Targeted Next-Generation Sequencing Panel for Clinical Diagnostic in Inherited Bone Marrow Failure Syndromes Benefit for Pediatric HSCT

Objective: Inherited bone marrow failure syndromes (IBMFS) are a heterogeneous group of genetic disorders characterized by bone marrow failure, congenital anomalies, and an increased risk of malignant disease. Because of phenotypic variability, diagnosis can be challenging for clinicians. This study is aimed to developed a targeted panel-based Next Generation Sequencing (NGS) pipeline to clinical diagnosis in IBMFS patients. Method: Agilent Haloplex method was used for target capture the IBMFS Library of known genes and related genes, Illumina platform was used for high-throughput sequencing, sequencing data was aligned by NextGENe® software, the variants were filtered and interpretation by the online tool Ingenuity Variant Analysis, and Sanger sequencing was used to confirm the variations. 21 patients with suspected IBMFS were studied and DNA from members of each pedigree were collected for this study. Results: More than 95% of the sequencing reads aligned to human genome reference sequence and more than 85% of the reads are in the target sequence. The 20× coverage area is >95% and the uniformity is >85%. Of the 21 patients with suspected IBMFS, pathogenic mutations have been identified in 12 patients. Including 6 cases with Fanconi anemia (FA), 2 cases of Dyskeratosis congenital (DC), 2 cases of Severe congenital neutropenia (SCN), 1 case of Diamond-Blackfan anemia (DBA), and 1 case of Shwachman-Diamond syndrome (SDS). After hematopoietic stem cell transplantation, 5 patients were successfully cured. Prenatal diagnosis has been successfully performed in 3 families. Conclusion: This study successfully established the target panel sequencing method to molecular diagnosis of IBMFS. The clinical results showed that our method can effectively detect and identify pathogenic genes in monogenic disorders and to provide a strong basis for completely cure and prenatal diagnosis, because the efficiency of captured target region is excellent, the quality of sequencing data is reliable, and the analysis by the bioinformatics software is very comprehensive.