MLPA‐Detected CFTR Exon Deletions in Children With Inconclusive CFTR Sequencing: A Single‐Center Experience From Türkiye

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Abstract
Introduction: Cystic fibrosis (CF) is an autosomal recessive disorder caused by variants in the CFTR gene and shows marked genetic heterogeneity in diverse populations. Although next‐generation sequencing (NGS) has significantly improved CFTR variant detection, it may fail to identify large exon deletions or duplications, leaving the CFTR genotype incomplete in some patients. This study evaluated the diagnostic contribution of the multiplex ligation‐dependent probe amplification (MLPA) method in pediatric CF cases with incomplete CFTR genotyping after NGS. Methods: A total of 51 pediatric patients who were evaluated for CF diagnosis or suspicion at our center between 2019 and 2024 and had incomplete CFTR genotyping after NGS were retrospectively reviewed. MLPA analysis was performed on these patients. Clinical data, sweat chloride test results, genetic analysis findings, and eligibility for modulator treatment were evaluated. Results: MLPA analysis detected deletions in the CFTR gene in 12 cases (23.5%). The most frequently observed deletions were at exons 2 and 11. In 6 cases where no pathogenic CFTR variant was detected by NGS analysis, large exon deletions were identified by MLPA. The remaining 39 cases were evaluated after NGS and MLPA. CF was excluded in 22 of these cases, whereas clinical suspicion persisted in 17 patients despite negative genetic results. This group was referred for further molecular analysis. Conclusion: MLPA is a complementary method that contributes to the detection of gene rearrangements in cases where CFTR genotyping is incomplete after NGS. Using MLPA as an additional analytical tool in populations with significant genetic heterogeneity may help characterize CFTR variants more comprehensively.

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