in a structured manner.

For the use of its software, Phosphorus charges a per-sample license fee, which is a few hundred dollars per sample, and that cost covers the analysis and variant calling. In addition to the software, labs can also use the company's library preparations and all the chemistry needed to perform the genetic test that they are interested in doing in house – customers purchase the actual materials they need for the test directly from the manufacturers. "It's a very cost effective way for labs to bring in this type of testing if they don't have the facility to do this in house," Bisignano said.

In terms of its clinical tests, LabCorp and Quest have offerings for some of the genes that Phosphorus' cardiovascular panels will test for. But Bisignano believes that Phosphorus tests will be able to compete especially in terms of cost. "We are able to develop [a] test for all these genes at once at a significantly reduced price than any individual test of these genes," he said. Also "we've built really good software for our physician partners to manage the family pedigrees and made ordering and tracking tests for family members much easier. A big part of cardiogenetics is making sure the family members are all tested to identify risk."

On the software side, Bisignano sees solutions from Omicia and Sophia Genetics as potential competitors. Just last week, Sophia Genetics unveiled plans to release new technology in the next release of its software that provides mode accurate and precise predictions of variant pathogenicity. However, he noted, Phosphorus software offers more features beyond variant analysis and interpretation, including, for example, tools for assay design and laboratory management. "These are major blockers for a lot of organizations," he said. Also compared to some other solutions on the market, "ours is far more turnkey," he added. "A lab with very limited current NGS capabilities would have the full ability to operate."

He and Phosphorus Cofounder Santiago Munne launched the company to commercialize software that used to be part of Recombine, a reproductive genetics company that they founded. Recombine developed and sold a genetic test called CarrierMap to fertility clinics. The test is used to screen couples looking to become pregnant or in the early stages of pregnancy to determine their risk of passing on more than 300 genetic diseases including cystic fibrosis and Tay Sachs to their progeny. 

That company also launched a research study called FertilityMap that aims to examine genetic factors that affect fertility and develop predictive algorithms to inform infertility diagnosis, prognosis, and treatment. As part of the study, Recombine researchers collected sequence data from consenting patients at fertility clinics and then mapped the information to patients' clinical records including hormone levels and andrology reports. "We've been slowly determining more variants and mapping out gene networks to be able to start predicting different types of infertility," Bisignano said.

Bisignano and Munne sold Recombine's commercial test portfolio to CooperSurgical earlier this year for $85 million and then launched Phosphorus to commercialize the underlying computational technology it previously used to support the tests. "With Cooper Surgical purchasing CarrierMap, we see that test going further into the Ob/Gyn network," Bisignano said. Under the terms of the agreement, Phosphorus will continue to support the CarrierMap test and will have access to all the data generated from patients who take the test. Phosphorus will use that data to continue to grow its network of genetic and clinical data it is building in addition to expanding the Fertility Map study, Bisignano said. The company will also expand the network with data from its new clinical genetic tests, he added.