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.

The post Maximizing next-generation sequencing in newborn screening through bioinformatics appeared first on APHL Lab Blog.

Small multiples pizza baby

For each month in her child’s first year, Amanda Makulec took a picture of her baby and a pizza. Each slice represents a month. Hence, pizza baby.

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Blanket pattern visualizes baby’s sleep data

Seung Lee collected sleep data for his son’s first year. Then he knitted a blanket to visualize the data. The blanket is impressive. Collecting a baby’s sleep data for a year? More so.

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Addition of lysosomal storage disorders to newborn screening panels is complex and highly emotional

Addition of lysosomal storage disorders to newborn screening panels is complex and highly emotional | www.APHLblog.org

By Michelle Forman, senior specialist, media, APHL

When it comes to newborn screening, the primary goal, simply stated, is to save or improve the lives of babies who otherwise may have died or been severely disabled. While the goal of the program is rather straightforward, achieving that goal can be very complicated. The addition of lysosomal storage disorders (LSDs) to newborn screening panels fully exemplifies how complex and emotional this critical public health program can be.

While newborn screening is a program managed by each state, there is a federal panel that reviews and recommends conditions to be added to state screening panels. The Secretary of the US Department of Health and Human Services’ Advisory Committee on Heritable Disorders in Newborns and Children (ACHDNC) uses strict criteria when considering which conditions should be recommended for addition to the Recommended Uniform Screening Panel (RUSP). Disorders added to the RUSP are evaluated based on scientific evidence that demonstrates:

  • The potential benefit of routinely screening all newborn babies,
  • Public health laboratories’ ability to perform the test and
  • Availability of effective treatments for the disorder.

LSDs consist of 50 rare metabolic diseases that are characterized by vital enzyme deficiencies which cause build-up of toxic materials in a person’s tissues and organs. If left untreated, the patient’s physical and mental functions will begin to deteriorate, likely leading to death. Krabbe, Pompe, Niemann-Pick A/B, MPS I and Fabry are all part of this group of diseases, and they have all been considered as potential additions to the RUSP. As of February 16, 2016, only Pompe and MPS 1 have been approved. The other conditions have not been formally recommended to the Secretary for consideration because they don’t meet the requirements listed above. Most often, the committee cited the lack of a perfected test and/or a lack of effective treatment for the condition.

However, some states have gone beyond the RUSP and have added or are planning to add certain LSDs to their newborn screening panels. On June 1, 2015, after a nearly seven month long pilot program, Illinois became one of three states to implement testing for LSDs joining New York and Missouri. Statewide testing in Illinois was implemented for five LSDs (Gaucher, Fabry, MPS I, Niemann-Pick A/B and Pompe) – state law requires two additional conditions, MPS II and Krabbe, which will be added at a later date.

Addition of lysosomal storage disorders to newborn screening panels is complex and highly emotional | www.APHLblog.orgAdding LSDs to newborn screening programs requires extensive work. The Illinois newborn screening program chose to use the most common testing platform, tandem mass spectrometry (MS/MS), for LSD screening because it lends itself to multiplexing (screening for multiple conditions at once) and high specimen throughput (screening lots of samples quickly). In order to accommodate these instruments, the Illinois public health laboratory needed to undergo renovations such as adding higher voltage outlets and additional air conditioning units. The renovations combined with the cost of renting the MS/MS instruments and other necessary equipment, buying reagents, staff labor and laboratory overhead totaled $1.45 million just to get the laboratory portion of the program off the ground. The follow-up costs are close to $150,000 annually. (The Illinois newborn screening program increased fees to cover this cost. Every state handles costs differently. Within each of the state profiles on NewSTEPs’ website, you can see how they handle fees.)

