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Baby Genes Plans to Supplement Metabolic Newborn Screening with NGS-Based Panel

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NEW YORK (GenomeWeb) – Baby Genes plans to expand conventional metabolic newborn screening with targeted genetic testing in order to provide faster definite diagnoses.

The Golden, Colorado-based startup recently launched a next-gen sequencing newborn screening panel, targeting 89 genes that have been linked to more than 60 metabolic conditions. It has been offering the assay for $330 and with a turnaround time of 96 hours or less as a reflex or diagnostic test, a supplemental newborn screening test, or a carrier screening test. 

Each US state has its own mandatory metabolic newborn screening program, with varying numbers of conditions included. But according to Baby Genes CEO Richard Sjogren, current screening yields a significant number of false negative and false positive results, and following up on positive tests can be a lengthy process, often involving confirmatory metabolic and subsequent genetic testing.

Other genetic tests that follow up on metabolic screening results are generally more expensive than Baby Genes' panel, often only test for a small number of genes, and have a longer turnaround time, he said. And in contrast to whole-exome or whole-genome sequencing, the Baby Genes panel produces fewer incidental findings, and 90 percent of the conditions it covers are treatable.

Sjogren and an undisclosed partner with expertise in NGS and library preparation founded Baby Genes in 2013 in order to provide a genetic screening test that could serve both as a supplement and as a confirmatory test for metabolic newborn screening. "We focus on giving answers to neonatologists quickly," he told GenomeWeb.

So far, the company, which has five employees and plans to expand, has been funded by private individuals. Its laboratory, which opened a year ago, recently became CLIA-certified and the firm is in the process of applying to states like California and New York that have additional requirements for clinical testing.

Baby Genes accepts either dried blood spots or buccal swabs for its laboratory-developed test, though the quality tends to be better with blood samples. The 89 genes are amplified using a customized Enzymatics Archer Anchored Multiplex PCR panel, followed by sequencing on the Illumina MiSeq.

The company has been able to keep prices low by focusing on a single test and establishing a streamlined laboratory process, Sjogren said.

Baby Genes is currently wrapping up a clinical validation study of its test on the MiSeq Dx that involves 150 de-identified samples of patients, including those with known metabolic conditions, and plans to publish the results within the next month, according to Kaylee Dollerschell, the firm's laboratory scientist and business analyst. In addition to the MiSeq Dx, it has a regular MiSeq in house.

The company's panel covers all core and secondary metabolic disorders recommended by the American College of Medical Genetics and Genomics for newborn screening. In addition, it includes genes for conditions that are not usually part of routine newborn screening, such as Krabbe, Gaucher, Fabry, Niemann Pick C, Pompe, MPS I, and X-ALD.

The test, which sequences the exons of the 89 genes, reports on almost 2,000 variants that have been classified as pathogenic or likely pathogenic, as well as variants of unknown significance.

So far, the company has run about 100 patient samples. Most of them were paid for by patient families, but the firm is in the process of filing insurance claims and can also bill institutions.

In the case of one patient from Montana, the initial metabolic screen came back normal, but less than a week after birth, the child developed a serious condition and was admitted to the neonatal intensive care unit. His doctor suspected a fatty acid disorder and ordered Baby Genes' panel, which provided results within a little more than 48 hours and confirmed a homozygous mutation in a gene that causes the condition.

In another case, the patient's metabolic screen showed an abnormal result but Baby Genes' panel found there was no genetic mutation. Since the patient's phenotype was normal, the initial screening result was likely a false positive.

So far, marketing for its test has been limited, but in the future Baby Genes plans to target physicians, including OB-GYNs and pediatricians, as well as parents.

It also plans to form partnerships, for example with a chord blood banking company that might be interested in distributing its test, and has been in discussions with several hospitals about offering the test as a follow up to abnormal metabolic screens, and eventually, as a supplemental screening test. According to Dollerschell, the test could be especially attractive to neonatal intensive care units who want a quick diagnosis for sick newborns with inconclusive metabolic screening results.

Longer term, Baby Genes also plans to seek 510(k) approval for its test from the US Food and Drug Administration, and to have it CE-marked in Europe.

A clinical trial that would compare the utility of its test to metabolic screening alone is also "definitely something we would like to do" in the future, said Dollerschell. The company emphasizes, however, that it does not consider its test as a replacement for metabolic screening. "They give you two different types of information. Hand in hand, they can give you some great answers very quickly," she said.

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