Multi-omics to the rescue – genome sequencing and RNA analysis decipher the cause of previously unresolved propionic acidemia
2Department of Genetics, Hadassah Medical Organization, Israel
3Genomics Unit, The Center for Cancer Research, Sheba Medical Center, Israel
4National Newborn Screening Program, Public Health Services, Ministry of Health, Israel
5Sackler Faculty of Medicine, Tel Aviv University, Israel
Background: Propionic acidemia (PA) is an autosomal recessive metabolic disorder caused by variants in PCCA or PCCB, both sub-units of the propionyl-CoA carboxylase (PCC) enzyme. PCC is required for the catabolism of certain amino acids and odd-chain fatty acids. In its absence, the accumulated toxic metabolites cause metabolic acidosis, neurologic symptoms, multi-organ dysfunction, and possible death. The clinical presentation of PA is highly variable, with typical onset in the neonatal or early infantile period.
Methods: We encountered two reportedly unrelated and non-consanguineous Muslim Arab families whose children’s newborn screening suggested PA. Exome sequencing (ES) failed to identify the pathogenic variant. We proceeded with enzyme assays, genome sequencing (GS) and RNA studies to reach a diagnosis.
Results: Enzymatic assays confirmed low levels of PCC. GS in both children demonstrated homozygosity to a deep intronic variant in PCCB. RNA analysis showed that this variant creates a pseudo-exon with a premature stop codon. The parents are variant carriers, though three of them are hemizygotes due to a common large intronic deletion (40% population frequency) on the second allele, which does not affect splicing and results in a normal allele.
Discussion: Arriving at a rapid diagnosis can be crucial in directing lifesaving care. In this instance, although we reached a biochemical diagnosis, one of the children could not be saved. Nevertheless, a diagnosis concludes the diagnostic odyssey and allows the family prenatal diagnosis in subsequent pregnancies. This case demonstrates the power of multi-omics in reaching a diagnosis, using GS and RNA analysis to overcome ES limitations and define pathogenicity. Moreover, intronic deletions in the variant region should be taken into consideration when analyzing genomic data, so that hemizygosity would not be misinterpreted as homozygosity, and variants will not be mislabeled as benign.
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