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Introduction: Paroxysmal Nocturnal Hemoglobinuria (PNH) is an acquired clonal disease of hematopoietic stem cells. It is caused by somatic mutation of the X‐linked PIGA gene, resulting in a deficient expression of glycosylphosphatidylinositol‐anchored proteins (GPI‐APs). In this study, we aimed to explore the diagnostic value of next‐generation sequencing (NGS) and potential molecular basis in PNH patients. Methods: Genomic DNA of 85 PNH patients was analyzed by a 114‐gene NGS panel. Results: Mutational analysis of PIGA identified 124 mutations in 92% PNH patients, including 101 distinct mutations and 23 recurrent mutations. Among them, 102 mutations were newly reported. Most mutations were located in exon 2 of PIGA gene, and truncated mutation was the most common one. Other mutations were detected in 26 out of 85 cases, including five cases of DNMT3A variants, four cases of ASXL1 variants, and four cases of U2AF1 variants. Clonal analysis was performed in one case and outlined a linear evolution pattern in classic PNH. There was a positive correlation between number of PIGA mutations and fraction of GPI‐APs deficient granulocytes. Conclusion: The detection of PIGA mutations and additional variants by targeted NGS not only shed light on the genetic characteristics of PNH, but also provided an important reference value in the diagnosis of PNH at molecular level. [ABSTRACT FROM AUTHOR]