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Maximizing next-generation sequencing in newborn screening through bioinformatics

A baby sleeps with his dad

by Samantha Marcellus, MPH, APHL-CDC Newborn Screening Bioinformatics Fellow

We live in the era of rapid access to near limitless information, over-the-counter DNA testing, and emerging gene therapies. As genetic testing, technology, and treatments advance, newborn screening must broadly utilize bioinformatics to keep up with the ever-changing rare disease arena and other areas of public health. Infectious diseases groups have widely adopted bioinformatics and next-generation sequencing over the last decade, and many laboratories have the capability to sequence and interpret the whole genome of a pathogen in hours or days. Through bioinformatics, cases can be linked via their specific strains and outbreaks can be declared more rapidly than ever before.

For the states that have harnessed the power of next-generation sequencing and bioinformatics for second- or third-tier screens, test times have been reduced and more detailed genetic information is presented to the providers. Continued and widespread implementation of bioinformatics in NBS is vital for programs to keep up with advances in technology and to offer providers and parents a more complete picture of the newborn’s risk profile.

Getting Started in Texas
In spring 2019, APHL and the Newborn Screening and Molecular Biology Branch at the US Centers for Disease Control and Prevention (CDC) selected the inaugural class of Newborn Screening Bioinformatics Fellows—myself and three others. We were matched with state public health laboratories to enhance or implement bioinformatics in their NBS programs.

At the Texas Department of State Health Services Laboratory we are building a bioinformatics program from the ground up. We are developing and refining a program to efficiently and accurately analyze and interpret severe combined immunodeficiency (SCID) next generation sequencing data. The public health bioinformatics community has already developed many great pipelines and analysis tools, so we plan to draw from those tools while adding some of our own programs to best fit the needs of Texas newborns. While all states utilize bioinformatics in different ways, we can still learn a great deal from our collective experiences.

In Texas, geneticists and consultants from around the state have shown interest in receiving sequencing information from the newborn screening program. The results from next-generation sequencing can be used to complement currently available newborn screening results and provide parents with a more complete picture of their child’s risk for a screened disease. As gene therapy is developed for an increasing number of disorders and those diseases are added to the Recommended Uniform Screening Panel (RUSP), the need for rapid DNA sequencing may increase in kind.

Looking Forward
With in-house bioinformaticians, laboratories will be able to process and analyze next-generation and Sanger sequencing data more rapidly and with programs that are designed to fit the state’s specific needs. These capabilities can allow for faster test times, higher accuracy and precision in results, and quicker result reporting. In the case of newborn screening, that could mean referring a baby to a specialist more quickly and with more complete information. Through programs such as the APHL/CDC Newborn Screening Bioinformatics Fellowship, state laboratories have the opportunity to develop staff and infrastructure to meet the evolving needs of newborn screening programs and public health in general.

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