Reconciling newborn screening and a novel splice variant in BTD associated with partial biotinidase deficiency: a BabySeq Project case report

Abstract

Here, we report a newborn female infant from the well-baby cohort of the BabySeq Project who was identified with compound heterozygous BTD gene variants. The two identified variants included a well-established pathogenic variant (c.1612C>T, p.Arg538Cys) that causes profound biotinidase deficiency (BTD) in homozygosity. In addition, a novel splice variant (c.44+1G>A, p.?) was identified in the invariant splice donor region of intron 1, potentially predictive of loss of function. The novel variant was predicted to impact splicing of exon 1; however, given the absence of any reported pathogenic variants in exon 1 and the presence of alternative splicing with exon 1 absent in most tissues in the GTEx database, we assigned an initial classification of uncertain significance. Follow-up medical record review of state-mandated newborn screen (NBS) results revealed an initial out-of-range biotinidase activity level. Levels from a repeat NBS sample barely passed cutoff into the normal range. To determine whether the infant was biotinidase-deficient, subsequent diagnostic enzyme activity testing was performed, confirming partial BTD, and resulted in a change of management for this patient. This led to reclassification of the novel splice variant based on these results. In conclusion, combining the genetic and NBS results together prompted clinical follow-up that confirmed partial BTD and informed this novel splice site's reclassification, emphasizing the importance of combining iterative genetic and phenotypic evaluations.

Interpretation of Genomic Sequencing Results in Healthy and Ill Newborns: Results from the BabySeq Project

“…As a result of the postlingual onset of KCNQ4-related hearing loss, the effects of a likely pathogenic variant in this gene are not expected to be detected by audiological screening at birth. In another newborn enrolled from the well-baby nursery, 16 nGS identified compound heterozygosity for two BTD variants; one was classified as pathogenic (GenBank: NM_000060.4; c.1612C>T [p.Arg538Cys]) and the other (c.44þ1G>A (p.?)) as a VUS during the initial assessment on the basis of the existence of transcripts without the relevant exon 1 that might abrogate the effects of predicted splicing disruption.…”

“…To clarify the clinical significance of the c.44þ1G>A variant, we further investigated the baby's NBS results and discovered borderline NBS results for BTD; a subsequent diagnostic measure of enzyme levels also confirmed partial BTD. 16 As a result, we classified the c.44þ1G>A variant as likely pathogenic, and the newborn was placed on biotin supplementation. Two variants in CYP21A2 were identified in a female baby with severe chronic lung disease.…”

“…Although many individuals with partial BTD might not experience any symptoms throughout their lifetime and detecting partial BTD in the newborn period might not be critical, symptoms can effectively be prevented with a simple and inexpensive treatment of biotin supplementation, as was prescribed in this case. 16 Finally, NBS rarely detects nonclassic CAH. 57 Identifying individuals at risk for nonclassic CAH might be beneficial for facilitating early diagnosis and therapies, if needed, although many individuals with this condition might not need treatment.…”

Quantifying Downstream Healthcare Utilization in Studies of Genomic Testing

“…A more detailed summary of the BabySeq Project, molecular findings, and parental attitudes at enrollment has been published previously. 16,[22][23][24][25][26][27][28] The study included healthy newborns born at Brigham and Women's Hospital (BWH) and newborns in intensive care units (ICUs) at BWH, Boston Children's Hospital (BCH), and Massachusetts General Hospital (MGH). Newborns were randomized to a modified standard of care (standard newborn screening and an in-depth family history analyses) or standard of care plus nGS.…”

Discordant results between conventional newborn screening and genomic sequencing in the BabySeq Project

“…2,5,6 Exome or genome sequencing (ES/GS) may complement traditional NBS in identifying risk for disease, ideally prior to the development of symptoms. We 5,7 and others 8 have previously described cases of inborn errors of metabolism that had been missed by traditional newborn screening and later detected by sequencing, raising the question of whether ES/GS should be incorporated during infancy for genetic risk assessment. Of the 35 disorders included in the Recommended Uniform Screening Panel (RUSP) that are tested using the dried blood spot, nearly all have a Mendelian genetic basis, including sickle cell disease, cystic fibrosis, and maple syrup urine disease, among others.…”