The California Department of Public Health started universal newborn screening for Pompe disease in August 2018 with a two-tier process including: (1) acid alpha-glucosidase (GAA) enzyme activity assay followed by, (2) GAA gene sequencing analysis. This study examines results from the first year of screening in a large and diverse screening population. With 453,152 screened newborns, the birth prevalence and GAA enzyme activity associated with various types of Pompe disease classifications are described. The frequency of GAA gene mutations and allele variants are reported. Of 88 screen positives, 18 newborns were resolved as Pompe disease, including 2 classic infantile-onset and 16 suspected late-onset form. The c.-32-13T>G variant was the most common pathogenic mutation reported. African American and Asian/Pacific Islander newborns had higher allele frequencies for both pathogenic and pseudodeficiency variants. After the first year of Pompe disease screening in California, the disease distribution in the population is now better understood. With the ongoing long-term follow-up system currently in place, our understanding of the complex genotype-phenotype relationships will become more evident in the future, and this should help us better understand the clinical significance of identified cases.

X-linked adrenoleukodystrophy (ALD) is a recent addition to the Recommended Uniform Screening Panel, prompting many states to begin screening newborns for the disorder. We provide California’s experience with ALD newborn screening, highlighting the clinical and epidemiological outcomes observed as well as program implementation challenges. In this retrospective cohort study, we examine ALD newborn screening results and clinical outcomes for 1,854,631 newborns whose specimens were received by the California Genetic Disease Screening Program from 16 February 2016 through 15 February 2020. In the first four years of ALD newborn screening in California, 355 newborns screened positive for ALD, including 147 (41%) with an ABCD1 variant of uncertain significance (VUS) and 95 males diagnosed with ALD. After modifying cutoffs, we observed an ALD birth prevalence of 1 in 14,397 males. Long-term follow-up identified 14 males with signs of adrenal involvement. This study adds to a growing body of literature reporting on outcomes of newborn screening for ALD and offering a glimpse of what other large newborn screening programs can expect when adding ALD to their screening panel.

Since the start of X-linked adrenoleukodystrophy (ALD) newborn screening in California, more than half of the diagnosed cases were found to have an ATP binding cassette subfamily D member 1 (ABCD1) gene variant of uncertain significance (VUS). To determine retrospectively the likelihood that these were true positive cases, we used a web-based post-analytical tool in Collaborative Laboratory Integrated Reports (CLIR). Confirmatory plasma very long-chain fatty-acids (VLCFA) profiles for ALD screen positive infant boys were run through the CLIR ALD tool. We compared the distribution by ABCD1 variant classification (pathogenic, likely pathogenic, VUS, and no variant) with the CLIR tool score interpretation (non-informative, possibly ALD, likely ALD, and very likely ALD) and the current case diagnosis. The study showed that CLIR tool positive interpretations were consistent with 100% of the pathogenic and likely pathogenic variants on the ABCD1 gene if a more conservative guideline was used. The tool interpretations were also consistent with screened cases that were determined to not have disease (our no-disorder group). The CLIR tool identified 19 diagnosed ALD cases with VUS to be potential false positives, representing a 40% reduction among all diagnosed ALD cases with VUS. The reduction could be extended to 65% if a more aggressive threshold was used. Identifying such preventable false positives could alleviate the follow-up burden for patients, their families, and California Special Care Centers.

The California Genetic Disease Screening Program (GDSP) employs a fixed immunoreactive trypsinogen (IRT) cutoff followed by molecular testing to screen newborns for cystic fibrosis (CF). The cutoffs approximate a 1.6% yearly IRT screen-positive rate; however, seasonal variation in IRT population means has led us to develop a model to establish fixed IRT cutoffs that anticipate seasonal variation and minimize missed cases below cutoff. We utilized an ARIMA model to fit monthly IRT screen-positive percentiles and estimated regular seasonal expectations. We established a retrospective cohort followed for at least 1.5 years to capture missed false-negative CF cases. We compared missed CF cases identified by seasonal cutoffs vs. floating cutoffs. GDSP screened 7,410,003 newborns, from July 2007 to December 2022, and missed 36 CF cases below the fixed cutoff; five of the 36 were within 3 ng/mL below the cutoff. There was a regular, seasonal cycle that varied from 1.4% in summer to 1.8% in winter. We would have missed 59 CF cases using a 1.6% daily floating cutoff. California would need to use a 4% daily floating cutoff to improve our current detection rate, which would double the number of specimens sent for costly molecular analysis.

The California Genetic Disease Screening Program (GDSP) employs a fixed immunoreactive trypsinogen (IRT) cutoff followed by molecular testing to screen newborns for Cystic Fibrosis (CF). The cutoffs approximate a 1.6% yearly IRT screen positive rate, however seasonal variation in IRT population means led us to develop a model to establish fixed IRT cutoffs that anticipate seasonal variation and minimize missed cases below cutoff. We utilized an ARIMA model to fit monthly IRT screen-positive percentiles and estimated regular seasonal expectations. We established a retrospective cohort followed for at least 1.5 years to capture missed false negative CF cases. We compared missed CF cases identified by seasonal cutoffs vs floating cutoffs. GDSP screened 7,410,016 newborns, from July 2007 to Dec. 2022, and missed 36 CF cases below the fixed cutoff; five of the 36 were within 3 ng/mL below the cutoff. There was a regular, seasonal cycle that varied from 1.4% in summer to 1.8% in winter. We would have missed 59 CF cases using a 1.6% daily floating cutoff. California would need to use a 4% daily floating cutoff to improve our current detection rate which would double the number of specimens sent for costly molecular analysis.