There is still controversy surrounding LSD screening. One concern is that the results aren’t necessarily straight-forward. An abnormal result could mean the baby is an asymptomatic carrier, will experience late onset with milder symptoms, needs treatment immediately to prevent serious outcomes, or other possibilities depending on the condition. In order to fully understand what abnormal results mean and to provide a definitive diagnosis, further diagnostic and genetic testing is required. However, in Illinois many insurance companies won’t cover that additional testing. For some families, paying for genetic testing out of pocket (often around $2,000) simply isn’t an option. Some families have refused.

As of January 2016 (over a year since the pilot program began), Illinois has screened over 110,000 specimens. Of those, 276 babies had abnormal results. Here is a breakdown of those newborns:

  • After undergoing further testing, 17 were diagnosed with a lysosomal storage disease. Most of these cases were Pompe and MPS I.
  • Fewer than 10 have refused additional genetic testing. That means there was enough information to warrant additional testing, but without it there is no official diagnosis.
  • There are still 74 cases pending. Some of these cases are awaiting additional testing while some are trying to determine how they will pay for that testing; there are many possible reasons for these pending cases.

While speaking with staff in the Illinois newborn screening program, their strong desire to help newborn babies and their families was abundantly clear. They were driven to perform their job as they were expected and as best they could. But the challenges they faced were also clear. For example, one of the conditions on their LSD panel is Niemann-Pick A/B, a neurological disorder that has no FDA approved treatment yet; the outcome for the baby is typically death. This makes it extremely hard to explain the results and what it means for the family.

Illinois is paving the way for other states to implement similar testing when the time is right. Many of their peers look to them for guidance on this issue.

Articulating the value of newborn screening can be very simple when discussing metabolic conditions for which we have been screening for decades and treatments are readily available. But newborn screening for LSDs is still very new, just as PKU screening once was. And just like with PKU, the desire to perfect LSD testing in order to save babies’ lives is eminently clear.

 

Q&A with NewSTEPs: Bringing routine CCHD newborn screening to every state

The latest release of CDC’s Morbidity and Mortality Weekly Report (MMWR) highlights the rapidly expanding program to routinely test all newborns for critical congenital heart disease (CCHD). In September 2011, CCHD was added to the HHS secretary’s Recommended Uniform Screening Panel (RUSP) for all newborns in the United States. Currently, the vast majority of states require CCHD screening for newborns while others have policies in the pipeline.

Read how this simple test saved Baby Dylan’s life

As noted in the MMWR, in 2014 CDC began partnering with the Newborn Screening Technical assistance and Evaluation Program (NewSTEPs), a program of APHL in collaboration with the Colorado School of Public Health. NewSTEPs is a national newborn screening program designed to provide data, technical assistance and training to state newborn screening programs across the country.

Sikha Singh, manager of NewSTEPs (APHL), and Marci Sontag, associate director of NewSTEPs (Colorado School of Public Health), answered some questions about bringing routine CCHD screening to all 50 states.

A primary role for NewSTEPs in the success of the CCHD newborn screening program has been data collection. Why is data collection a key contributor to this program’s success?

As with all newborn screening, it is important to have continuous quality assurance programs for CCHD screening. Data shows us what is working and where improvements can be made. At the public health level (as opposed to clinical care), we are always asking these questions:

– How many newborns were screened?
– Were there any newborns who were not screened but should have been?
– How many newborns had abnormal screening results and what happened to them?
– Did the newborns who had abnormal results receive the appropriate follow-up and care?
– Is the testing algorithm being appropriately implemented?
– Can changes be made to the algorithm to decrease inaccurate results?

CCHD newborn screening is done right in the hospital with a pulse-oximeter that is placed on the baby’s foot. No sample is sent to a public health laboratory like with other newborn screening tests. So why is APHL involved in this aspect of the newborn screening program?

Q&A with NewSTEPs: Bringing routine CCHD newborn screening to every state | www.APHLblog.orgAPHL and NewSTEPs are a newborn screening resource, so we are responsible for supporting that system. CCHD screening is one of two point-of-care newborn screening tests that are not laboratory- based (hearing loss detection is the other.) In many cases, newborn screening program staff are covering all aspects of the state’s newborn screening program. If our members and partners are focused on the entire system, we need to be as well.

