Posted 1/31/2019 by Candice Brannen, PhD, Senior Director of Lab Products

Benefits of Second Tier Sequencing for Newborn Screening Programs

Babies born in the U.S. are screened for an average of 40 disorders through state universal newborn screening programs. If screening identifies a baby with the potential to have one of the disorders, this is considered a positive result and is handled by the newborn screening program in one of two ways:

1. Refer any positive result from the original screen to the follow-up program.

The follow-up program then notifies the family and physician of the result. The follow-up staff either collects a second sample for retesting at the public health lab or refers the baby for confirmatory testing.

The state program avoids the cost of running a second tier test.
Instead, the families bear the cost burden. One of the tests frequently administered to confirm abnormal follow-up test results is genetic sequencing, which may not be covered by the family’s insurance.
More families experience unnecessary anxiety while putting the newborn through additional tests and awaiting follow-up results.
While cost to the lab is lower, the follow-up program must serve an increased number of families due to a higher rate of referred cases.

2. Perform a second tier test using the original dried blood spot.

Second tier testing can reduce false positive results by ruling out ‘normals’ such as carriers and pseudodeficiencies before the follow-up program and family get involved.

By reducing the rate of follow-up referral cases, second tier testing can decrease the burden and costs to clinics from cases needlessly getting pushed into the system. This allows more timely and focused treatment for confirmed positive cases.
Second tier testing prevents unnecessary family anxiety.
Second tier testing by genetic sequencing avoids healthcare disparity by providing equity of care to all families.
The newborn screening program pays for the second tier test.

Why is additional testing necessary following a positive screen?

A newborn screening test indicates the potential that a baby has a particular disorder. For example, newborn screening for lysosomal storage disorders measures the level of enzyme activity in the baby’s blood. If the activity is below a certain “cut-off”, the baby has the potential to have the disorder – but requires further testing to complete the diagnosis. This cut-off level is set to maximize sensitivity so that all potential cases are identified, which avoids false negative results (missing an affected baby) but allows for false positive results.

Second tier testing helps reduce false positive results. Second tier can be performed as a biochemical test or genetic sequencing.

What are the benefits of Second Tier Sequencing vs. Second Tier Biochemical Testing for lysosomal storage disorders (LSDs)?

When considering second tier testing for LSDs, biochemical tests only address the level of the enzyme based on activity in the dried blood spot. Therefore, biochemical assays do not obtain information on variations or severity of disease, which can lead to delay of therapeutic intervention.

Second tier sequencing is a good mechanism to understand the child’s specific case because it can provide genotype differentiated data to improve the quality of referrals and promptly inform treatment decisions. For example: with Pompe disease, variant identification can help distinguish infantile onset (IOPD) from late-onset (LOPD), both of which have progressively worsening symptoms that can start to manifest shortly after birth. Sequencing can help better inform the physician to start early treatment before life-threatening symptoms appear.

In addition, sequencing can provide the family a marker for which other family members can be tested.

So, why not do genetic sequencing as the original screening test?

Second Tier Sequencing with Baebies

Baebies now offers second tier testing in our CLIA-certified lab using the original dried blood spot to perform targeted genetic sequencing. Baebies comprehensive molecular characterization service identifies specific mutations in the GAA (Pompe disease) and IDUA genes (MPS I, including Hurler, Hurler-Scheie and Scheie subcategories) – as well as mutations in the GBA (Gaucher disease), GLA (Fabry disease), GALC (Krabbe disease), and ASM genes (Niemann-Pick Disease).

If your state public health lab is currently testing for Pompe disease and MPS I or considering adding these disorders to your newborn screening panel, Baebies second tier sequencing provides the following benefits:

Reduces the false positive rate which saves follow-up programs time and money
Prevents unnecessary family anxiety incurred while awaiting follow-up results
Provides a precise genetic characterization to inform referral and treatment decision
Avoids healthcare disparity by providing equity of care to all families - moving insurance-based DNA sequencing follow-up to NBS-based universal screening

Want to introduce second tier sequencing to your newborn screening program? Request more info: