Susceptibility haplotypes in non-cystic fibrosis newborns with elevated immunoreactive trypsinogen

Cystic fibrosis (CF) represents the most prevalent life-threatening autosomal recessive disorder in Europe, primarily affecting the respiratory tract, exocrine pancreatic function, and lipid metabolism. Immunoreactive trypsinogen (IRT) quantification constitutes the first-tier test in neonatal CF screening programs; however, elevated IRT levels may also be detected in infants who do not develop CF, generating false-positive (FP) results. The biological basis underlying increased IRT in these cases remains poorly understood and may involve genetic determinants independent of CFTR. Dried blood spot (DBS) samples were collected from full-term neonates with normal growth parameters, classified as true negatives (TN) or FP through CF newborn screening programs across multiple European centers. IRT levels were measured via standardized immunoassay, and genomic DNA extracted from DBS underwent whole-exome sequencing (WES). Bioinformatic analyses integrated functional prediction, evolutionary conservation, and allele frequency data, with variant prioritization restricted to a curated panel of genes implicated in pancreatic disease. Following quality control, 212 samples (94 FP, 118 TN) were included. Comparative analyses identified significant enrichment of variants in five genes among FP subjects. Notably, top loci localized to regulatory regions and genes involved in oxidative stress, suggesting a mechanistic link with pancreatic inflammation and elevated IRT. Several variants clustered within high linkage disequilibrium regions, supporting the presence of susceptibility haplotypes. Burden testing of rare variants confirmed significant associations for CFTR, PRSS1, and PRSS2 after multiple testing corrections. These results suggest that genetic variation beyond CFTR is associated with elevated neonatal IRT in infants without CF and support further investigation of pancreatic-related pathways in false-positive CF newborn screening.