Why was the addition of CCHD testing so significant for the newborn screening program?

Addressing CCHD screenings is very different from other newborn screens because abnormal results mean a baby requires immediate follow-up care prior to leaving the hospital. Abnormal results would indicate a dire situation and, in many cases, the solution is open heart surgery. CCHD screening therefore sets off a completely different chain of events than other newborn screens.

From the direct perspective of NewSTEPs, the exchange of information is different. With laboratory- based newborn screening, data is typically sent from the state public health laboratories to birthing facilities. With CCHD, we are working to get data from birthing facilities to newborn screening programs, which poses significant financial and logistical challenges.

More broadly speaking, the addition of CCHD to newborn screening panels has expanded public health’s commitment to addressing severe conditions in the very early stages of life before permanent damage can be done. While newborn screening once referred only to metabolic conditions, it now includes many other types of heritable diseases as well. The addition of both CCHD and hearing loss detection brought newborn screening into completely new territories but under the same goal of saving and improving babies’ lives.

What needs to happen to have all 50 states routinely screening every newborn for CCHD?

As the MMWR indicates, we are very close to having all states routinely screening for CCHD. In fact, additional states have begun mandatory CCHD screenings since the MMWR was written. NewSTEPs works closely with each state to evaluate the best mechanism for moving routine CCHD screening forward. In some states, legislative action has been necessary to move CCHD screening forward, but other states have mandated screening through regulatory action, and yet other states have implemented statewide screening absent a legislative or regulatory mandate. Through our ongoing data collection and analysis, along with the help of partner organizations and parent advocates, we have the tools and the momentum necessary to ensure that CCHD newborn screening becomes the standard of care in all states.

Learn more about NewSTEPs

Newborn Screening: This Tiny Test is a Big Job That’s Always Improving

By Scott J. Becker, executive director, APHL

Newborn screening saves or improves lives – 12,000 each year, to be specific. Every year over four million babies born in the United States have their heels pricked during the first days of life to check for certain devastating conditions that are not otherwise apparent at birth. The small number of babies who test positive for those conditions may suffer serious and irreversible damage without early detection. Newborn screening enables health professionals to identify and, in most cases, treat those babies allowing them to grow up to live healthy, normal lives. The newborn screening program is one of our nation’s greatest public health achievements, but that doesn’t mean it is perfect.

Newborn Screening: This Tiny Test is a Big Job That’s Always Improving | www.aphlblog.org

Last year a series in the Milwaukee Journal Sentinel drew public attention to some of the areas in which the newborn screening program needed to improve. That story and a recent editorial in USA Today focused on the amount of time between specimen collection, testing and reporting of results. Timeliness is critical for the newborn screening program to be a success, and we acknowledge the valuable contribution these articles have made.

Continual quality improvements – including timeliness – have been and continue to be a priority for public health laboratories, the agencies responsible for identifying and reporting positive newborn screening test results. In fact, APHL recognized the efforts of many state programs during the 2014 Newborn Screening and Genetic Testing Symposium. Many state newborn screening programs have conducted hospital site visits; conducted targeted outreach to lagging performers and publicly recognized top performers; provided hospitals and other specimen submitters with guidelines for collection of specimens; reinforced regulatory requirements; and provided training for use of overnight courier shipping software. Program changes like these in states around the country have significantly improved specimen transit times.

APHL and its members have collaborated with the Department of Health and Human Services Discretionary Advisory Committee on Heritable Disorders in Newborns and Children to develop updated recommendations on timeliness guidelines. These activities occur in tandem with a series of other quality improvement activities including proficiency testing, evaluation of emerging technologies and implementation of quality practices pertaining to screening, confirmation and results reporting.

I am proud of the work state newborn screening programs are doing every day. We do not take the public health laboratories’ role in this life-saving program lightly, and I thank the staff for their dedication to improving it. Our focus is on the babies – it always has been and always will be.