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Baebies Enters Phase II of NIH Funding for Droplet-based Neonatal Saliva Screen for CMV


NEW YORK (GenomeWeb) — Headed by a co-founder of Advanced Liquid Logic, startup company Baebies has entered the second stage of Small Business Innovation Research funding from the National Institutes of Health to develop a point-of-care cytomegalovirus assay appropriate for routine screening of newborns.

The assay will be an integrated lab-on-chip device to detect CMV DNA in saliva samples, performing real-time PCR on droplets shuttled between thermal zones, as opposed to traditional thermal cycling.

Vamsee Pamula, president and founder of the Durham, NC-based startup, told PCR Insider in an email this week that Baebies also "has a robust pipeline of several other new assays," and the company "has a singular focus on newborn screening."

"We perform real-time PCR on droplets that are shuttled between thermal zones … set up on the cartridge, as opposed to thermal cycling [of] a droplet in place," Pamula said, since "shuttling just a sub-microliter droplet between thermal zones allows faster heating and cooling."

CMV is a leading cause of late-onset and progressive hearing loss in babies, and Baebies' current funding, which totals just under $500,000 over the next fiscal year, was awarded by the National Institute on Deafness and Other Communication Disorders.

Diagnosis and treatment of congenital hearing loss is often delayed until one or two years of age, while auditory stimulation during the first six months of life is critical to the development of speech and language skills, Pamula said.

Universal newborn hearing screening and subsequent early intervention have been demonstrated to improve language and development outcomes. Unfortunately, "most of the estimated 30,000 congenitally [CMV]-infected infants born each year in the US have no clinically detectable symptoms at birth and are not identified by current universal newborn hearing screens," Pamula said.

"Without early detection and intervention therapies, 15 percent of asymptomatic infants develop CMV-related hearing loss," he added.

A rapid and reliable nucleic acid test for CMV was recently described by Baebies collaborator Suresh Boppana, a professor of pediatrics and microbiology at the University of Alabama, Birmingham, Pamula said. That test detects pathogen DNA in saliva, an increasingly common PCR sample type.

The Boppana study, published in May in The Journal of Infectious Diseases, compared rapid CMV culture to PCR analyses of both urine and saliva specimens to determine the clinical utility of the real-time PCR assay for diagnosis of congenital CMV infection. In the study, "saliva was found to be [a more] appropriate sample for CMV than the conventional dried blood spot[s]" that are currently collected from newborns to screen for a number of diseases, Pamula explained. A similar study of CMV in neonatal saliva samples was done by a group in Ireland, and published in March in the Journal of Clinical Virology.

A PCR-based CMV test could be useful, but "current newborn screening programs do not have the infrastructure necessary to perform screening using saliva samples," Pamula explained.

The Baebies on-chip PCR device, therefore, may provide "a turnkey solution for performing nucleic acid testing on saliva samples from newborns," he said.

The droplet-shuttling method used in the device has been described in three recent publications.

The first was a 2010 Analytical Chemistry paper detailing a digital microfluidic platform for multiplex real-time PCR using a closed-loop, flow-through format. In this proof-of-concept study, the researchers showed the platform, with built-in magnetic microbead capture, was able to detect methicillin-resistant Staphylococcus aureus, Mycoplasma pneumoniae, and Candida albicans from whole blood. While continuous-flow PCR is not completely novel — researchers have recently adapted it for robotic sampling of deep sea microbes, for example — it is not common.

Next, a study published in Diagnostic Microbiology and Infectious Diseases used the device for sensitive, fast, and inexpensive detection of Mycoplasma pneumoniae, a common cause of hospital-acquired pneumonia, from nasopharyngeal specimens.

Most recently, a study published in the European Journal of Clinical Microbiology and Infectious Diseases showed the microfluidic device was able to detect C. albicans DNA in low volumes of blood. That study evaluated blood from a mouse model of systemic candidiasis, as well as clinical samples from patients with culture-proven infection.

As reported last year in In Sequence, Illumina acquired Advanced Liquid Logic primarily for ALL's sequencing technologies. At that time, the ALL newborn screening platform for lysosomal storage disorder was an example of technology that Illumina was still deciding whether it would pursue.

According to Pamula, Baebies continues to develop that platform, which performs biochemical assays on dried blood spots and is also referred to as the LSD-100 Lysosomal Storage Enzyme Analyzer. It is being evaluated in a pilot study in Missouri, with over 150,000 babies screened thus far. It has also been subjected to a product comparison study by the Mayo Clinic on about 100,000 newborn samples, Pamula said.

The microfluidic device measures lysosomal storage enzyme activities in 40 dried blood samples at a time, and effectively screens for four different rare genetic disorders — Pompe, Fabre, and Gaucher diseases, and Hurler syndrome. In 2012, ALL received a $3 million grant from the National Institute of Child Health and Human Development to further develop the platform

For the CMV test, Baebies is currently further developing the technology, demonstrating proof of concept of the utility of the device to detect CMV in newborn saliva, and performing a method comparison with clinical gold standard techniques, Pamula said.

Baebies "is a very early stage company," he added, and has not yet established any relationships for commercialization of this test.