Arndt Rolfs

Background Rare diseases affect over 300 million people worldwide, with more than half of these cases presenting in childhood. Despite advances in genomic technologies, significant diagnostic delays remain, particularly in underrepresented populations. Although whole-genome sequencing is expected to be more effective than whole-exome sequencing, there are currently no direct patient-level comparisons from Albania. Methods We conducted a prospective, head-to-head comparison of whole-genome sequencing and whole-exome sequencing in 72 pediatric patients from Albania with suspected rare genetic disorders. Both technologies were applied in parallel using ISO-accredited pipelines. Variants were classified according to the ACMG guidelines and assessed for clinical relevance. Primary and secondary findings, as well as dual diagnoses, were recorded and compared. Results A molecular diagnosis was achieved in 72.2% of patients. Whole genome sequencing yielded diagnostic or secondary findings in 68.1% of cases, while whole exome sequencing identified primary diagnoses in 30.6% of cases. WGS made a primary diagnosis in 37.5% of cases, resolving complex or blended phenotypes and detecting variant types that were missed by WES, including deep intronic, regulatory and structural variants. Furthermore, WGS identified medically actionable secondary findings in 15.3% of patients, providing direct information for clinical management. Overall, WGS outperformed WES across variant classes and inheritance modes. Conclusion WGS demonstrated clear diagnostic superiority over WES in this pediatric cohort, particularly in identifying complex phenotypes and structural variants. These results suggest that WGS should be considered a primary diagnostic tool and highlight the importance of ensuring equitable access to genomic technologies for underrepresented populations.

Progressive familial intrahepatic cholestasis (PFIC) is a rare group of genetic disorders that typically present in infants and children, often progressing to end-stage liver disease. Using whole genome sequencing (WGS) for diagnosis, we aimed to assess phenotypic features and outcomes, in Pakistani children with different types of PFIC. The study included 116 pediatric participants with five PFIC types: PFIC1, ATP8B1 gene (n=19); PFIC2, ABCB11 (n=28); PFIC3, ABCB4 (n=52); PFIC4 TJP2 (n=15); and PFIC5 NR1H4 (n=2). Seventy unique variants were identified across the five genes. Age at genetic diagnosis was higher in PFIC3 patients. Clinical and laboratory findings showed significant overlap among all PFIC types. PFIC3 had a less aggressive course and better survival outcomes than PFIC1, PFIC2, and PFIC4. The cumulative survival rate was significantly higher at 89% (95% CI 43-98%) for patients who underwent liver transplantation, compared to 9% (95% CI 1-29%) for those who did not (p=0.016). The study provides the first comprehensive analysis of PFIC in Pakistani children, highlighting significant clinical overlap and the critical need for early genetic diagnosis using WGS. The findings underscore the importance of personalized treatment approaches, including early consideration for liver transplantation, to improve patient outcomes.